About | BLOGS | Portfolio | Misc | Recommended | What's New | What's Hot

About | BLOGS | Portfolio | Misc | Recommended | What's New | What's Hot


Bibliography Options Menu

27 Sep 2020 at 01:35
Hide Abstracts   |   Hide Additional Links
Long bibliographies are displayed in blocks of 100 citations at a time. At the end of each block there is an option to load the next block.

Bibliography on: Species Concept


Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 27 Sep 2020 at 01:35 Created: 

Species Concept

Wikipedia: The species problem is the set of questions that arises when biologists attempt to define what a species is. Such a definition is called a species concept; there are at least 26 recognized species concepts. A species concept that works well for sexually reproducing organisms such as birds is useless for species that reproduce asexually, such as bacteria. The scientific study of the species problem has been called microtaxonomy. One common, but sometimes difficult, question is how best to decide which species an organism belongs to, because reproductively isolated groups may not be readily recognizable, and cryptic species may be present. There is a continuum from reproductive isolation with no interbreeding, to panmixis, unlimited interbreeding. Populations can move forward or backwards along this continuum, at any point meeting the criteria for one or another species concept, and failing others. Many of the debates on species touch on philosophical issues, such as nominalism and realism, and on issues of language and cognition. The current meaning of the phrase "species problem" is quite different from what Charles Darwin and others meant by it during the 19th and early 20th centuries. For Darwin, the species problem was the question of how new species arose. Darwin was however one of the first people to question how well-defined species are, given that they constantly change.

Created with PubMed® Query: "species concept" NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2020-09-19

Sterling KA, ML Warren (Jr) (2020)

Description of a new species of cryptic snubnose darter (Percidae: Etheostomatinae) endemic to north-central Mississippi.

PeerJ, 8:e9807.

Many subclades within the large North American freshwater fish genus Etheostoma (Percidae) show brilliant male nuptial coloration during the spring spawning season. Traditionally, perceived differences in color were often used to diagnose closely related species. More recently, perceived differences in male nuptial color have prompted further investigation of potential biodiversity using genetic tools. However, cryptic diversity among Etheostoma darters renders male nuptial color as unreliable for detecting and describing diversity, which is foundational for research and conservation efforts of this group of stream fishes. Etheostoma raneyi (Yazoo Darter) is an imperiled, range-limited fish endemic to north-central Mississippi. Existing genetic evidence indicates cryptic diversity between disjunctly distributed E. raneyi from the Little Tallahatchie and Yocona river watersheds despite no obvious differences in male color between the two drainages. Analysis of morphological truss and geometric measurements and meristic and male color characters yielded quantitative differences in E. raneyi from the two drainages consistent with genetic evidence. Morphological divergence is best explained by differences in stream gradients between the two drainages. Etheostoma faulkneri, the Yoknapatawpha Darter, is described as a species under the unified species concept. The discovery of cryptic diversity within E. raneyi would likely not have occurred without genetic tools. Cryptic diversity among Etheostoma darters and other stream fishes is common, but an overreliance on traditional methods of species delimitation (e.g., identification of a readily observable physical character to diagnose a species) impedes a full accounting of the diversity in freshwater fishes in the southeastern United States.

RevDate: 2020-08-26

Gu J, Jiang B, Wang H, et al (2020)

Phylogeny and species delimitation of the genus Longgenacris and Fruhstorferiola viridifemorata species group (Orthoptera: Acrididae: Melanoplinae) based on molecular evidence.

PloS one, 15(8):e0237882 pii:PONE-D-20-12129.

Phylogenetic positions of the genus Longgenacris and one of its members, i.e. L. rufiantennus are controversial. The species boundaries within both of L. rufiantennus+Fruhstorferiola tonkinensis and F. viridifemorata species groups are unclear. In this study, we explored the phylogenetic positions of the genus Longgenacris and the species L. rufiantennus and the relationships among F. viridifemorata group based on the 658-base fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) barcode and the complete sequences of the internal transcribed spacer regions (ITS1 and ITS2) of the nuclear ribosomal DNA. The phylogenies were reconstructed in maximum likelihood framework using IQ-TREE. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. Phylogenetic species concept and NJ tree, K2P distance, the statistical parsimony network as well as the generalized mixed Yule coalescent model (GMYC) were employed to delimitate the species boundaries in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups. The results demonstrated that the genus Longgenacris should be placed in the subfamily Melanoplinae but not Catantopinae, and L. rufiantennus should be a member of the genus Fruhstorferiola but not Longgenacris. Species boundary delimitation confirmed the presence of oversplitting in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups and suggested that each group should be treated as a single species.

RevDate: 2020-08-21

Campbell DL, Thessen AE, L Ries (2020)

A novel curation system to facilitate data integration across regional citizen science survey programs.

PeerJ, 8:e9219 pii:9219.

Integrative modeling methods can now enable macrosystem-level understandings of biodiversity patterns, such as range changes resulting from shifts in climate or land use, by aggregating species-level data across multiple monitoring sources. This requires ensuring that taxon interpretations match up across different sources. While encouraging checklist standardization is certainly an option, coercing programs to change species lists they have used consistently for decades is rarely successful. Here we demonstrate a novel approach for tracking equivalent names and concepts, applied to a network of 10 regional programs that use the same protocols (so-called "Pollard walks") to monitor butterflies across America north of Mexico. Our system involves, for each monitoring program, associating the taxonomic authority (in this case one of three North American butterfly fauna treatments: Pelham, 2014; North American Butterfly Association, Inc., 2016; Opler & Warren, 2003) that shares the most similar overall taxonomic interpretation to the program's working species list. This allows us to define each term on each program's list in the context of the appropriate authority's species concept and curate the term alongside its authoritative concept. We then aligned the names representing equivalent taxonomic concepts among the three authorities. These stepping stones allow us to bridge a species concept from one program's species list to the name of the equivalent in any other program, through the intermediary scaffolding of aligned authoritative taxon concepts. Using a software tool we developed to access our curation system, a user can link equivalent species concepts between data collecting agencies with no specialized knowledge of taxonomic complexities.

RevDate: 2020-07-29

McCoy SJ, Krueger-Hadfield SA, N Mieszkowska (2020)

Evolutionary phycology: Towards a macroalgal species conceptual framework.

Journal of phycology [Epub ahead of print].

Species concepts formalize evolutionary and ecological processes, but often conflict with one another when considering the mechanisms that ultimately lead to species delimitation. Evolutionary biologists are, however, recognizing that the conceptualization of a species is separate and distinct from the delimitation of species. Indeed, if species are generally defined as separately evolving metapopulation lineages, then characteristics, such as reproductive isolation or monophyly, can be used as evidence of lineage separation and no longer conflict with the conceptualization of a species. However, little of this discussion has addressed the formalization of this evolutionary conceptual framework for macroalgal species. This may be due to the complexity and variation found in macroalgal life cycles. While macroalgal mating system variation and patterns of hybridization and introgression have been identified, complex algal life cycles generate unique eco-evolutionary consequences. Moreover, the discovery of frequent macroalgal cryptic speciation has not been accompanied by the study of the evolutionary ecology of those lineages, and, thus, an understanding of the mechanisms underlying such rampant speciation remain elusive. In this perspective, we aim to further the discussion and interest in species concepts and speciation processes in macroalgae. We propose a conceptual framework to enable phycological researchers and students alike to portray these processes in a manner consistent with dialogue at the forefront of evolutionary biology. We define a macroalgal species as an independently evolving metapopulation lineage, whereby we can test for reproductive isolation or the occupation of distinct adaptive zones, among other mechanisms, as secondary lines of supporting evidence.

RevDate: 2020-07-29

Bangs MR, Douglas MR, Chafin TK, et al (2020)

Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus).

Ecology and evolution, 10(13):6477-6493 pii:ECE36384.

The delimitation of species boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life histories codistributed in the highly modified Colorado River (i.e., flannelmouth sucker, Catostomus latipinnis; bluehead sucker, C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double-digest restriction site-associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in bluehead sucker, supporting elevation of C. (P.) virescens to species status and recognizing C. (P.) discobolus yarrowi (Zuni bluehead sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate flannelmouth sucker lineages as ESUs (evolutionarily significant units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the agreement of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolation versus secondary contact.

RevDate: 2020-07-22

Quilodrán CS, Montoya-Burgos JI, M Currat (2020)

Harmonizing hybridization dissonance in conservation.

Communications biology, 3(1):391 pii:10.1038/s42003-020-1116-9.

A dramatic increase in the hybridization between historically allopatric species has been induced by human activities. However, the notion of hybridization seems to lack consistency in two respects. On the one hand, it is inconsistent with the biological species concept, which does not allow for interbreeding between species, and on the other hand, it is considered either as an evolutionary process leading to the emergence of new biodiversity or as a cause of biodiversity loss, with conservation implications. In the first case, we argue that conservation biology should avoid the discussion around the species concept and delimit priorities of conservation units based on the impact on biodiversity if taxa are lost. In the second case, we show that this is not a paradox but an intrinsic property of hybridization, which should be considered in conservation programmes. We propose a novel view of conservation guidelines, in which human-induced hybridization may also be a tool to enhance the likelihood of adaptation to changing environmental conditions or to increase the genetic diversity of taxa affected by inbreeding depression. The conservation guidelines presented here represent a guide for the development of programmes aimed at protecting biodiversity as a dynamic evolutionary system.

RevDate: 2020-07-03

Jiao X, Z Yang (2020)

Defining Species When There is Gene Flow.

Systematic biology pii:5866754 [Epub ahead of print].

Whatever one's definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with continuous-time migration or episodic introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a genetic sequence to be on average more closely related to a sequence from another species than to a sequence from the same species. Our results highlight the extraordinary impact that even a small amount of gene flow may have on the genetic history of the species. We suggest that contrasting long-term migration rate and short-term hybridization rate, both of which can be estimated using genetic data, may be a powerful approach to detecting the presence of reproductive barriers and to define species boundaries.

RevDate: 2020-06-12

Xu J (2020)

Fungal Species Concepts in the Genomics Era.

Genome [Epub ahead of print].

The 140,000 or so fungal species reported so far are heterogeneously defined based on varying criteria such as morphological, physiological, mating, and/or molecular features. Incongruences are common among traits used to separating closely related species and it is often difficult to compare fungal taxonomic groups defined based on different species recognition criteria. Though DNA sequence-based classification and identification have been made, a consensus has not been reached, primarily due to intrinsic limitations in the proposed one or a few genes. Here, I argue that the fundamental reason for the observed inconsistencies is that speciation is a stochastic process with the emergence and fixation of different traits influenced differently by many non-deterministic factors such as population size, random mutation, mode(s) of reproduction, selection imposed by interacting biotic and abiotic factors, and chance events. Each species concept attempts to capture one or a few traits emerged in the continuous process of speciation. I propose that a genome sequence-based classification and identification system could unify and stabilize fungal taxonomy and help integrate taxonomy with other fields of fungal biology. The genomic species concept could be similarly argued for other groups of eukaryotic microbes as well as for plants and animals.

RevDate: 2020-05-29

Heuchert B, Braun U, Diederich P, et al (2018)

Taxonomic monograph of the genus Taeniolella s. lat. (Ascomycota).

Fungal systematics and evolution, 2:69-261.

A taxonomic monograph of the ascomycete genus Taeniolella (asexual dematiaceous hyphomycetes, sexual morphs unknown) is provided. Recent phylogenetic analyses demonstrated the polyphyly of this genus. The type species of Taeniolella pertains to the Kirschsteiniotheliaceae within Dothideomycetes, while other saprobic species clustered far away within Sordariomycetes, Savoryellaceae s. lat., and Lindgomycetaceae, whereas lichenicolous species belong to a monophyletic clade that represents the order Asterotexiales, but for most species assigned to Taeniolella sequence data and phylogenetic analyses are not yet available. The main focus of the present taxonomic study was on a revision of the lichenicolous Taeniolella species. Since the currently available phylogenetic analyses do not allow final taxonomic conclusions at generic rank, the exclusion of lichenicolous species from Taeniolella s. lat. has been postponed pending a broader sampling and more phylogenetic data of allied ascomycete genera within the order Asterotexiales. For the interim, Taeniolella s. lat., including lichenicolous and saprobic species, is maintained. The taxonomic background, history, generic description and discrimination from morphologically confusable genera, phylogeny, biology, host range and distribution, and species concept of Taeniolella species are briefly outlined and discussed. Keys to the species of Taeniolella divided by ecological groups (lichenicolous taxa, saprobic taxa) are provided, supplemented by a tabular key to lichenicolous species based on host (lichen) families and genera. Twenty-nine lichenicolous species and a Taeniolella sp. (putative asexual morph of Sphaerellothecium thamnoliae) as well as 16 saprobic species are described in detail and illustrated by drawings, macroscopic photographs, light microscopic and SEM micrographs, including six new lichenicolous species (T. arctoparmeliae on Arctoparmelia separata, T. lecanoricola on Lecanora rupicola, T. thelotrematis on Thelotrema, T. umbilicariae and T. umbilicariicola on Umbilicaria, T. weberi on Thelotrema weberi), three new saprobic species (T. filamentosa on Salix, T. ravenelii on Quercus, T. stilbosporoides on Salix caprea), and one new combination, T. arthoniae. Most saprobic Taeniolella species are wood-inhabiting (on bark, decorticated trunks and twigs, rotten wood), whereas lichenicolous species grow on thalli and fruiting bodies (mostly apothecia) of lichens, mostly without causing any evident damage, but they are nevertheless confined to their host lichens, or they are obviously pathogenic and cause either disease of the thalli (e.g., Taeniolella chrysothricis and T. delicata) or at least thallus discolorations or necroses (e.g., T. christiansenii, T. chrysothricis, T. cladinicola, T. pseudocyphellariae, and T. strictae). Taeniolella atricerebrina and T. rolfii induce the formation of distinct galls. The range of micro-morphological traits for taxonomic purposes is limited in Taeniolella species, but size, shape and septation of conidiophores and conidia, including surface ornamentation, provided basic characters. Mycelium, stromata and arrangement of conidiophores are less important for the differentiation of species. Lichenicolous species are widespread on a wide range of lichens, with a focus in the northern hemisphere, mainly in northern temperate regions, including arctic-subartic habitats (18 species, i.e., 62 % of the lichenicolous species). Eleven lichenicolous species, e.g., T. pseudocyphellariae, T. santessonii, T. thelotrematis, T. umbilicariae, are also known from collections in non-temperate Asia, Australia and South America (38 % of the species). Most collections deposited in herbaria are from northern temperate to arctic-subarctic regions, which may reflect activities of lichenologists and mycologist dealing with lichenicolous fungi in general and Taeniolella in particular. Most lichenicolous Taeniolella species are confined to hosts of a single lichen genus or few closely allied genera (26 species, i.e., 97 % of the lichenicolous species), but only three species, T. delicata, T. punctata, and T. verrucosa, have wider hosts ranges. Excluded, doubtful and insufficiently known species assigned to Taeniolella are listed at the end, discussed, described and in some cases illustrated, including Talpapellis beschiana comb. nov. (≡ Taeniolella beschiana), Corynespora laevistipitata (≡ Taeniolella laevistipitata), Stanjehughesia lignicola comb. nov. (≡ Taeniolella lignicola), Sterigmatobotrys rudis (≡ Taeniolella rudis), and Taeniolina scripta (≡ Taeniolella scripta).

RevDate: 2020-05-26

Newton LG, Starrett J, Hendrixson BE, et al (2020)

Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex.

Molecular ecology [Epub ahead of print].

Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth's quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, the Antrodiaetus unicolor species complex containing two sympatric species, exhibits this pattern of relative morphological stasis with considerable genetic divergence across its distribution. A past study using two molecular markers, COI and 28S, revealed that A. unicolor is paraphyletic with respect to A. microunicolor. To better investigate species boundaries in the complex, we implement the cohesion species concept and employ multiple lines of evidence for testing genetic exchangeability and ecological interchangeability. Our integrative approach includes extensively sampling homologous loci across the genome using a RADseq approach (3RAD), assessing population structure across their geographic range using multiple genetic clustering analyses that include STRUCTURE, PCA, and a recently developed unsupervised machine learning approach (Variational Autoencoder). We evaluate ecological similarity by using large-scale ecological data for niche-based distribution modeling. Based on our analyses, we conclude that this complex has at least one additional species as well as confirm species delimitations based on previous less comprehensive approaches. Our study demonstrates the efficacy of genomic-scale data for recognizing cryptic species, suggesting that species delimitation with one data type, whether one mitochondrial gene or morphology, may underestimate true species diversity in morphologically homogenous taxa with low vagility.

RevDate: 2020-05-15

Mosier SL (2019)

Policies as species Viewing and classifying policy from an evolutionary biology perspective.

Politics and the life sciences : the journal of the Association for Politics and the Life Sciences, 38(2):117-131.

This article proposes equating policies as species to develop a better understanding of how policies emerge, change, and diffuse across policymaking environments. Scholars have long shown an interest in understanding policy change and reinvention, whether incremental or nonincremental. The two subfields of public policy that can answer how and why policies change are not unified, leading to difficulty in comprehensively assessing policy emergence and change. The policy species concept bridges knowledge of the policy process and knowledge in the policy process by creating an operationalized definition of public policy and suggesting a process for classifying policies to observe subsequent behavior. Drawing from the field of biology, the policy species framework outlines how policies possess genotypes and phenotypes, which dictate what a policy is and how it can change. In tracing genotypic and phenetic change over time, policy evolution and change is more easily discernible. In turn, a more precise picture of how policies function is painted.

RevDate: 2020-05-15

Sterling KA, Nielsen SV, Brown AJ, et al (2020)

Cryptic diversity among Yazoo Darters (Percidae: Etheostoma raneyi) in disjunct watersheds of northern Mississippi.

PeerJ, 8:e9014 pii:9014.

The Yazoo Darter, Etheostoma raneyi (Percidae), is an imperiled freshwater fish species endemic to tributaries of the Yocona and Little Tallahatchie rivers of the upper Yazoo River basin, in northern Mississippi, USA. The two populations are allopatric, isolated by unsuitable lowland habitat between the two river drainages. Relevant literature suggests that populations in the Yocona River represent an undescribed species, but a lack of data prevents a thorough evaluation of possible diversity throughout the range of the species. Our goals were to estimate phylogenetic relationships of the Yazoo Darter across its distribution and identify cryptic diversity for conservation management purposes. Maximum likelihood (ML) phylogenetic analyses of the mitochondrial cytochrome b (cytb) gene returned two reciprocally monophyletic clades representing the two river drainages with high support. Bayesian analysis of cytb was consistent with the ML analysis but with low support for the Yocona River clade. Analyses of the nuclear S7 gene yielded unresolved relationships among individuals in the Little Tallahatchie River drainage with mostly low support, but returned a monophyletic clade for individuals from the Yocona River drainage with high support. No haplotypes were shared between the drainages for either gene. Additional cryptic diversity within the two drainages was not indicated. Estimated divergence between Yazoo Darters in the two drainages occurred during the Pleistocene (<1 million years ago) and was likely linked to repeated spatial shifts in suitable habitat and changes in watershed configurations during glacial cycles. Individuals from the Yocona River drainage had lower genetic diversity consistent with the literature. Our results indicate that Yazoo Darters in the Yocona River drainage are genetically distinct and that there is support for recognizing Yazoo Darter populations in the Yocona River drainage as a new species under the unified species concept.

RevDate: 2020-04-20

Karasiewicz S, Chapelle A, Bacher C, et al (2020)

Harmful algae niche responses to environmental and community variation along the French coast.

Harmful algae, 93:101785.

Distribution, frequency and intensity of harmful phytoplanktonic species are impacted by changes in environmental conditions. In the Bay of Brest, Alexandrium minutum has been responsible for several harmful algal blooms (HABs) associated with toxin production causing paralytic shellfish poisoning (PSP). Additionally, Lepidodinium chlorophorum causes green water and hypoxia locally in the Bay of Biscay. Previous studies revealed that L. chlorophorum's success was related to possible competitive exclusion. Therefore, the phytoplankton composition and the environmental conditions should be taken into account. This study aims to assess the combined effect of changes in habitat conditions and community structure with the occurrence of HAB species, on a spatial-temporal scale. For the investigation we first used the Hutchinson's niche concept by means of the Outlying Mean Index (OMI) analysis. The OMI analysis enable us to observe the environmental variables defining the ecological niche of the harmful species among the community. Secondly, we used the subniche theory to highlight the environmental variables defining the subniches in cases of high and low abundance of HABs with an estimation of the biological constraint restricting the species' subniche. This was undertaken using the Within Outlying Mean indexes (WitOMI) calculated under environmental conditions promoting high (H) and low (L) abundance bloom. Thirdly, we used the Indicator Species Concept from the Indicator Species Analysis (ISA) to link the biological restriction with potential competing or indicator species. We combined a data set from the French National Phytoplankton and Phycotoxin Monitoring Network (REPHY), the Velyger network (oyster monitoring program) and satellite imagery. A total of 44 stations, over the period of 1998-2017 using 50 taxonomic units. 36 taxa had significant niche and were mostly distributed along nutrient and salinity gradients. The two species of interest L. chlorophorum and A. minutum seemed to have similar affinity for summer-like environmental conditions and both used a marginal habitat compared to the rest of the community. A. minutum had a larger niche due to a greater affinity to the estuarine-like conditions. The subniche of the two species had a similar response to the environmental variation; their respective abundance was partly caused by greater environmental restrains. Their success in abundance appeared to be linked to local hydrodynamics which increases or reduces resources. On the other hand, the biotic pressure exerted upon A. minutum and L. chlorophorum were antagonistic. A possible competitor assemblage was exposed but the analysis was inconclusive. The methodological limitations were discussed as well as a perspective for future similar studies.

RevDate: 2020-04-16

Seifert B (2020)

The Gene and Gene Expression (GAGE) species concept - an universal approach for all eukaryotic organisms.

Systematic biology pii:5820980 [Epub ahead of print].

The Gene and Gene Expression (GAGE) species concept, a new version of the Pragmatic Species Concept of Seifert (2014), is proposed as a concept applicable to any described recent or fossil eukaryotic organism independent from its mode of reproduction or evolutionary history. In addition to presenting the concept as such, the paper also provides practical recommendations for taxonomists when delimiting species and describing taxa. The wording of the new concept contains a heading core sentence plus five attached sentences addressing essential conditions for its translation into a sound taxonomic practice: "Species are separable clusters that have passed a threshold of evolutionary divergence and are exclusively defined by nuclear DNA sequences and/or their expression products. Nuclear DNA sequences and their expression products are different character systems but have a highly correlated indicative function. Character systems with the least risk of epigenetic or ontogenetic modification have superior indicative value when conflicts between character systems of integrative studies arise. All character systems have to be described by an adequate numerics allowing cluster formation and determination of thresholds. Thresholds for each character system should be fixed by consensus among the experts under the principle of avoiding oversplitting or lumping. Clusters must not be the expression of intraspecific polymorphism." Recognizing the distortions and conflicts caused to taxonomy through barcoding or through assessment on the basis of association with other organisms, the GAGE species concept strongly downgrades the use of cytoplasmic DNA of endosymbiotic origin (mtDNA, cpDNA) or DNA of closely associated microbes (e.g. Wolbachia bacteria) for final taxonomic decision making. Recognizing the distortion of phylogenies by the high frequency of reticulate evolution, it is argued that delimiting and naming species has to be separated from constructing bifurcating phylogenetic trees.

RevDate: 2020-04-04

Corduneanu A, Ursache TD, Taulescu M, et al (2020)

Detection of DNA of Babesia canis in tissues of laboratory rodents following oral inoculation with infected ticks.

Parasites & vectors, 13(1):166 pii:10.1186/s13071-020-04051-z.

BACKGROUND: Babesia spp. are apicomplexan parasites which infect a wide range of mammalian hosts. Historically, most Babesia species were described based on the assumed host specificity and morphological features of the intraerythrocytic stages. New DNA-based approaches challenge the traditional species concept and host specificity in Babesia. Using such tools, the presence of Babesia DNA was reported in non-specific mammalian hosts, including B. canis in feces and tissues of insectivorous bats, opening questions on alternative transmission routes. The aim of the present study was to evaluate if B. canis DNA can be detected in tissues of laboratory rodents following oral inoculation with infected ticks.

METHODS: Seventy-five questing adult Dermacentor reticulatus ticks were longitudinally cut in two halves and pooled. Each pool consisted of halves of 5 ticks, resulting in two analogous sets. One pool set (n = 15) served for DNA extraction, while the other set (n = 15) was used for oral inoculation of experimental animals (Mus musculus, line CD-1 and Meriones unguiculatus). Blood was collected three times during the experiment (before the inoculation, at 14 days post-inoculation and at 30 days post-inoculation). All animals were euthanized 30 days post-inoculation. At necropsy, half of the heart, lung, liver, spleen and kidneys were collected from each animal. The presence of Babesia DNA targeting the 18S rRNA gene was evaluated from blood and tissues samples. For histopathology, the other halves of the tissues were used. Stained blood smears were used for the light microscopy detection of Babesia.

RESULTS: From the 15 pools of D. reticulatus used for the oral inoculation, six were PCR-positive for B. canis. DNA of B. canis was detected in blood and tissues of 33.3% of the animals (4 out of 12) inoculated with a B. canis-positive pool. No Babesia DNA was detected in the other 18 animals which received B. canis-negative tick pools. No Babesia was detected during the histological examination and all blood smears were microscopically negative.

CONCLUSIONS: Our findings demonstrate that B. canis DNA can be detected in tissues of mammalian hosts following ingestion of infected ticks and opens the question of alternative transmission routes for piroplasms.

RevDate: 2020-04-03

Tatarenkov A, Earley RL, Taylor DS, et al (2020)

Extensive hybridization and past introgression between divergent lineages in a quasi-clonal hermaphroditic fish: ramifications for species concepts and taxonomy.

Journal of evolutionary biology [Epub ahead of print].

Extreme inbreeding is expected to reduce the incidence of hybridization, serving as a prezygotic barrier. Mangrove rivulus is a small killifish that reproduces predominantly by self-fertilization, producing highly homozygous lines throughout its geographic range. The Bahamas and Caribbean are inhabited by two highly diverged phylogeographic lineages of mangrove rivulus, Kryptolebias marmoratus and a "Central clade" closely related to K. hermaphroditus from Brazil. The two lineages are largely allopatric, but recently were found in syntopy on San Salvador, Bahamas, where a single hybrid was reported. To better characterize the degree of hybridization and the possibility of secondary introgression, here we conducted a detailed genetic analysis of the contact zone on San Salvador. Two mixed populations were identified, one of which contained sexually mature hybrids. The distribution of heterozygosity at diagnostic microsatellite loci in hybrids showed that one of these hybrids was an immediate offspring from the K. marmoratus x Central clade cross, whereas the remaining five hybrids were products of reproduction by self-fertilization for 1-3 generations following the initial cross. Two hybrids had mitochondrial haplotypes of K. marmoratus and the remaining four hybrids had a haplotype of the Central clade, indicating that crosses go in both directions. In hybrids, alleles of parental lineages were represented in equal proportions suggesting lack of recent backcrossing to either of the parental lineages. However, sympatric populations of two lineages were less diverged than allopatric populations, consistent with introgression. Results are discussed in terms of applicability of the biological species concept for isogenic, effectively clonal, organisms.

RevDate: 2020-03-12

Li ZZ, Ngarega BK, Lehtonen S, et al (2020)

Cryptic diversity within the African aquatic plant Ottelia ulvifolia (Hydrocharitaceae) revealed by population genetic and phylogenetic analyses.

Journal of plant research pii:10.1007/s10265-020-01175-2 [Epub ahead of print].

Revealing cryptic diversity is of great importance for effective conservation and understanding macroevolution and ecology of plants. Ottelia, a typical example of aquatic plants, possesses extremely variable morphology and the presence of cryptic diversity makes its classification problematic. Previous studies have revealed cryptic Ottelia species in Asia, but very little is known about the molecular systematics of this genus in Africa, a center of species diversity of Ottelia. In this study, we sampled Ottelia ulvifolia, an endemic species of tropical Africa, from Zambia and Cameroon. We used six chloroplast DNA regions, nrITS and six polymorphic microsatellite markers to estimate the molecular diversity and population genetic structure in O. ulvifolia. The phylogenetic inference, STACEY and STRUCTURE analyses supported at least three clusters within O. ulvifolia, each representing unique flower types (i.e., bisexual yellow flower, unisexual yellow flower and bisexual white flower types). Although abundant genetic variation (> 50%) was observed within the populations, excessive anthropogenic activities may result in genetic drift and bottlenecks. Here, three cryptic species of O. ulvifolia complex are defined, and insights are provided into the taxonomy of Ottelia using the phylogenetic species concept.

RevDate: 2020-03-12

Wang P, Chen B, Zheng J, et al (2020)

Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp (Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China.

Frontiers in genetics, 11:118.

The kuruma shrimp (Marsupenaeus japonicus) includes two cryptic species, which are distributed mostly allopatrically but co-occur in the northern South China Sea (from Huilai to Beihai). To obtain a better understanding of the fine-scale genetic structure and parapatric diversification of these two varieties in the northwestern Pacific region, we used a genotyping-by-sequencing (GBS) and comparative transcriptomics approach to establish their phylogenetic relationships. Using the GBS technique, we genotyped 28891 SNPs in 160 individuals in the Northwest Pacific. The results supported two highly diverged evolutionary lineages of kuruma shrimp (var. I and II). The ND and XM populations showed complex genetic patterns, which might be affected by the complex environment of the Taiwan Strait. In addition, the migration rates and inbreeding coefficients of XM and BH were much lower than those of the other populations, which might be related to the land-sea changes and complex ocean currents in the Taiwan Strait and Qiongzhou Strait. Based on the synonymous substitution rates (ds) of 2,491 candidate orthologs, we estimated that the divergence time between the two varieties was 0.26~0.69 Mya. Choice and no-choice interbreeding experiments provided support for the biological species concept, by showing the existence of reproductive isolation or incompatibility. In view of these differences between the two Marsupenaeus species, we believe that it is essential and urgent to establish a genetic database for each and reevaluate their ecological suitable conditions in order to improve species-specific culturing techniques. Moreover, this research can serve as a case study for future research on speciation and hybridization.

RevDate: 2020-01-28

Malavin S, L Shmakova (2020)

Isolates from ancient permafrost help to elucidate species boundaries in Acanthamoeba castellanii complex (Amoebozoa: Discosea).

European journal of protistology, 73:125671 pii:S0932-4739(20)30001-8 [Epub ahead of print].

Acanthamoeba castellanii species complex (genotype T4) comprises of more than ten species with unclear synonymy. Its molecular phylogeny has several conflicts with published morphological data. In this paper, we analyze morphometric traits and temperature preferences in six new strains belonging to A. castellanii complex isolated from Arctic permafrost in the framework of molecular phylogeny. This integrative approach allows us to cross-link genotypic and phenotypic variability and identify species-level boundaries inside the complex. We also analyze previously known and newly found discrepancies between the nuclear and mitochondrial gene-based phylogenies. We hypothesize that one reason for these discrepancies may be the intragenomic polymorphism of ribosomal RNA genes.

RevDate: 2020-01-24

Cheng JY, T Mailund (2020)

Ancestral Population Genomics with Jocx, a Coalescent Hidden Markov Model.

Methods in molecular biology (Clifton, N.J.), 2090:167-189.

Coalescence theory lets us probe the past demographics of present-day genetic samples and much information about the past can be gleaned from variation in rates of coalescence event as we trace genetic lineages back in time. Fewer and fewer lineages will remain, however, so there is a limit to how far back we can explore. Without recombination, we would not be able to explore ancient speciation events because of this-any meaningful species concept would require that individuals of one species are closer related than they are to individuals of another species, once speciation is complete. Recombination, however, opens a window to the deeper past. By scanning along a genomic alignment, we get a sequential variant of the coalescence process as it looked at the time of the speciation. This pattern of coalescence times is fixed at speciation time and does not erode with time; although accumulated mutations and genomic rearrangements will eventually hide the signal, it enables us to glance at events in the past that would not be observable without recombination. So-called coalescence hidden Markov models allow us to exploit this, and in this chapter, we present the tool Jocx that uses a framework of these models to infer demographic parameters in ancient speciation events.

RevDate: 2020-01-22

Martin D, Gil J, Zanol J, et al (2020)

Digging the diversity of Iberian bait worms Marphysa (Annelida, Eunicidae).

PloS one, 15(1):e0226749 pii:PONE-D-19-22833.

During a visit to polychaete-rearing facilities in the vicinity of Bay of Cádiz (SW Iberian Peninsula, Atlantic Ocean), we sampled two populations of Marphysa (Annelida, Eunicidae) originally occurring at nearby intertidal soft bottoms, one being more than twice as long as the other at the same age. We analysed them using partial sequences of two mitochondrial genes, 16S rDNA and Cytochrome Oxidase I, and classical morphological observations. Our molecular results confirmed that the two populations corresponded to two different species, with PTP species delimitation values ranging from 0.973 (long-bodied species) to 0.999 (short-bodied species). Morphologically, the short-bodied species resembles the recently redescribed M. sanguinea (Montagu, 1813), but differs mainly in having some parapodia with two subacicular hooks (one bidentate and one unidentate) and three types of pectinate chaetae, Two isodont present all along the body, and one particularly large anodont asymmetric appearing only from mid-posterior parapodia. The long-bodied species resembles Marphysa aegypti Elgetany, El-Ghobashy, Ghoneim and Struck, 2018 both in size and in having very robust, unidentate subacicular hooks (single in most parapodia, two-both similar in size and form-in some posterior parapodia), but differs, among other features, in the maxillary formula, the number of acicula per parapodia and the number and shape of pectinate chaetae. Accordingly, we are here fully illustrating and formally describing the two Iberian populations as Marphysa gaditana sp. nov. (short-bodied) and Marphysa chirigota sp. nov. (long-bodied) and we are emending the description of M. aegypti based on our revision of the type material. Also, we discuss on the distribution of the species of the sanguinea-group and on the relevancy of taxonomically robust studies when dealing with species of commercial interest having the potential of being globally spread through human activities, as well as on the misunderstandings caused by the incorrect use of the "cosmopolitan species" concept.

RevDate: 2020-01-24

Walther G, Wagner L, O Kurzai (2019)

Updates on the Taxonomy of Mucorales with an Emphasis on Clinically Important Taxa.

Journal of fungi (Basel, Switzerland), 5(4):.

Fungi of the order Mucorales colonize all kinds of wet, organic materials and represent a permanent part of the human environment. They are economically important as fermenting agents of soybean products and producers of enzymes, but also as plant parasites and spoilage organisms. Several taxa cause life-threatening infections, predominantly in patients with impaired immunity. The order Mucorales has now been assigned to the phylum Mucoromycota and is comprised of 261 species in 55 genera. Of these accepted species, 38 have been reported to cause infections in humans, as a clinical entity known as mucormycosis. Due to molecular phylogenetic studies, the taxonomy of the order has changed widely during the last years. Characteristics such as homothallism, the shape of the suspensors, or the formation of sporangiola are shown to be not taxonomically relevant. Several genera including Absidia, Backusella, Circinella, Mucor, and Rhizomucor have been amended and their revisions are summarized in this review. Medically important species that have been affected by recent changes include Lichtheimia corymbifera,Mucor circinelloides, and Rhizopus microsporus. The species concept of Rhizopus arrhizus (syn. R. oryzae) is still a matter of debate. Currently, species identification of the Mucorales is best performed by sequencing of the internal transcribed spacer (ITS) region. Ecologically, the Mucorales represent a diverse group but for the majority of taxa, the ecological role and the geographic distribution remain unknown. Understanding the biology of these opportunistic fungal pathogens is a prerequisite for the prevention of infections, and, consequently, studies on the ecology of the Mucorales are urgently needed.

RevDate: 2019-11-15

Cabarroi-Hernández M, Villalobos-Arámbula AR, Mabel Gisela Torres-Torres , et al (2019)

The Ganoderma weberianum-resinaceum lineage: multilocus phylogenetic analysis and morphology confirm G. mexicanum and G. parvulum in the Neotropics.

MycoKeys, 59:95-131.

Many species of Ganoderma exhibit a high phenotypic plasticity. Hence, particularly among them, the morphological species concept remains difficult to apply, resulting in a currently confused taxonomy; as a consequence, the geographical distribution range of many species also remains very uncertain. One of the areas with a strong uncertainty, as far as morphological species concept is concerned, is the Neotropics. It is common that names of species described from other regions, mainly from northern temperate areas, have been applied to Neotropical species. The aim of the present study was to determine which species might lay behind the G. weberianum complex in the Neotropics, using morphological studies and phylogenetic inferences based on both single (ITS) and multilocus (ITS, rpb2, and tef1-α) sequences. The results indicated that G. weberianumsensu Steyaert, which is the usually accepted concept for this taxon, was absent from the Neotropics. In this area, G. weberianumsensu Steyaert encompassed at least two phylogenetic species, which are tentatively, for the time being, identified as belonging to G. mexicanum and G. parvulum. These two species could be distinguished morphologically, notably by the ornamentation or its absence on their chlamydospores. The results also showed that additional species from the Neotropics might still exist, including, e.g., G. perzonatum, but their circumscription remains uncertain until now because of the paucity of material available. Furthermore, it was found that the current concept of G. resinaceum embraced a complex of species.

RevDate: 2020-01-08
CmpDate: 2019-11-18

Smith BP, Cairns KM, Adams JW, et al (2019)

Taxonomic status of the Australian dingo: the case for Canis dingo Meyer, 1793.

Zootaxa, 4564(1):zootaxa.4564.1.6 pii:zootaxa.4564.1.6.

The taxonomic status and systematic nomenclature of the Australian dingo remain contentious, resulting in decades of inconsistent applications in the scientific literature and in policy. Prompted by a recent publication calling for dingoes to be considered taxonomically as domestic dogs (Jackson et al. 2017, Zootaxa 4317, 201-224), we review the issues of the taxonomy applied to canids, and summarise the main differences between dingoes and other canids. We conclude that (1) the Australian dingo is a geographically isolated (allopatric) species from all other Canis, and is genetically, phenotypically, ecologically, and behaviourally distinct; and (2) the dingo appears largely devoid of many of the signs of domestication, including surviving largely as a wild animal in Australia for millennia. The case of defining dingo taxonomy provides a quintessential example of the disagreements between species concepts (e.g., biological, phylogenetic, ecological, morphological). Applying the biological species concept sensu stricto to the dingo as suggested by Jackson et al. (2017) and consistently across the Canidae would lead to an aggregation of all Canis populations, implying for example that dogs and wolves are the same species. Such an aggregation would have substantial implications for taxonomic clarity, biological research, and wildlife conservation. Any changes to the current nomen of the dingo (currently Canis dingo Meyer, 1793), must therefore offer a strong, evidence-based argument in favour of it being recognised as a subspecies of Canis lupus Linnaeus, 1758, or as Canis familiaris Linnaeus, 1758, and a successful application to the International Commission for Zoological Nomenclature - neither of which can be adequately supported. Although there are many species concepts, the sum of the evidence presented in this paper affirms the classification of the dingo as a distinct taxon, namely Canis dingo.

RevDate: 2020-01-08

Chase AB, Arevalo P, Brodie EL, et al (2019)

Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria.

mBio, 10(5):.

For free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several obstacles to the study of the processes contributing to microbial diversification. These obstacles are particularly high in soil, where high bacterial diversity inhibits the study of closely related genotypes and therefore the factors structuring microbial populations. Here, we isolated strains within a single Curtobacterium ecotype from surface soil (leaf litter) across a regional climate gradient and investigated the phylogenetic structure, recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. Our results indicate that microbial populations are delineated by gene flow discontinuities, with distinct populations cooccurring at multiple sites. Bacterial population structure was further delineated by genomic features allowing for the identification of candidate genes possibly contributing to local adaptation. These results suggest that the genetic structure within this bacterium is maintained both by ecological specialization in localized microenvironments (isolation by environment) and by dispersal limitation between geographic locations (isolation by distance).IMPORTANCE Due to the promiscuous exchange of genetic material and asexual reproduction, delineating microbial species (and, by extension, populations) remains challenging. Because of this, the vast majority of microbial studies assessing population structure often compare divergent strains from disparate environments under varied selective pressures. Here, we investigated the population structure within a single bacterial ecotype, a unit equivalent to a eukaryotic species, defined as highly clustered genotypic and phenotypic strains with the same ecological niche. Using a combination of genomic and computational analyses, we assessed the phylogenetic structure, extent of recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. To our knowledge, this study is the first to do so for a dominant soil bacterium. Our results indicate that bacterial soil populations, similarly to those in other environments, are structured by gene flow discontinuities and exhibit distributional patterns consistent with both isolation by distance and isolation by environment. Thus, both dispersal limitation and local environments contribute to the divergence among closely related soil bacteria as observed in macroorganisms.

RevDate: 2019-10-24

König K, Zundel P, Krimmer E, et al (2019)

Reproductive isolation due to prezygotic isolation and postzygotic cytoplasmic incompatibility in parasitoid wasps.

Ecology and evolution, 9(18):10694-10706.

The reproductive barriers that prevent gene flow between closely related species are a major topic in evolutionary research. Insect clades with parasitoid lifestyle are among the most species-rich insects and new species are constantly described, indicating that speciation occurs frequently in this group. However, there are only very few studies on speciation in parasitoids. We studied reproductive barriers in two lineages of Lariophagus distinguendus (Chalcidoidea: Hymenoptera), a parasitoid wasp of pest beetle larvae that occur in human environments. One of the two lineages occurs in households preferably attacking larvae of the drugstore beetle Stegobium paniceum ("DB-lineage"), the other in grain stores with larvae of the granary weevil Sitophilus granarius as main host ("GW-lineage"). Between two populations of the DB-lineage, we identified slight sexual isolation as intraspecific barrier. Between populations from both lineages, we found almost complete sexual isolation caused by female mate choice, and postzygotic isolation, which is partially caused by cytoplasmic incompatibility induced by so far undescribed endosymbionts which are not Wolbachia or Cardinium. Because separation between the two lineages is almost complete, they should be considered as separate species according to the biological species concept. This demonstrates that cryptic species within parasitoid Hymenoptera also occur in Central Europe in close contact to humans.

RevDate: 2019-11-16

Zhao L, de Hoog S, Hagen F, et al (2019)

Species borderlines in Fusarium exemplified by F. circinatum/F. subglutinans.

Fungal genetics and biology : FG & B, 132:103262.

Fusarium species are known as cross-kingdom pathogens, causing infections in both plants and animals. This ecological variation challenges the species concept of closely similar lineages in the genus. The present paper describes various types of genetic interaction between strains of two neighboring model species with different predilection, F. circinatum and F. subglutinans. Parameters include sequencing of the translation elongation factor 1α (TEF1) and the second largest subunit of RNA polymerase (RPB2), sexual crossing, and vegetative compatibility groups (VCGs). Successful interspecific crosses resulted in either recombination or in homothallic fruiting, the latter being limited to F. subglutinans MAT1 parents. Crossings were skewed, as Fusarium circinatum recombined more often than F. subglutinans. We hypothesize that genetic exchange in Fusarium species is finely regulated with an arsenal of options, which are applied when partners are phylogenetically closely related, leading to fluent species borderlines.

RevDate: 2019-08-09

Arevalo P, VanInsberghe D, Elsherbini J, et al (2019)

A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations.

Cell, 178(4):820-834.e14.

Delineating ecologically meaningful populations among microbes is important for identifying their roles in environmental and host-associated microbiomes. Here, we introduce a metric of recent gene flow, which when applied to co-existing microbes, identifies congruent genetic and ecological units separated by strong gene flow discontinuities from their next of kin. We then develop a pipeline to identify genome regions within these units that show differential adaptation and allow mapping of populations onto environmental variables or host associations. Using this reverse ecology approach, we show that the human commensal bacterium Ruminococcus gnavus breaks up into sharply delineated populations that show different associations with health and disease. Defining populations by recent gene flow in this way will facilitate the analysis of bacterial and archaeal genomes using ecological and evolutionary theory developed for plants and animals, thus allowing for testing unifying principles across all biology.

RevDate: 2020-01-08

McKenzie JL, Chung DJ, Healy TM, et al (2019)

Mitochondrial Ecophysiology: Assessing the Evolutionary Forces That Shape Mitochondrial Variation.

Integrative and comparative biology, 59(4):925-937.

The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.

RevDate: 2019-06-28

Guzmán-Verri C, Suárez-Esquivel M, Ruíz-Villalobos N, et al (2019)

Genetic and Phenotypic Characterization of the Etiological Agent of Canine Orchiepididymitis Smooth Brucella sp. BCCN84.3.

Frontiers in veterinary science, 6:175.

Members of the genus Brucella cluster in two phylogenetic groups: classical and non-classical species. The former group is composed of Brucella species that cause disease in mammals, including humans. A Brucella species, labeled as Brucella sp. BCCN84.3, was isolated from the testes of a Saint Bernard dog suffering orchiepididymitis, in Costa Rica. Following standard microbiological methods, the bacterium was first defined as "Brucella melitensis biovar 2." Further molecular typing, identified the strain as an atypical "Brucella suis." Distinctive Brucella sp. BCCN84.3 markers, absent in other Brucella species and strains, were revealed by fatty acid methyl ester analysis, high resolution melting PCR and omp25 and omp2a/omp2b gene diversity. Analysis of multiple loci variable number of tandem repeats and whole genome sequencing demonstrated that this isolate was different from the currently described Brucella species. The smooth Brucella sp. BCCN84.3 clusters together with the classical Brucella clade and displays all the genes required for virulence. Brucella sp. BCCN84.3 is a species nova taxonomical entity displaying pathogenicity; therefore, relevant for differential diagnoses in the context of brucellosis. Considering the debate on the Brucella species concept, there is a need to describe the extant taxonomical entities of these pathogens in order to understand the dispersion and evolution.

RevDate: 2020-01-08
CmpDate: 2020-01-08

Darienko T, Kang W, Orzechowski AK, et al (2019)

Pleurastrosarcina terriformae, a new species of a rare desert trebouxiophycean alga discovered by an integrative approach.

Extremophiles : life under extreme conditions, 23(5):573-586.

Biological soil crusts of extreme habitats (semi-deserts and deserts) are dominated by cyanobacteria and microalgae. The most abundant taxa are green algae belonging to the classes Chlorophyceae and Trebouxiophyceae. Specimens with sarcinoid-like morphology (cells arranged in packages) represent one group of these microalgae. The genus Pleurastrosarcina consists of two species, which were originally described as Chlorosarcina (P. brevispinosa and P. longispinosa). Both species are exclusively found from arid soils. However, these species were only reported few times and probably overlooked especially if no akinetes were present. During studying soil samples collected from different regions of the Atacama desert (Chile), we isolated two strains, which were morphologically similar to both Pleurastrosarcina species. The phylogenetic analyses confirmed that they belong to this genus. The ITS-2/CBC approach revealed that both new isolates represent a new species, P. terriformae. The comparison with other available strains demonstrated that this new species is not restricted to South America and was also found in coastal area in Europe. The six investigated strains showed a high phenotypic plasticity, which is reflected in the descriptions of several varieties.

RevDate: 2019-09-12

Su H, Packeu A, Ahmed SA, et al (2019)

Species Distinction in the Trichophyton rubrum Complex.

Journal of clinical microbiology, 57(9): pii:JCM.00352-19.

The Trichophyton rubrum species complex comprises commonly encountered dermatophytic fungi with a worldwide distribution. The members of the complex usually have distinct phenotypes in culture and cause different clinical symptoms, despite high genome similarity. In order to better delimit the species within the complex, molecular, phenotypic, and physiological characteristics were combined to reestablish a natural species concept. Three groups, T. rubrum, T. soudanense, and T. violaceum, could be distinguished based on the sequence of the internal transcribed spacer (ITS) ribosomal DNA barcode gene. On average, strains within each group were similar by colony appearance, microscopy, and physiology, but strains between groups showed significant differences. Trichophyton rubrum strains had higher keratinase activity, whereas T. violaceum strains tended to be more lipophilic; however, none of the phenotypic features were diagnostic. The results of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and amplified fragment length polymorphism (AFLP) were partially consistent with the ITS data but failed to distinguish the species unambiguously. Despite their close similarity, T. violaceum, T. soudanense, and T. rubrum can be regarded as independent species with distinct geographical distributions and clinical predilections. Trichophyton soudanense is pheno- and genotypically intermediate between T. rubrum and T. violaceum For routine diagnostics, ITS sequencing is recommended.

RevDate: 2020-01-25

Wagner L, de Hoog S, Alastruey-Izquierdo A, et al (2019)

A Revised Species Concept for Opportunistic Mucor Species Reveals Species-Specific Antifungal Susceptibility Profiles.

Antimicrobial agents and chemotherapy, 63(8): pii:AAC.00653-19.

Recently, the species concept of opportunistic Mucor circinelloides and its relatives has been revised, resulting in the recognition of its classical formae as independent species and the description of new species. In this study, we used isolates of all clinically relevant Mucor species and performed susceptibility testing using the EUCAST reference method to identify potential species-specific susceptibility patterns. In vitro susceptibility profiles of 101 mucoralean strains belonging to the genus Mucor (72), the closely related species Cokeromyces recurvatus (3), Rhizopus (12), Lichtheimia (10), and Rhizomucor (4) to six antifungals (amphotericin B, natamycin, terbinafine, isavuconazole, itraconazole, and posaconazole) were determined. The most active drug for all Mucorales was amphotericin B. Antifungal susceptibility profiles of pathogenic Mucor species were specific for isavuconazole, itraconazole, and posaconazole. The species formerly united in M. circinelloides showed clear differences in their antifungal susceptibilities. Cokeromyces recurvatus, Mucor ardhlaengiktus, Mucor lusitanicus (M. circinelloides f. lusitanicus), and Mucor ramosissimus exhibited high MICs to all azoles tested. Mucor indicus presented high MICs for isavuconazole and posaconazole, and Mucor amphibiorum and Mucor irregularis showed high MICs for isavuconazole. MIC values of Mucor spp. for posaconazole, isavuconazole, and itraconazole were high compared to those for Rhizopus and the Lichtheimiaceae (Lichtheimia and Rhizomucor). Molecular identification combined with in vitro susceptibility testing is recommended for Mucor species, especially if azoles are applied in treatment.

RevDate: 2019-10-23

Li M, Zhao H, Zhao F, et al (2019)

Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae).

Annals of botany, 124(2):233-243.

BACKGROUND AND AIMS: Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models.

METHODS: We examined the phylogenetic implications of the CBC process by using a comprehensive sampling of ITS2 from ten closely related species of Corydalis. We predicted ITS2 secondary structures by using homology modelling, which was then used for a structure-based alignment. Paired and unpaired regions were analysed separately and in combination by using both RNA-specific substitution models and conventional DNA models. We mapped all base-pair states of CBCs on the phylogenetic tree to infer their evolution and relative timing.

KEY RESULTS: Our results indicate that selection acted to increase the thermodynamic stability of the secondary structure. Thus, the unpaired and paired regions did not evolve under a common substitution model. Only two CBCs occurred within the lineage sampled and no striking differences in topology or support for the shared clades were found between trees constructed using DNA- or RNA-specific substitution models.

CONCLUSIONS: Although application of RNA-specific substitution models remains preferred over more conventional DNA models, we infer that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within closely related lineages wherein few CBCs are observed. Each of the two CBCs was found within the same lineages but was not observed within a given species, which supports application of the CBC species concept.

RevDate: 2019-10-11

Hundsdoerfer AK, Lee KM, Kitching IJ, et al (2019)

Genome-wide SNP Data Reveal an Overestimation of Species Diversity in a Group of Hawkmoths.

Genome biology and evolution, 11(8):2136-2150.

The interface between populations and evolving young species continues to generate much contemporary debate in systematics depending on the species concept(s) applied but which ultimately reduces to the fundamental question of "when do nondiscrete entities become distinct, mutually exclusive evolutionary units"? Species are perceived as critical biological entities, and the discovery and naming of new species is perceived by many authors as a major research aim for assessing current biodiversity before much of it becomes extinct. However, less attention is given to determining whether these names represent valid biological entities because this is perceived as both a laborious chore and an undesirable research outcome. The charismatic spurge hawkmoths (Hyles euphorbiae complex, HEC) offer an opportunity to study this less fashionable aspect of systematics. To elucidate this intriguing systematic challenge, we analyzed over 10,000 ddRAD single nucleotide polymorphisms from 62 individuals using coalescent-based and population genomic methodology. These genome-wide data reveal a clear overestimation of (sub)species-level diversity and demonstrate that the HEC taxonomy has been seriously oversplit. We conclude that only one valid species name should be retained for the entire HEC, namely Hyles euphorbiae, and we do not recognize any formal subspecies or other taxonomic subdivisions within it. Although the adoption of genetic tools has frequently revealed morphologically cryptic diversity, the converse, taxonomic oversplitting of species, is generally (and wrongly in our opinion) accepted as rare. Furthermore, taxonomic oversplitting is most likely to have taken place in intensively studied popular and charismatic organisms such as the HEC.

RevDate: 2019-11-20

Petrželová I, M Sochor (2019)

How useful is the current species recognition concept for the determination of true morels? Insights from the Czech Republic.

MycoKeys, 52:17-43 pii:32335.

The phylogentic diversity of the genus Morchella has only been sporadically studied in Central Europe. In this study, a molecular taxonomic revision of the Morchella species of the Czech Republic was performed using available fungarium specimens, fresh collections, and axenic cultures. Molecular phylogenetic analyses based on either ITS or five-locus (ITS, LSU, RPB1, RPB2, and EF-1α) sequencing and the application of principles of the genealogical concordance phylogenetic species recognition (GCPSR) have revealed the occurrence of 11 phylogenetic species in the region, but only six of them could be assigned unequivocally to the previously published phylospecies: Mel-3 (M.semilibera), Mel-10 (M.importuna), Mel-19 (M.eohespera), Mes-4 (M.americana), Mes-5 and Mes-8 (M.esculenta). One lineage was identified as a new phylospecies and is designated as Mel-39. Four lineages grouped together with two or more previously published phylospecies: Mel-13/26 (M.deliciosa), Mel-15/16 (M.angusticeps / M.eximioides), Mel-20/34 (M.purpurascens), and Mel-23/24/31/32 (M.pulchella). Our phylogenetic analyses and literature review shed light on the pitfalls of current molecular taxonomy of morels and highlight the ambiguities of present species recognition concepts. The main source of the problems seems to be rooted in the application of different methods (multigene vs single-gene sequencing, phenotypic determination) and approaches (monophyly vs paraphyly, the application or not of GCPSR, degree of differentiation between accepted species, etc.) by various authors for the delimitation of new phylospecies. Therefore, we propose five criteria for distinguishing new phylospecies in the genus Morchella based on molecular data, and recommend a more conservative approach in species delimitation.

RevDate: 2019-08-08
CmpDate: 2019-08-08

Haelewaters D, Boer P, Báthori F, et al (2019)

Studies of Laboulbeniales on Myrmica ants (IV): host-related diversity and thallus distribution patterns of Rickia wasmannii.

Parasite (Paris, France), 26:29.

Fungal species identities are often based on morphological features, but current molecular phylogenetic and other approaches almost always lead to the discovery of multiple species in single morpho-species. According to the morphological species concept, the ant-parasitic fungus Rickia wasmannii (Ascomycota, Laboulbeniales) is a single species with pan-European distribution and a wide host range. Since its description, it has been reported from ten species of Myrmica (Hymenoptera, Formicidae), of which two belong to the rubra-group and the other eight to the phylogenetically distinct scabrinodis-group. We found evidence for R. wasmannii being a single phylogenetic species using sequence data from two loci. Apparently, the original morphological description (dating back to 1899) represents a single phylogenetic species. Furthermore, the biology and host-parasite interactions of R. wasmannii are not likely to be affected by genetic divergence among different populations of the fungus, implying comparability among studies conducted on members of different ant populations. We found no differences in total thallus number on workers between Myrmica species, but we did observe differences in the pattern of thallus distribution over the body. The locus of infection is the frontal side of the head in Myrmica rubra and M. sabuleti whereas in M. scabrinodis the locus of infection differs between worker ants from Hungary (gaster tergites) and the Netherlands (frontal head). Possible explanations for these observations are differences among host species and among populations of the same species in (i) how ant workers come into contact with the fungus, (ii) grooming efficacy, and (iii) cuticle surface characteristics.

RevDate: 2019-09-25
CmpDate: 2019-09-24

Brasch J, R Gläser (2019)

[Dynamic diversity of dermatophytes].

Der Hautarzt; Zeitschrift fur Dermatologie, Venerologie, und verwandte Gebiete, 70(8):575-580.

BACKGROUND: Many dermatologists do not understand the perpetual adjustments in the dermatophyte nomenclature.

OBJECTIVES: The aim is to explain the background and the development of methods that have led to previous and current changes of dermatophyte taxonomy and to the detection of new dermatophytes.

METHODS: In this article we evaluate the recent literature on this topic and our own results in the fields of dermatophyte identification, their detection, and of the associated taxonomic developments.

RESULTS: Today, the phylogenetic species concept is the basis of taxonomic classification, including that of dermatophytes. Genetic techniques have decisively advanced this and are state of the art nowadays. The detection of new dermatophyte species was often triggered by clinical observations and by morphologically conspicuous cultures that prompted their subsequent exact mycological characterization. Even today not all species of dermatophytes are unequivocally defined.

CONCLUSIONS: By exclusively using selected genetic characteristics for the construction of phylogenetic trees additional taxonomically relevant features are neglected. Therefore it is necessary to better integrate data derived from morphologic, physiologic, ecologic and pathophysiologic observations into phylogenetic analyses. Dermatologists are still asked to contribute such information.

RevDate: 2019-11-20

Korshunova T, Picton B, Furfaro G, et al (2019)

Multilevel fine-scale diversity challenges the 'cryptic species' concept.

Scientific reports, 9(1):6732 pii:10.1038/s41598-019-42297-5.

'Cryptic' species are an emerging biological problem that is broadly discussed in the present study. Recently, a cryptic species definition was suggested for those species which manifest low morphological, but considerable genetic, disparity. As a case study we present unique material from a charismatic group of nudibranch molluscs of the genus Trinchesia from European waters to reveal three new species and demonstrate that they show a dual nature: on one hand, they can be considered a 'cryptic' species complex due to their overall similarity, but on the other hand, stable morphological differences as well as molecular differences are demonstrated for every species in that complex. Thus, this species complex can equally be named 'cryptic', 'pseudocryptic' or 'non-cryptic'. We also present evidence for an extremely rapid speciation rate in this species complex and link the species problem with epigenetics. Available metazoan-wide data, which are broadly discussed in the present study, show the unsuitability of a 'cryptic' species concept because the degree of crypticity represents a continuum when a finer multilevel morphological and molecular scale is applied to uncover more narrowly defined species making the 'cryptic' addition to 'species' redundant. Morphological and molecular methods should be applied in concordance to form a fine-scale multilevel taxonomic framework, and not necessarily implying only an a posteriori transformation of exclusively molecular-based 'cryptic' species into morphologically-defined 'pseudocryptic' ones. Implications of the present study have importance for many fields, including conservation biology and fine-scale biodiversity assessments.

RevDate: 2019-08-13

González-Resendiz L, Johansen JR, León-Tejera H, et al (2019)

A bridge too far in naming species: a total evidence approach does not support recognition of four species in Desertifilum (Cyanobacteria).

Journal of phycology, 55(4):898-911.

A population of Desertifilum (Cyanobacteria, Oscillatoriales) from an oligotrophic desertic biotope was isolated and characterized using a polyphasic approach including molecular, morphological, and ecological information. The population was initially assumed to be a new species based on ecological and biogeographic separation from other existing species, however, phylogenetic analyses based on sequences of the 16S rRNA gene and 16S-23S ITS region, placed this strain clearly within the type species, Desertifilum tharense. Comparative analysis of morphology, 16S rRNA gene similarity, 16S-23S ITS secondary structure, and percent dissimilarity of the ITS regions for all characterized strains supports placing the six Desertifilum strains (designated as PD2001/TDC17, UAM-C/S02, CHAB7200, NapGTcm17, IPPAS B-1220, and PMC 872.14) into D. tharense. The recognition of Desertifilum salkalinema and Desertifilum dzianense is not supported, although our analysis does support continued recognition of Desertifilum fontinale. Pragmatic criteria for recognition of closely related species are proposed based on this study and others, and more rigorous review of future taxonomic papers is recommended.

RevDate: 2019-11-20

Galtier N (2019)

Delineating species in the speciation continuum: A proposal.

Evolutionary applications, 12(4):657-663 pii:EVA12748.

Delineating species is a difficult and seemingly uninteresting issue that is still essential to address. Taxonomic methodology is heterogeneous according to the taxa and scientists involved due to the disparate data quality and quantity and disagreements over the species concept. This has negative impacts on basic and applied research. Genomic data substantially enhance our understanding of the speciation process but do not provide a ubiquitous solution to the species problem. The relevance of comparative approaches in speciation research has nevertheless recently been demonstrated. I suggest moving towards a more unified taxonomic classification through a reference-based decision procedure.

RevDate: 2019-12-19
CmpDate: 2019-12-19

Aguado MT, Capa M, Lago-Barcia D, et al (2019)

Species delimitation in Amblyosyllis (Annelida, Syllidae).

PloS one, 14(4):e0214211 pii:PONE-D-18-21574.

Amblyosyllis is a worldwide distributed group of annelids mainly found in coastal environments. It is well known among the polychaete specialists mostly because of its notable beauty, showing bright colourful patterns and outstanding long and coiled appendices. Amblyosyllis is a monophyletic genus easy to identify due to its distinct diagnostic features; however, the species and their boundaries are, in most cases, not well defined. Herein, we provide an extensive sample of Amblyosyllis material (115 specimens) from several world geographic areas. We have studied the morphological features of each specimen and photographed them alive. Two mitochondrial DNA markers (COI and 16S) and one nuclear gene fragment (28S, D1 region) were sequenced. We performed phylogenetic analyses based on each DNA partition, as well as the combined data sets, obtaining congruent results. Species delimitation methods such as distance analyses, statistical parsimony networks and multi-rate Poisson tree processes were also applied. The combined results obtained from different methodologies and data sets are used to differentiate between, at least, 19 lineages compatible with the separately evolving meta-populations species concept. Four of these lineages are identified as nominal species, including the type species of Amblyosyllis, A. rhombeata. For three other lineages previously synonymized names are recovered, and seven lineages are described as new species. All of these species are described and supported by appropriate iconography. We recognize several morphological characters useful to identify species of Amblyosyllis, which in some cases should also be combined with molecular methods for species delineation. The genetic divergence in the genus is high, contrary to the morphological homogeneity observed. Two species show a wide geographical distribution, while the rest have a more restricted distribution. There are several examples of species with overlapping distribution patterns.

RevDate: 2019-06-11

Velamala GR, Naranji MK, Kondamudi RB, et al (2019)

DNA barcoding of commercially important snapper species (Lutjaniformes; Lutjanidae; Lutjanus) from Visakhapatnam, Central Eastern coast of India.

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis, 30(4):585-591.

Snappers are commercially important fishes in Indian waters, currently belonging to the order Lutjaniformes, family Lutjanidae. Generally, recognizing species of Lutjanus is a challenging task not only because of overlapping morphological characters, such as shapes, size groups, or colour patterns, but also based on the definition of the species concept or the definition of the threshold for speciation. In India there has not been any updated and accurate study of the genus so far. Besides, identification of the group based on ecological aspects and DNA barcoding tools were confined to limited laboratories. In the present study, ten species of snappers were identified from samples obtained from the major fish landing centres in the Visakhapatnam, Central Eastern coast of India. Snapper species were identified using COI (Cytochrome oxidase I) sequences for DNA barcoding. The validity of the conjecture species-level taxonomy based on COI is assisted with high equivalence search (98-100%) both in BOLD and BLAST, well-distributed genetic distance values.

RevDate: 2020-01-08

Hill GE (2019)

Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression.

Integrative and comparative biology, 59(4):912-924.

The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.

RevDate: 2019-11-20

Gao YD, Gao XF, A Harris (2019)

Species Boundaries and Parapatric Speciation in the Complex of Alpine Shrubs, Rosa sericea (Rosaceae), Based on Population Genetics and Ecological Tolerances.

Frontiers in plant science, 10:321.

Discerning species boundaries among closely related taxa is fundamental to studying evolution and biodiversity. However, species boundaries can be difficult to access in plants because ongoing divergence and speciation may leave an evolutionary footprint similar to introgression, which occurs frequently among species and genera. In this study, we sought to determine species boundaries between two closely related alpine shrubs, Rosa sericea and Rosa omeiensis, using population genetics, environmental data and ecological niche modeling, and morphological traits. We analyzed populations of R. sericea and R. omeiensis using genetic markers comprising a fragment of the single-copy nuclear gene, LEAFY, micro-satellites (EST-SSR), and plastid DNA sequences. The DNA sequence data suggested clusters of populations consistent with geography but not with previously proposed species boundaries based on morphology. Nevertheless, we found that the ecological niches of the previously proposed species only partially overlap. Thus, we suspect that these species are in the process of parapatric speciation; that is, differentiating along an ecological gradient, so that they exhibit differing morphology. Morphology has previously been the basis of recognizing the species R.sericea and R. omeiensis, which are the most widely distributed species within a broader R. sericea complex that includes several other narrow endemics. Here, we recognize R.sericea and R. omeiensis as independent species based on morphological and ecological data under the unified species concept, which emphasizes that these data types are of equal value to DNA for determining species boundaries and refining taxonomic treatments. While the DNA data did not delimit species within the R.sericea complex, we expect to develop and utilize new, robust DNA tools for understanding speciation within this group in future studies.

RevDate: 2019-11-20

Telschow A, Gadau J, Werren JH, et al (2019)

Genetic Incompatibilities Between Mitochondria and Nuclear Genes: Effect on Gene Flow and Speciation.

Frontiers in genetics, 10:62.

The process of speciation is, according to the biological species concept, the reduction in gene flow between genetically diverging populations. Most of the previous theoretical studies analyzed the effect of nuclear genetic incompatibilities on gene flow. There is, however, an increasing number of empirical examples suggesting that cytoplasmically inherited genetic elements play an important role in speciation. Here, we present a theoretical analysis of mitochondrial driven speciation, in which genetic incompatibilities occur between mitochondrial haplotypes and nuclear alleles. Four population genetic models with mainland-island structure were analyzed that differ with respect to the type of incompatibility and the underlying genetics. Gene flow reduction was measured on selectively neutral alleles of an unlinked locus and quantified by the effective migration rate. Analytical formulae for the different scenarios were derived using the fitness graph method. For the models with haploid genetics, we found that mito-nuclear incompatibilities (MtNI) are as strong as nuclear-nuclear incompatibilities (NNI) in reducing gene flow at the unlinked locus, but only if males and females migrate in equal number. For models with diploid genetics, we found that MtNI reduce gene flow stronger than NNI when incompatibilities are recessive, but weaker when they are dominant. For both haploid and diploid MtNI, we found that gene flow reduction is stronger if females are the migrating sex, but weaker than NNI when males are the migrating sex. These results encourage further examination on the role of mitochondria on genetic divergence and speciation and point toward specific factors (e.g., migrating sex) that could be the focus of an empirical test.

RevDate: 2019-07-08
CmpDate: 2019-07-08

Aghová T, Palupčíková K, Šumbera R, et al (2019)

Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny.

BMC evolutionary biology, 19(1):69 pii:10.1186/s12862-019-1380-9.

BACKGROUND: Spiny mice of the genus Acomys are distributed mainly in dry open habitats in Africa and the Middle East, and they are widely used as model taxa for various biological disciplines (e.g. ecology, physiology and evolutionary biology). Despite their importance, large distribution and abundance in local communities, the phylogeny and the species limits in the genus are poorly resolved, and this is especially true for sub-Saharan taxa. The main aims of this study are (1) to reconstruct phylogenetic relationships of Acomys based on the largest available multilocus dataset (700 genotyped individuals from 282 localities), (2) to identify the main biogeographical divides in the distribution of Acomys diversity in dry open habitats in Afro-Arabia, (3) to reconstruct the historical biogeography of the genus, and finally (4) to estimate the species richness of the genus by application of the phylogenetic species concept.

RESULTS: The multilocus phylogeny based on four genetic markers shows presence of five major groups of Acomys called here subspinosus, spinosissimus, russatus, wilsoni and cahirinus groups. Three of these major groups (spinosissimus, wilsoni and cahirinus) are further sub-structured to phylogenetic lineages with predominantly parapatric distributions. Combination of alternative species delimitation methods suggests the existence of 26 molecular operational taxonomic units (MOTUs), potentially corresponding to separate species. The highest genetic diversity was found in Eastern Africa. The origin of the genus Acomys is dated to late Miocene (ca. 8.7 Ma), when the first split occurred between spiny mice of eastern (Somali-Masai) and south-eastern (Zambezian) savannas. Further diversification, mostly in Plio-Pleistocene, and the current distribution of Acomys were influenced by the interplay of global climatic factors (e.g., Messinian salinity crisis, intensification of Northern Hemisphere glaciation) with local geomorphology (mountain chains, aridity belts, water bodies). Combination of divergence dating, species distribution modelling and historical biogeography analysis suggests repeated "out-of-East-Africa" dispersal events into western Africa, the Mediterranean region and Arabia.

CONCLUSIONS: The genus Acomys is very suitable model for historical phylogeographic and biogeographic reconstructions of dry non-forested environments in Afro-Arabia. We provide the most thorough phylogenetic reconstruction of the genus and identify major factors that influenced its evolutionary history since the late Miocene. We also highlight the urgent need of integrative taxonomic revision of east African taxa.

RevDate: 2019-11-20

Murphy JC, Braswell AL, Charles SP, et al (2019)

A new species of Erythrolamprus from the oceanic island of Tobago (Squamata, Dipsadidae).


Tobago is a small island on the southeast edge of the Caribbean Plate with a continental flora and fauna. Using DNA sequences from Genbank, new sequences, and morphological data from the snakes Erythrolamprusepinephalus, E.melanotus, E.reginae, and E.zweifeli, the species status of specimens of a Tobago snake previously considered to be Erythrolamprusreginae was assessed. Erythrolampruszweifeli, long considered a subspecies of E.reginae, was found to be a northern Venezuela-Trinidad endemic and the sister to E.reginae. The trans-Andean species E.epinephalus is shown to be non-monophyletic while the Costa Rican lineage of E.epinephalus is weakly supported as the sister to the Tobago population. The Tobago Erythrolamprus is described as a distinct taxon based upon five specimens from four localities in lower montane rainforest. Much of the new species range includes the Main Ridge Forest Reserve of Tobago, the oldest protected forest in the Western Hemisphere. All known locations fall within a 400-ha area, and its total geographic distribution is likely to be less than 4,566 ha. The restricted distribution of this new snake makes it a likely candidate for threatened status. The new species also becomes another biogeographic link between northern Venezuela and Tobago.

RevDate: 2019-02-15
CmpDate: 2019-02-04

Freyhof J, BayÇelebİ E, M Geiger (2018)

Review of the genus Cobitis in the Middle East, with the description of eight new species (Teleostei: Cobitidae).

Zootaxa, 4535(1):1-75 pii:zootaxa.4535.1.1.

The diversity of Cobitis in the Middle East is reviewed, resulting in the recognition of 30 species, of which eight are described herein as new. Two species, C. amphilekta and C. kellei, seem to be extinct. Hypotheses on species-level diversity derived from distance and Poisson tree process analyses of DNA barcode data are tested against morphometric and morphological characters including colour patterns. For species pairs separated by small K2P distances in COI sequence data we follow a practitioner-oriented diagnostic species concept, in which we recognise species only if differentiated morphologically (including by colour pattern). For all 30 species we provide diagnoses and identification keys. Cobitis afifeae, new species, from the Büyük Menderes River drainage in the Aegean Sea basin, is distinguished by having two laminae circularis in the male, a row of blotches below Z4, a small, roundish or comma-shaped black spot at the upper caudal-fin base, and elevated mental lobes. Cobitis aliyeae, new species, from the lower Seyhan and Ceyhan River drainages, is distinguished by having two laminae circularis in the male, the blotches in Z2 and Z4 anterior to the dorsal-fin origin usually well separated from each other, and the pigmentation in Z1 well distinguished from the pigmentation in Z2. Cobitis anabelae, new species, from the lower Orontes River drainage, is distinguished by having two laminae circularis in the male, the pigmentation in Z2 formed by small, brown spots, always much smaller than blotches in Z3, much smaller than the pupil diameter, Z2 and Z3 well separated, and no pigmentation below Z4. Cobitis erkakanae, new species, from the Gölbasi Lakes, adjacent to the Ceyhan River drainage, is distinguished by having two laminae circularis in the male, no blotches below Z4, the blotches in Z2 and Z4 being horizontally elongated and often fused with adjacent ones, and the caudal fin with 4-6 wide, regularly-shaped, brown bands. Cobitis emrei, new species, from the Lake Sapanca basin is distinguished by having one lamina circularis in the male, a large black spot at the upper caudal-fin base, and Z3 fully covered by very small spots forming a sand-like pattern. Cobitis joergbohleni, new species, from the Sultan marshes in Central Anatolia is distinguished by having two laminae circularis in the male, and the flank colour pattern being completely disorganised, not following the Gambetta zones. Cobitis pirii, new species, from the endorheic Lake Eğirdir basin and the Mediterranean Aksu and Köprü Rivers, is distinguished by having two laminae circularis in the male, a simple external part of the suborbital spine and two distinct rows of small blotches in Z4, one along the lateral midline and one distinctly below. Cobitis troasensis, new species, from the Tuzla River drainage, is distinguished by having one lamina circularis in the male and 25-36 small, comma-shaped brown blotches in Z4. A lectotype is designated for Cobitis battalgilae. As First Revisers, priority is given to Cobitis fahireae over C. kurui. Cobitis damlae and C. kurui are treated as synonyms of C. fahireae. Cobitis strumicae and C. taenia are recorded for the first time from Anatolia and C. saniae is newly documented from the Black Sea basin in Georgia. The Poisson tree process analysis of COI data proposed 31 groups, most of which could be distinguished by morphological characters. Cobitis troasensis is described based on morphological data alone.

RevDate: 2019-11-20

Lawrence DP, Holland LA, Nouri MT, et al (2018)

Molecular phylogeny of Cytospora species associated with canker diseases of fruit and nut crops in California, with the descriptions of ten new species and one new combination.

IMA fungus, 9:333-370.

Cytospora species are destructive canker and dieback pathogens of woody hosts in natural and agroecosystems around the world. In this genus, molecular identification has been limited due to the paucity of multi-locus sequence typing studies and the lack of sequence data from type specimens in public repositories, stalling robust phylogenetic reconstructions. In most cases a morphological species concept could not be applied due to the plasticity of characters and significant overlap of morphological features such as spore dimensions and fruiting body characters. In this study, we employed a molecular phylogenetic framework with the inclusion of four nuclear loci (ITS, translation elongation factor 1-alpha, actin, and beta-tubulin) to unveil the biodiversity and taxonomy of this understudied important genus of plant pathogens. Phylogenetic inferences based on 150 Californian isolates revealed 15 Cytospora species associated with branch and twig cankers and dieback of almond, apricot, cherry, cottonwood, olive, peach, pistachio, plum, pomegranate, and walnut trees in California. Of the 15 species recovered in this study, 10 are newly described and typified, in addition to one new combination. The pathogenic status of the newly described Cytospora species requires further investigation as most species were associated with severe dieback and decline of diverse and economically important fruit and nut crops in California.

RevDate: 2019-04-30
CmpDate: 2019-04-30

El-Sherry S, Ogedengbe ME, Hafeez MA, et al (2019)

Cecal coccidiosis in turkeys: Comparative biology of Eimeria species in the lower intestinal tract of turkeys using genetically typed, single oocyst-derived lines.

Parasitology research, 118(2):583-598.

Differentiating the Eimeria species causing cecal coccidiosis in turkeys is challenging. To obtain benchmark biological data for Eimeria gallopavonis Hawkins 1952 and Eimeria meleagridis Tyzzer 1929 and to support the stability of the species concept for each, genetically typed, single oocyst-derived lines of E. gallopavonis Weybridge strain and E. meleagridis USAR97-01 were used to redescribe the biological, pathological, and morphological features of these parasites. Oocysts of E. meleagridis and E. gallopavonis overlap in dimensions, but oocysts of the former have a single polar granule compared with multiple in the latter. Mature first-generation meronts of E. gallopavonis were observed histologically as early as 48 h post-inoculation alongside the villi in jejunum (before and after Meckel's diverticulum), ileum, cecal neck and rectum, but not cecal pouches. Three asexual cycles were observed suggesting that early workers apparently overlooked one asexual cycle. Examination of endogenous development of a culture labeled "Eimeria adenoeides Weybridge strain" suggested that this strain (found in a number of publications as a large oocyst strain of "Eimeria adenoeides") matched the species description of E. gallopavonis and so has been renamed herein. Macroscopic lesions induced by E. gallopavonis consisted of caseous material distally from posterior of the yolk stalk through the remaining intestinal tract, excluding the cecal pouches. For E. meleagridis, only the first asexual generation was observed outside of the cecal pouches within the jejunum around the yolk stalk. Second- and 3rd-generation asexual stages developed almost exclusively in the cecal pouches (but not cecal necks). Macroscopic lesions described for E. meleagridis were similar to those of E. adenoeides. Marked corrugation of the cecal serosal surface was observed. Cecal pouches contained creamy colored, caseous material varying from loose material to granular. Distinguishing features of the Eimeria species infecting the lower part of the small intestine are summarized in the present study, and new type specimens were designated for E. gallopavonis and E. meleagridis to provide a stable reference for future work with these parasites.

RevDate: 2019-11-20

Manceau M, A Lambert (2019)

The Species Problem from the Modeler's Point of View.

Bulletin of mathematical biology, 81(3):878-898.

How to define a partition of individuals into species is a long-standing question called the species problem in systematics. Here, we focus on this problem in the thought experiment where individuals reproduce clonally and both the differentiation process and the population genealogies are explicitly known. We specify three desirable properties of species partitions: (A) Heterotypy between species, (B) Homotypy within species and (M) Genealogical monophyly of each species. We then ask: How and when is it possible to delineate species in a way satisfying these properties? We point out that the three desirable properties cannot in general be satisfied simultaneously, but that any two of them can. We mathematically prove the existence of the finest partition satisfying (A) and (M) and the coarsest partition satisfying (B) and (M). For each of them, we propose a simple algorithm to build the associated phylogeny out of the genealogy. The ways we propose to phrase the species problem shed new light on the interaction between the genealogical and phylogenetic scales in modeling work. The two definitions centered on the monophyly property can readily be used at a higher taxonomic level as well, e.g., to cluster species into monophyletic genera.

RevDate: 2019-11-20

Chung M, Munro JB, Tettelin H, et al (2018)

Using Core Genome Alignments To Assign Bacterial Species.

mSystems, 3(6):.

With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method to assign species designations is needed that is consistent with classically obtained taxonomic analyses. This is particularly acute for unculturable, obligate intracellular bacteria with which classically defined methods, like DNA-DNA hybridization, cannot be used, such as those in the Rickettsiales. In this study, we generated nucleotide-based core genome alignments for a wide range of genera with classically defined species, as well as those within the Rickettsiales. We created a workflow that uses the length, sequence identity, and phylogenetic relationships inferred from core genome alignments to assign genus and species designations that recapitulate classically obtained results. Using this method, most classically defined bacterial genera have a core genome alignment that is ≥10% of the average input genome length. Both Anaplasma and Neorickettsia fail to meet this criterion, indicating that the taxonomy of these genera should be reexamined. Consistently, genomes from organisms with the same species epithet have ≥96.8% identity of their core genome alignments. Additionally, these core genome alignments can be used to generate phylogenomic trees to identify monophyletic clades that define species and neighbor-network trees to assess recombination across different taxa. By these criteria, Wolbachia organisms are delineated into species different from the currently used supergroup designations, while Rickettsia organisms are delineated into 9 distinct species, compared to the current 27 species. By using core genome alignments to assign taxonomic designations, we aim to provide a high-resolution, robust method to guide bacterial nomenclature that is aligned with classically obtained results. IMPORTANCE With the increasing availability of genome sequences, we sought to develop and apply a robust, portable, and high-resolution method for the assignment of genera and species designations that can recapitulate classically defined taxonomic designations. Using cutoffs derived from the lengths and sequence identities of core genome alignments along with phylogenetic analyses, we sought to evaluate or reevaluate genus- and species-level designations for diverse taxa, with an emphasis on the order Rickettsiales, where species designations have been applied inconsistently. Our results indicate that the Rickettsia genus has an overabundance of species designations, that the current Anaplasma and Neorickettsia genus designations are both too broad and need to be divided, and that there are clear demarcations of Wolbachia species that do not align precisely with the existing supergroup designations.

RevDate: 2019-11-20

Doungsa-Ard C, McTaggart AR, Geering ADW, et al (2018)

Diversity of gall-forming rusts (Uromycladium, Pucciniales) on Acacia in Australia.

Persoonia, 40:221-238.

Uromycladium tepperianum has been reported on over 100 species of Acacia, as well as on the closely related plant genera, Falcataria, Racosperma and Paraserianthes. Previous studies have indicated that U. tepperianum may represent a complex of host-specific, cryptic species. The phylogenetic relationships between 79 specimens of Uromycladium were determined based on a concatenated dataset of the Small Subunit, the Internal Transcribed Spacer and the Large Subunit regions of nuclear ribosomal DNA, and the mitochondrial cytochrome c oxidase subunit 3. This study showed that the host range of U. tepperianum s.str. was restricted to species of Acacia in the 'A. bivenosa group' sensu Chapman & Maslin (1992). An epitype of U. tepperianum on A. ligulata is designated to create a stable taxonomy for the application of this name. Sixteen novel species of Uromycladium are described, based on host preference, morphology and a phylogenetic species concept.

RevDate: 2019-01-15
CmpDate: 2018-12-19

Beaulieu F, JJ Beard (2018)

Acarine biocontrol agents Neoseiulus californicus sensu Athias-Henriot (1977) and N. barkeri Hughes (Mesostigmata: Phytoseiidae) redescribed, their synonymies assessed, and the identity of N. californicus (McGregor) clarified based on examination of types.

Zootaxa, 4500(4):451-507 pii:zootaxa.4500.4.1.

In 1954, McGregor described two species of phytoseiids from lemon, in California, USA: Typhlodromus californicus McGregor and T. mungeri McGregor, the former represented by one male, and the latter by two females. Since its description, T. mungeri was synonymised under T. californicus, and the name T. (now Neoseiulus) californicus has been used extensively to represent a species that is now commonly used as a biocontrol agent of crop pests worldwide. However, the true identity of the biocontrol agent is uncertain because the original descriptions of T. californicus and T. mungeri were not adequate enough to allow an irrefutable identification, with each description being based on specimens of a single sex. An examination of the types of N. californicus and N. mungeri revealed that they are morphologically identical to the male and female of N. barkeri Hughes, 1948, respectively, and that they are in fact junior synonyms of N. barkeri-and are therefore distinct from the biocontrol agent globally called N. californicus (sensu Athias-Henriot, 1977; see Griffiths, 2015). This is further supported by a comparison with male and female syntypes of N. barkeri, as well as other specimens of N. barkeri including some collected from the type host in the vicinity of the type location (i.e. lemon in southern California, 1952-1958). We redescribe the male and female of both N. barkeri and N. californicus sensu Athias-Henriot (1977), based on representative specimens from at least 14 and 19 populations, respectively. Based on examination of types, we confirm the synonymy of N. mckenziei (Schuster Pritchard, 1963), N. picketti (Specht, 1968), and N. oahuensis (Prasad, 1968) with N. barkeri, and that the names N. chilenensis (Dosse, 1958b) and N. wearnei (Schicha, 1987) represent the same species as N. californicus sensu Athias-Henriot (1977). We also provide a hypothesis as to why Chant (1959) had erroneously synonymised T. californicus and T. mungeri under T. marinus (Willmann). Finally, we suggest maintaining the prevailing usage of the name N. californicus (McGregor) for the species concept of Athias-Henriot (1977) as followed by subsequent authors, through submission of a separate application to the International Commission of Zoological Nomenclature (ICZN). In the meantime, the current meaning of N. californicus should be maintained until a ruling by the ICZN is made on the application.

RevDate: 2019-01-10
CmpDate: 2019-01-10

Jacobs RL, BW Baker (2018)

The species dilemma and its potential impact on enforcing wildlife trade laws.

Evolutionary anthropology, 27(6):261-266.

The varied answers to the question "What is a species?" provoke more than lively debates in academic circles. They pose practical problems for law enforcement. Commercial wildlife trade threatens many primate species and is regulated through such laws and international agreements as the U.S. Endangered Species Act and the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Enforcing legislation relies on the ability to identify when violations occur. Species-defining characters may not be preserved in wildlife trade items. For example, pelage patterns and behavioral characters (e.g., vocalizations) are absent from skulls. Accordingly, identifying victims of illegal trade can be difficult, which hinders enforcement. Moreover, identifying new species and "splitting" of currently recognized species can result in enforcement lags and regulatory loopholes. Although such negative consequences should not hinder scientific advancement, we suggest that they be considered by primate taxonomists and provide recommendations to prevent unintended conservation consequences.

RevDate: 2019-04-18
CmpDate: 2019-04-18

Koch JB, Rodriguez J, Pitts JP, et al (2018)

Phylogeny and population genetic analyses reveals cryptic speciation in the Bombus fervidus species complex (Hymenoptera: Apidae).

PloS one, 13(11):e0207080.

Bumble bees (Bombus Latrielle) are significant pollinators of flowering plants due to their large body size, abundant setae, and generalist foraging strategies. However, shared setal coloration patterns among closely and distantly related bumble bee species makes identification notoriously difficult. The advent of molecular genetic techniques has increased our understanding of bumble bee evolution and taxonomy, and enables effective conservation policy and management. Individuals belonging to the North American Bombus fervidus species-complex (SC) are homogenous in body structure but exhibit significant body color phenotype variation across their geographic distribution. Given the uncertainty of the genealogical boundaries within the SC, some authors have synonymized all members of the B. fervidus SC within a single taxon, while others propose an alternative two taxa hypothesis. Operating under the phylogenetic species concept, our analysis supports the hypothesis that there are two independent lineages of bumble bees within the B. fervidus SC. With the current evidence, however, it is not possible to assign valid names to either of them, because both lineages include the color phenotypes found in the original species descriptions of B. fervidus and B. californicus. Cryptic speciation does not seem to be the product of Müllerian mimicry between the clades, because diverging coloration patterns are observed when the distribution of the clades overlaps. Furthermore, within each lineage there is evidence for strong population differentiation that is correlated with geographic distribution rather than color phenotype. In our study, we demonstrate the importance of obtaining a broad sample of multiple populations when conducting lower-level phylogenetic analyses. In addition to improving our knowledge of bumble bee diversification patterns, characterizing the evolutionary history of these pollinators provides the foundation needed to guide contemporary conservation assessments and management strategies.

RevDate: 2019-04-01
CmpDate: 2019-04-01

Schuler GA, Tice AK, Pearce RA, et al (2018)

Phylogeny and Classification of Novel Diversity in Sainouroidea (Cercozoa, Rhizaria) Sheds Light on a Highly Diverse and Divergent Clade.

Protist, 169(6):853-874.

Sainouroidea is a molecularly diverse clade of cercozoan flagellates and amoebae in the eukaryotic supergroup Rhizaria. Previous 18S rDNA environmental sequencing of globally collected fecal and soil samples revealed great diversity and high sequence divergence in the Sainouroidea. However, a very limited amount of this diversity has been observed or described. The two described genera of amoebae in this clade are Guttulinopsis, which displays aggregative multicellularity, and Rosculus, which does not. Although the identity of Guttulinopsis is straightforward due to the multicellular fruiting bodies they form, the same is not true for Rosculus, and the actual identity of the original isolate is unclear. Here we isolated amoebae with morphologies like that of Guttulinopsis and Rosculus from many environments and analyzed them using 18S rDNA sequencing, light microscopy, and transmission electron microscopy. We define a molecular species concept for Sainouroidea that resulted in the description of 4 novel genera and 12 novel species of naked amoebae. Aggregative fruiting is restricted to the genus Guttulinopsis, but other than this there is little morphological variation amongst these taxa. Taken together, simple identification of these amoebae is problematic and potentially unresolvable without the 18S rDNA sequence.

RevDate: 2019-08-06
CmpDate: 2019-08-06

Meziti A, Tsementzi D, Rodriguez-R LM, et al (2019)

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient.

The ISME journal, 13(3):767-779.

Recent diversity studies have revealed that microbial communities of natural environments are dominated by species-like, sequence-discrete populations. However, how stable the sequence and gene-content diversity are within these populations and especially in highly dynamic lotic habitats remain unclear. Here we quantified the dynamics of intra-population diversity in samples spanning two years and five sites in the Kalamas River (Northwest Greece). A significant positive correlation was observed between higher intra-population sequence diversity and longer persistence over time, revealing that more diverse populations tended to represent more autochthonous (vs. allochthonous) community members. Assessment of intra-population gene-content changes caused by strain replacement or gene loss over time revealed different profiles with the majority of populations exhibiting gene-content changes close to 10% of the total genes, while one population exhibited ~21% change. The variable genes were enriched in hypothetical proteins and mobile elements, and thus, were probably functionally neutral or attributable to phage predation. A few notable exceptions to this pattern were also noted such as phototrophy-related proteins in summer vs. winter populations. Taken together, these results revealed that some freshwater genomes are remarkably dynamic, even across short time and spatial scales, and have implications for the bacterial species concept and microbial source tracking.

RevDate: 2019-09-02
CmpDate: 2019-09-02

Castorani MCN, Reed DC, RJ Miller (2018)

Loss of foundation species: disturbance frequency outweighs severity in structuring kelp forest communities.

Ecology, 99(11):2442-2454.

Disturbances often cause the disproportionate loss of foundation species but understanding how the frequency and severity of disturbance to such organisms influence biological communities remains unresolved. This gap in knowledge exists in part because of the rarity of ecologically meaningful studies capable of disentangling different elements of disturbance. Hence, we carried out a long-term (9 yr), large-scale (2,000 m2 plots), spatially replicated (4 sites) field experiment in which we manipulated disturbance to a globally distributed marine foundation species, the giant kelp Macrocystis pyrifera, and tracked community responses over time. To distinguish the effects of disturbance frequency and severity on the biodiversity and composition of temperate rocky reef communities, we simulated the repeated loss of giant kelp from destructive winter waves across a background of natural variation in disturbance. By following the response of over 200 taxa from the surrounding community, we discovered that the frequency of disturbance to giant kelp changed the biomass, diversity, and composition of community guilds in a manner commensurate with their dependence on the physical (i.e., benthic light and space), trophic (i.e., living and detrital biomass), and habitat (i.e., biogenic structure) resources mediated by this foundation species. Annual winter disturbance to giant kelp reduced living and detrital giant kelp biomass by 57% and 40%, respectively, enhanced bottom light by 22%, and halved the seafloor area covered by giant kelp holdfasts. Concomitantly, the biomass of understory algae and epilithic sessile invertebrates more than doubled, while the biomass of rock-boring clams, mobile invertebrates, and fishes decreased 30-61%. Frequent loss of giant kelp boosted understory algal richness by 82% and lowered sessile invertebrate richness by 13% but did not affect the biodiversity of mobile fauna. In contrast to changes driven by disturbance frequency, interannual variation in the severity of disturbance to giant kelp had weaker, less consistent effects, causing only modest changes in assemblages of sessile invertebrates, mobile invertebrate herbivores, and fishes. Our results broaden the foundation species concept by demonstrating that repeated disturbance to a dominant habitat-forming species can outweigh the influence of less frequent but severe disturbances for the surrounding community.

RevDate: 2019-10-29
CmpDate: 2019-10-29

Haelewaters D, De Kesel A, DH Pfister (2018)

Integrative taxonomy reveals hidden species within a common fungal parasite of ladybirds.

Scientific reports, 8(1):15966.

Our understanding of fungal diversity is far from complete. Species descriptions generally focus on morphological features, but this approach may underestimate true diversity. Using the morphological species concept, Hesperomyces virescens (Ascomycota, Laboulbeniales) is a single species with global distribution and wide host range. Since its description 120 years ago, this fungal parasite has been reported from 30 species of ladybird hosts on all continents except Antarctica. These host usage patterns suggest that H. virescens could be made up of many different species, each adapted to individual host species. Using sequence data from three gene regions, we found evidence for distinct clades within Hesperomyces virescens, each clade corresponding to isolates from a single host species. We propose that these lineages represent separate species, driven by adaptation to different ladybird hosts. Our combined morphometric, molecular phylogenetic and ecological data provide support for a unified species concept and an integrative taxonomy approach.

RevDate: 2019-04-08
CmpDate: 2019-04-08

Zink RM, H Vázquez-Miranda (2019)

Species Limits and Phylogenomic Relationships of Darwin's Finches Remain Unresolved: Potential Consequences of a Volatile Ecological Setting.

Systematic biology, 68(2):347-357.

Island biotas have become paradigms for illustrating many evolutionary processes. The fauna of the Galapagos Islands includes several taxa that have been focal points for evolutionary studies. Perhaps their most famous inhabitants, Darwin's finches, represent a go-to icon when thinking about how species originate and adapt to the environment. However, unlike other adaptive radiations, past morphological and molecular studies of Darwin's finches have yielded inconsistent hypotheses of species limits and phylogenetic relationships. Expecting that idiosyncrasies of prior data and analytic methods explained different proposed classifications, we were surprised to observe that three new phylogenetic hypotheses derived mostly from the same genomics data were topologically inconsistent. We found that the differences between some of these genomics trees were as great as one would expect between two random trees with the same number of taxa. Thus, the phylogeny of Darwin's finches remains unresolved, as it has for more than a century. A component of phylogenetic uncertainty comes from unclear species limits, under any species concept, in the ground finches (Geospiza) and tree finches (Camarhynchus). We suggest that past authors should have tested the species limits of Lack, rather than uncritically accepting them. In fact, the impressive amount of genomics data do not provide unambiguous hypotheses of the number of species of Geospiza or Camarhynchus, although they imply greater species diversity than Lack's taxonomy. We suggest that insufficient sampling of species populations across islands (35.6% for morphometrics and 20.4% for genomics) prevents accurate diagnoses of species limits. However, it is unknown whether samples from a greater number of islands might result in bridging differences between species, or reveal many new ones. We conclude that attempts to interpret patterns of variation among the finches under standard evolutionary paradigms have obscured some major messages, most specifically the ongoing reciprocal interactions between geographic isolation and lineage divergence, and dispersal and gene flow caused by the volatile ecological conditions in the islands. Although the finches provide textbook examples of natural selection, better understanding of species limits and a robust phylogenetic hypothesis are required to corroborate past hypotheses of speciation and adaptive radiation in the finches of the Galapagos.

RevDate: 2019-02-15
CmpDate: 2019-02-11

Vernygora OV, Davis CS, Murray AM, et al (2018)

Delimitation of Alosa species (Teleostei: Clupeiformes) from the Sea of Azov: integrating morphological and molecular approaches.

Journal of fish biology, 93(6):1216-1228.

Shads of the genus Alosa are essential to commercial fisheries across North America and Europe, but in some areas their species boundaries remain controversial. Traditional morphology-based taxonomy of Alosa spp. has relied heavily on the number of gill rakers and body proportions, but these can be highly variable. We use mitochondrial (mt)DNA (coI and cytb) and genome-wide single nucleotide polymorphisms (SNP) along with morphological characters to assess differentiation among endemic Ponto-Caspian shads in the Sea of Azov. Morphological species assignments based on gill-raker number were not congruent with genetic lineages shown by mtDNA and SNPs. Iterative analysis revealed that genetic lineages were associated with sampling location and several other morphometric traits (caudal peduncle depth, pre-anal length and head length). Phylogenetic analysis of the genus placed Ponto-Caspian Alosa spp. in the same evolutionary lineage as endangered Alosa spp. endemic to Greece, highlighting the importance of these findings to conservation management. We conclude that gill-raker number is not reliable for delimiting species of Alosa. This taxonomic uncertainty should be addressed by examining type material to provide a robust integrative classification for these commercially important fishes.

RevDate: 2019-03-20
CmpDate: 2019-02-20

Dantas-Torres F (2018)

Species Concepts: What about Ticks?.

Trends in parasitology, 34(12):1017-1026.

Since ancient times, philosophers and taxonomists have tried to classify forms of life. This is what taxonomy is about: the science of identifying, naming, classifying, and describing organisms. In this article I address the issue of the species concept in tick taxonomy. While the typological species concept is still the most widely used, the biological and phylogenetic species concepts are growing in popularity among tick taxonomists. The integrative approach is increasingly being used, but the question is how to define a tick species when using this approach, particularly if data are incongruent. The adoption of an integrative species concept is discussed, in light of recent advances in our understanding of the genetics, morphology, and biology of ticks.

RevDate: 2019-11-15
CmpDate: 2019-11-15

Suga H, Arai M, Fukasawa E, et al (2019)

Genetic Differentiation Associated with Fumonisin and Gibberellin Production in Japanese Fusarium fujikuroi.

Applied and environmental microbiology, 85(1): pii:AEM.02414-18.

Fusarium fujikuroi is a pathogenic fungus that infects rice. It produces several important mycotoxins, such as fumonisins. Fumonisin production has been detected in strains of maize, strawberry, and wheat, whereas it has not been detected in strains from rice seedlings infested with bakanae disease in Japan. We investigated the genetic relationships, pathogenicity, and resistance to a fungicide, thiophanate-methyl (TM), in 51 fumonisin-producing strains and 44 nonproducing strains. Phylogenetic analyses based on amplified fragment length polymorphism (AFLP) markers and two specific genes (a combined sequence of translation elongation factor 1α [TEF1α] and RNA polymerase II second-largest subunit [RPB2]) indicated differential clustering between the fumonisin-producing and -nonproducing strains. One of the AFLP markers, EATMCAY107, was specifically present in the fumonisin-producing strains. A specific single nucleotide polymorphism (SNP) between the fumonisin-producing and nonproducing strains was also detected in RPB2, in addition to an SNP previously found in TEF1α. Gibberellin production was higher in the nonproducing than in the producing strains according to an in vitro assay, and the nonproducing strains had the strongest pathogenicity with regard to rice seedlings. TM resistance was closely correlated with the cluster of fumonisin-nonproducing strains. The results indicate that intraspecific evolution in Japanese F. fujikuroi is associated with fumonisin production and pathogenicity. Two subgroups of Japanese F. fujikuroi, designated G group and F group, were distinguished based on phylogenetic differences and the high production of gibberellin and fumonisin, respectively.IMPORTANCEFusarium fujikuroi is a pathogenic fungus that causes rice bakanae disease. Historically, this pathogen has been known as Fusarium moniliforme, along with many other species based on a broad species concept. Gibberellin, which is currently known as a plant hormone, is a virulence factor of F. fujikuroi Fumonisin is a carcinogenic mycotoxin posing a serious threat to food and feed safety. Although it has been confirmed that F. fujikuroi produces gibberellin and fumonisin, production varies among strains, and individual production has been obscured by the traditional appellation of F. moniliforme, difficulties in species identification, and variation in the assays used to determine the production of these secondary metabolites. In this study, we discovered two phylogenetic subgroups associated with fumonisin and gibberellin production in Japanese F. fujikuroi.

RevDate: 2018-12-12
CmpDate: 2018-12-12

Zachos FE (2018)

(New) Species concepts, species delimitation and the inherent limitations of taxonomy.

Journal of genetics, 97(4):811-815.

The species problem, despite decades of heated debates, has not been resolved yet. Recently, two new species concepts have been published, the mitonuclear compatibility species concept and the inclusive species concept. I briefly discuss them, together with a recent attempt at standardizing taxonomic decisions, in the broader framework of what I believe is an inherent limitation of taxonomy-imposing a discrete system on a continuous process (evolution) that leads to fuzzy boundaries in nature. In the light of this, taxonomists, biologists in general and conservationists alike will have to accept the fact that completely nonarbitrary species delimitation is impossible. This has serious ramifications in all disciplines that rely on species, and particularly species counts, as a basic currency for quantitative analyses (ecology, evolutionary biology) and practical decision-making (conservation and environmental policy).

RevDate: 2019-10-25
CmpDate: 2019-10-25

Waters AJ, Capriotti P, Gaboriau DCA, et al (2018)

Rationally-engineered reproductive barriers using CRISPR & CRISPRa: an evaluation of the synthetic species concept in Drosophila melanogaster.

Scientific reports, 8(1):13125.

The ability to erect rationally-engineered reproductive barriers in animal or plant species promises to enable a number of biotechnological applications such as the creation of genetic firewalls, the containment of gene drives or novel population replacement and suppression strategies for genetic control. However, to date no experimental data exist that explores this concept in a multicellular organism. Here we examine the requirements for building artificial reproductive barriers in the metazoan model Drosophila melanogaster by combining CRISPR-based genome editing and transcriptional transactivation (CRISPRa) of the same loci. We directed 13 single guide RNAs (sgRNAs) to the promoters of 7 evolutionary conserved genes and used 11 drivers to conduct a misactivation screen. We identify dominant-lethal activators of the eve locus and find that they disrupt development by strongly activating eve outside its native spatio-temporal context. We employ the same set of sgRNAs to isolate, by genome editing, protective INDELs that render these loci resistant to transactivation without interfering with target gene function. When these sets of genetic components are combined we find that complete synthetic lethality, a prerequisite for most applications, is achievable using this approach. However, our results suggest a steep trade-off between the level and scope of dCas9 expression, the degree of genetic isolation achievable and the resulting impact on fly fitness. The genetic engineering strategy we present here allows the creation of single or multiple reproductive barriers and could be applied to other multicellular organisms such as disease vectors or transgenic organisms of economic importance.

RevDate: 2019-06-21
CmpDate: 2019-06-21

Lay CY, Hamel C, M St-Arnaud (2018)

Taxonomy and pathogenicity of Olpidium brassicae and its allied species.

Fungal biology, 122(9):837-846.

The classification and physiology of the zoosporic plant-pathogen Olpidium brassicae and its relationships with the closely-related species are often confusing. This review focuses on these species and intends to differentiate them based on the literatures published since the discovery and establishment of the species by Woronin in 1878 under the name of Chytridium brassicae to current molecular era. The goal of this review is to help researchers better understand the taxonomy, the host range, and the potential role in plant health of O. brassicae-related species. To reach the goal, we reviewed the rationales behind the creation or reduction in synonymy of the different names for O. brassicae and its allied species in order to elucidate the evolution of the species concept on them based on the traditional morphological studies. Furthermore, the studies by molecular biology methods improve our knowledge and perspectives on O. brassicae and its host specificity. In particular, we clarify the differences between O. brassicae and Olpidium virulentus, and propose potential new research avenues. We therefore hope that this review will give a better perspective on Olpidium spp. and their potential role in the root microbiome of plants in natural environments and in agricultural settings.

RevDate: 2019-02-15
CmpDate: 2019-02-07

Skovmand LH, Xu CCY, Servedio MR, et al (2018)

Keystone Genes.

Trends in ecology & evolution, 33(9):689-700.

The keystone species concept is used in ecology to describe individual species with disproportionately large effects on their communities. We extend this idea to the level of genes with disproportionately large effects on ecological processes. Such 'keystone genes' (KGs) would underlie traits involved in species interactions or causing critical biotic and/or abiotic changes that influence emergent community and ecosystem properties. We propose a general framework for how KGs could be identified, while keeping KGs under the umbrella of 'ecologically important genes' (EIGs) that also include categories such as 'foundation genes', 'ecosystem engineering genes', and more. Although likely rare, KGs and other EIGs could dominate certain ecological processes; thus, their discovery and study are relevant for understanding eco-evolutionary dynamics.

RevDate: 2019-06-13
CmpDate: 2019-06-11

Grodwohl JB, Porto F, CN El-Hani (2018)

The instability of field experiments: building an experimental research tradition on the rocky seashores (1950-1985).

History and philosophy of the life sciences, 40(3):45 pii:10.1007/s40656-018-0209-y.

In many experimental sciences, like particle physics or molecular biology, the proper place for establishing facts is the laboratory. In the sciences of population biology, however, the laboratory is often seen as a poor approximation of what occurs in nature. Results obtained in the field are usually more convincing. This raises special problems: it is much more difficult to obtain stable, repeatable results in the field, where environmental conditions vary out of the experimenter's control, than in the laboratory. We examine here how this problem affected an influential experimental research tradition in community ecology, the study of the ecology of the rocky seashores. In the 1960s, a handful of North-American ecologists, most notably Joseph Connell, Robert Paine and Paul Dayton, made the rocky seashores a model study system for experimenting in the field. Their experiments were deceptively simple: they removed species living on the seashore and described the resulting effects on the local ecology. These experiments exerted a deep influence on community ecology. They provided evidence for speculative developments concerning the theory of interspecific competition, the factors responsible for species richness and the ecology of food webs. They also stimulated novel conceptual developments. In particular, Paine developed the predation hypothesis, which states that the presence of predators can favour species richness, before introducing the keystone species concept, according to which some species exert disproportionate effects on ecological systems. More broadly, these experiments gave support to a methodological trend in favour of field experimentation. Only controlled perturbations in the field, it seemed, provided a reliable method to get insights into the structure of ecological communities. However, as experiments were continued in time and repeated in different sites, divergent results appeared. We analyse here how intertidal researchers coped with the variability of environmental conditions and tried to stabilize their results. In the process, they reconsidered not only their early conclusions, but also the exclusive status given to field experiments. Expanding on this case study, we discuss some significant differences between laboratory and field experiments.

RevDate: 2019-11-20

Korhonen A, Seelan JSS, O Miettinen (2018)

Cryptic species diversity in polypores: the Skeletocutis nivea species complex.


We propose a taxonomic revision of the two closely related white-rot polypore species, Skeletocutis nivea (Jungh.) Jean Keller and S. ochroalba Niemelä (Incrustoporiaceae, Basidiomycota), based on phylogenetic analyses of nuclear ribosomal internal transcribed spacer (ITS) and translation elongation factor EF-1α sequences. We show that prevailing morphological species concepts of S. nivea and S. ochroalba are non-monophyletic and we delineate new species boundaries based on phylogenetic inference. We recognise eleven species within the prevailing species concept of S. nivea (S. calidasp. nov., S. coprosmae comb. nov., S. futilissp. nov., S. imperviasp. nov., S. ipuletiisp. nov., S. lepidasp. nov., S. nemoralissp. nov., S. nivea sensu typi, S. semipileata comb. nov., S. unguinasp. nov. and S. yuchengiisp. nov.) and assign new sequenced epitypes for S. nivea and S. semipileata. The traditional concept of S. ochroalba comprises two independent lineages embedded within the S. nivea species complex. The Eurasian conifer-dwelling species S. cummatasp. nov. is recognised as separate from the North American S. ochroalba sensu stricto. Despite comprehensive microscopic examination, the majority of the recognised species are left without stable diagnostic character combinations that would enable species identification based solely on morphology and ecology.

RevDate: 2019-03-08
CmpDate: 2019-03-08

Niu YT, Jabbour F, Barrett RL, et al (2018)

Combining complete chloroplast genome sequences with target loci data and morphology to resolve species limits in Triplostegia (Caprifoliaceae).

Molecular phylogenetics and evolution, 129:15-26.

Species represent the most basic unit of taxonomy. As such, species delimitation represents a crucial issue for biodiversity conservation. Taxonomic practices were revolutionized in the last three decades due to the increasing availability of molecular phylogenetic data. The genus Triplostegia (Caprifoliaceae) traditionally consists of two species, T. glandulifera and T. grandiflora, distinguishable mainly based on quantitative morphological features. In this study, we sequenced nine chloroplast loci (i.e., accD, psbK-psbI, rbcL-accD, rpoB-trnC, rps16-trnQ, trnE-trnT, trnF-ndhJ, trnH-psbA, trnS-trnG) and one nuclear locus (ITS) of 16 individuals of Triplostegia representing the entire distribution range of both species recognized. Furthermore, we also obtained whole chloroplast sequences for 11 of the 16 individuals for which silica gel-dried leaves were available. Our phylogenetic analyses integrating chloroplast genome sequences and multiple loci data revealed that Triplostegia includes four main clades that largely match geography. Neither T. grandiflora nor T. glandulifera was recovered as monophyletic and no diagnosable differences in leaf, flower, and pollen traits were detected between the two species, indicating the need for a revised species circumscription within Triplostegia. Our study highlights the importance of combining data from different sources while defining species limits.

RevDate: 2019-11-20

Tsang CC, Tang JYM, Lau SKP, et al (2018)

Taxonomy and evolution of Aspergillus, Penicillium and Talaromyces in the omics era - Past, present and future.

Computational and structural biotechnology journal, 16:197-210.

Aspergillus, Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species important to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxonomic studies on these fungi are essential since they could provide invaluable information on their evolutionary relationships and define criteria for species recognition. With the advancement of various biological, biochemical and computational technologies, different approaches have been adopted for the taxonomy of Aspergillus, Penicillium and Talaromyces; for example, from traditional morphotyping, phenotyping to chemotyping (e.g. lipotyping, proteotypingand metabolotyping) and then mitogenotyping and/or phylotyping. Since different taxonomic approaches focus on different sets of characters of the organisms, various classification and identification schemes would result. In view of this, the consolidated species concept, which takes into account different types of characters, is recently accepted for taxonomic purposes and, together with the lately implemented 'One Fungus - One Name' policy, is expected to bring a more stable taxonomy for Aspergillus, Penicillium and Talaromyces, which could facilitate their evolutionary studies. The most significant taxonomic change for the three genera was the transfer of Penicillium subgenus Biverticillium to Talaromyces (e.g. the medically important thermally dimorphic 'P. marneffei' endemic in Southeast Asia is now named T. marneffei), leaving both Penicillium and Talaromyces as monophyletic genera. Several distantly related Aspergillus-like fungi were also segregated from Aspergillus, making this genus, containing members of both sexual and asexual morphs, monophyletic as well. In the current omics era, application of various state-of-the-art omics technologies is likely to provide comprehensive information on the evolution of Aspergillus, Penicillium and Talaromyces and a stable taxonomy will hopefully be achieved.

RevDate: 2019-01-31
CmpDate: 2019-01-31

De Decker S, Vanormelingen P, Pinseel E, et al (2018)

Incomplete Reproductive Isolation Between Genetically Distinct Sympatric Clades of the Pennate Model Diatom Seminavis robusta.

Protist, 169(4):569-583.

Incomplete reproductive isolation between genetically distinct taxa provides an interesting opportunity for speciation and adaptation studies. This phenomenon is well-described in macro-organisms, but less experimental evidence is available for unicellular eukaryotes. Here, we document the sympatric occurrence of genetically differentiated populations of the pennate model diatom Seminavis robusta in coastal subtidal biofilm communities and show widespread potential for gene flow between them. Based on sequence variation in the plastid-encoded rbcL gene, three distinct clades were identified. Morphological variation between the clades reflected their phylogenetic relationships, with subtle differences in valve morphology in the most distant clade compared to the other two clades, which were indistinguishable. Using a large number of experimental crosses we showed that, although reproductive output was significantly lower compared to the majority of within-clade crosses, approximately 34.5% of the inter-clade crosses resulted in viable and fertile progeny. While the nature of the incomplete reproductive isolation remains unknown, its occurrence in natural diatom populations represents an additional mechanism contributing to population genetic structuring and adaptation and can spur further research into the mechanisms of species divergence and the maintenance of species identity in the presence of gene flow.

RevDate: 2019-08-27
CmpDate: 2019-08-27

Tatarenkov A, Earley RL, Taylor DS, et al (2018)

Natural hybridization between divergent lineages in a selfing hermaphroditic fish.

Biology letters, 14(6):.

By definition, mating between individuals is infrequent in highly selfing organisms, and so too, therefore, hybridization should be rare between genetically divergent lineages in predominantly self-fertilizing species. Notwithstanding these expectations, here we report a remarkable case of natural hybridization between highly diverged phylogeographic lineages of the mangrove rivulus, a small killifish that reproduces predominantly by self-fertilization and typically is found as highly homozygous lines in most parts of its extensive geographical range. Two distinctive genetic lineages (Kryptolebias marmoratus and a 'Central clade' closely related to K. hermaphroditus) previously were not known in sympatry, but were found by us to co-occur on San Salvador, Bahamas. Genetic analyses of a mitochondrial and multiple nuclear markers determined the direction of a cross producing a hybrid fish. Furthermore, we show that this hybrid individual was viable, as it successfully reproduced by self-fertilization for two generations. Additional sampling of this population will be necessary to determine if backcrossing of hybrids to the parental lineages occurs in nature and to analyse whether such backcross progeny are viable. Application of the biological species concept (BSC) is traditionally difficult in clonally reproducing organisms. Our results show that although mangrove rivulus fish are mostly highly selfing in nature (resulting in isogenic, effectively clonal and homozygous progeny), classification within this taxonomic complex need not be incompatible with the BSC.

RevDate: 2019-11-07
CmpDate: 2019-10-09

Sutherland C, Fuller AK, Royle JA, et al (2018)

Large-scale variation in density of an aquatic ecosystem indicator species.

Scientific reports, 8(1):8958.

Monitoring indicator species is a pragmatic approach to natural resource assessments, especially when the link between the indicator species and ecosystem state is well justified. However, conducting ecosystem assessments over representative spatial scales that are insensitive to local heterogeneity is challenging. We examine the link between polychlorinated biphenyl (PCB) contamination and population density of an aquatic habitat specialist over a large spatial scale using non-invasive genetic spatial capture-recapture. Using American mink (Neovison vison), a predatory mammal and an indicator of aquatic ecosystems, we compared estimates of density in two major river systems, one with extremely high levels of PCB contamination (Hudson River), and a hydrologically independent river with lower PCB levels (Mohawk River). Our work supports the hypothesis that mink densities are substantially (1.64-1.67 times) lower in the contaminated river system. We demonstrate the value of coupling the indicator species concept with well-conceived and spatially representative monitoring protocols. PCBs have demonstrable detrimental effects on aquatic ecosystems, including mink, and these effects are likely to be profound and long-lasting, manifesting as population-level impacts. Through integrating non-invasive data collection, genetic analysis, and spatial capture-recapture methods, we present a monitoring framework for generating robust density estimates across large spatial scales.

RevDate: 2019-01-24
CmpDate: 2018-09-04

Bobay LM, H Ochman (2018)

Biological species in the viral world.

Proceedings of the National Academy of Sciences of the United States of America, 115(23):6040-6045.

Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.

RevDate: 2019-07-18
CmpDate: 2019-07-18

Laurimäe T, Kinkar L, Moks E, et al (2018)

Molecular phylogeny based on six nuclear genes suggests that Echinococcus granulosus sensu lato genotypes G6/G7 and G8/G10 can be regarded as two distinct species.

Parasitology, 145(14):1929-1937.

Tapeworms of the species complex of Echinococcus granulosus sensu lato (s. l.) are the cause of a severe zoonotic disease - cystic echinococcosis, which is listed among the most severe parasitic diseases in humans and is prioritized by the World Health Organization. A stable taxonomy of E. granulosus s. l. is essential to the medical and veterinary communities for accurate and effective communication of the role of different species in this complex on human and animal health. E. granulosus s. l. displays high genetic diversity and has been divided into different species and genotypes. Despite several decades of research, the taxonomy of E. granulosus s. l. has remained controversial, especially the species status of genotypes G6-G10. Here the Bayesian phylogeny based on six nuclear loci (7387 bp in total) demonstrated, with very high support, the clustering of G6/G7 and G8/G10 into two separate clades. According to the evolutionary species concept, G6/G7 and G8/G10 can be regarded as two distinct species. Species differentiation can be attributed to the association with distinct host species, largely separate geographical distribution and low level of cross-fertilization. These factors have limited the gene flow between genotypic groups G6/G7 and G8/G10, resulting in the formation of distinct species. We discuss ecological and epidemiological differences that support the validity of these species.

RevDate: 2019-11-01
CmpDate: 2019-10-17

Bobay LM, Ellis BS, H Ochman (2018)

ConSpeciFix: classifying prokaryotic species based on gene flow.

Bioinformatics (Oxford, England), 34(21):3738-3740.

Summary: Classification of prokaryotic species is usually based on sequence similarity thresholds, which are easy to apply but lack a biologically-relevant foundation. Here, we present ConSpeciFix, a program that classifies prokaryotes into species using criteria set forth by the Biological Species Concept, thereby unifying species definition in all domains of life.

ConSpeciFix's webserver is freely available at www.conspecifix.com. The local version of the program can be freely downloaded from https://github.com/Bobay-Ochman/ConSpeciFix. ConSpeciFix is written in Python 2.7 and requires the following dependencies: Usearch, MCL, MAFFT and RAxML.

RevDate: 2019-04-25
CmpDate: 2019-04-25

Stock SP, Campos-Herrera R, El-Borai FE, et al (2019)

Steinernema khuongi n. sp. (Panagrolaimomorpha, Steinernematidae), a new entomopathogenic nematode species from Florida, USA.

Journal of helminthology, 93(2):226-241.

In this study, molecular (ribosomal sequence data), morphological and cross-hybridization properties were used to identify a new Steinernema sp. from Florida, USA. Molecular and morphological data provided evidence for placing the novel species into Clade V, or the 'glaseri-group' of Steinernema spp. Within this clade, analysis of sequence data of the rDNA genes, 28S and internal transcribed spacer (ITS), depicted the novel species as a distinctive entity and closely related to S. glaseri and S. cubanum. Additionally, cross-hybridization assays showed that the new species is unable to interbreed with either of the latter two species, reinforcing its uniqueness from a biological species concept standpoint. Key morphological diagnostic characters for S. khuongi n. sp. include the mean morphometric features of the third-stage infective juveniles: total body length (average: 1066 μm), tail length (average: 65 μm), location of the excretory pore (average: 80.5 μm) and the values of c (average: 16.4), D% (average: 60.5), E% (average: 126) and H% (average: 46.6). Additionally, males can be differentiated from S. glaseri and S. cubanum by the values of several ratios: D% (average: 68), E% (average: 323) and SW% (average: 120). The natural distribution of this species in Florida encompasses both natural areas and citrus groves, primarily in shallow groundwater ecoregions designated as 'flatwoods'. The morphological, molecular, phylogenetic and ecological data associated with this nematode support its identity as a new species in the S. glaseri-group.

RevDate: 2018-12-02
CmpDate: 2018-05-28

Webb JM, Jacobus LM, SP Sullivan (2018)

The state of systematics of North American Baetis Leach, 1815 (Ephemeroptera: Baetidae), with recommendations for identification of larvae.

Zootaxa, 4394(1):105-127 pii:zootaxa.4394.1.6.

The North American species of Baetis Leach (Ephemeroptera: Baetidae) are reviewed. Nearly one-third of species are either unknown or inadequately described in the larval stage, a fact not reflected in most keys or standard taxonomic efforts for bioassessment, which typically recommend species-level identifications of larvae. Furthermore, our new observations indicate that some previously published stage associations should be viewed as only tentative, and molecular evidence suggests that current species taxonomy does not reflect biological species. In order to acknowledge these deficiencies, but at the same time provide a degree of higher taxonomic resolution beyond the genus level, we recommend a scheme for identifications incorporating previously established species groups and the species complexes and species included within them. Species complexes are proposed for instances when there are either multiple species that cannot be differentiated in the larval stage or when multiple lines of evidence indicate more than one actual species is included in a single species concept. Complexes include B. flavistriga complex (B. flavistriga McDunnough + B. phoebus McDunnough + B. rusticans McDunnough), B. intercalaris complex (B. intercalaris McDunnough), B. vernus complex (B. brunneicolor McDunnough + B. vernus Curtis), B. bicaudatus complex (B. bicaudatus Dodds), B. tricaudatus complex (B. tricaudatus Dodds), and B. piscatoris complex (B. piscatoris Traver + B. palisadi Mayo + B. persecutus McDunnough [=B. persecutor McCafferty n. obj. syn]). A new larval identification key incorporating the B. piscatoris complex is provided.

RevDate: 2019-11-20

Aldhebiani AY (2018)

Species concept and speciation.

Saudi journal of biological sciences, 25(3):437-440.

Defining and recognizing a species has been a controversial issue for a long time. To determine the variation and the limitation between species, many concepts have been proposed. When a taxonomist study a particular taxa, he/she must adopted a species concept and provide a species limitation to define this taxa. In this paper some of species concepts are discussed starting from the typological species concepts to the phylogenetic concept. Positive and negative aspects of these concepts are represented in addition to their application.

RevDate: 2018-11-14
CmpDate: 2018-07-23

Vaidya G, Lepage D, R Guralnick (2018)

The tempo and mode of the taxonomic correction process: How taxonomists have corrected and recorrected North American bird species over the last 127 years.

PloS one, 13(4):e0195736.

While studies of taxonomy usually focus on species description, there is also a taxonomic correction process that retests and updates existing species circumscriptions on the basis of new evidence. These corrections may themselves be subsequently retested and recorrected. We studied this correction process by using the Check-List of North and Middle American Birds, a well-known taxonomic checklist that spans 130 years. We identified 142 lumps and 95 splits across sixty-three versions of the Check-List and found that while lumping rates have markedly decreased since the 1970s, splitting rates are accelerating. We found that 74% of North American bird species recognized today have never been corrected (i.e., lumped or split) over the period of the checklist, while 16% have been corrected exactly once and 10% have been corrected twice or more. Since North American bird species are known to have been extensively lumped in the first half of the 20th century with the advent of the biological species concept, we determined whether most splits seen today were the result of those lumps being recorrected. We found that 5% of lumps and 23% of splits fully reverted previous corrections, while a further 3% of lumps and 13% of splits are partial reversions. These results show a taxonomic correction process with moderate levels of recorrection, particularly of previous lumps. However, 81% of corrections do not revert any previous corrections, suggesting that the majority result in novel circumscriptions not previously recognized by the Check-List. We could find no order or family with a significantly higher rate of correction than any other, but twenty-two genera as currently recognized by the AOU do have significantly higher rates than others. Given the currently accelerating rate of splitting, prediction of the end-point of the taxonomic recorrection process is difficult, and many entirely new taxonomic concepts are still being, and likely will continue to be, proposed and further tested.

RevDate: 2019-01-14
CmpDate: 2019-01-14

Zhou W, Ji X, Obata S, et al (2018)

Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling.

Molecular phylogenetics and evolution, 126:1-16.

Nyssa sylvatica complex consists of several woody taxa occurring in eastern North America. These taxa were recognized as two or three species including three or four varieties by different authors. Due to high morphological similarities and complexity of morphological variation, classification and delineation of taxa in the group have been difficult and controversial. Here we employ data from RAD-seq to elucidate the genetic structure and phylogenetic relationships within the group. Using the genetic evidence, we evaluate previous classifications and delineate species. We also employ Species Distribution Modeling (SDM) to evaluate impacts of climatic changes on the ranges of the taxa and to gain insights into the relevant refugia in eastern North America. Results from Molecular Variance Analysis (AMOVA), STRUCTURE, phylogenetic analyses using Maximum likelihood, Bayesian Inference, and Splittree methods of RAD-seq data strongly support a two-clade pattern, largely separating samples of N. sylvatica from those of N. biflora-N. ursina mix. Divergence time analysis with BEAST suggests the two clades diverged in the mid Miocene. The ancestor of the present trees of N. sylvatica was suggested to be in the Pliocene and that of N. biflora-N. ursina mix in the end of the Miocene. Results from SDM predicted a smaller range in the southern part of the species present range of each clade during the Last Glacial Maximum (LGM). A northward expansion of the ranges during interglacial period and a northward shift of the ranges in the future under a model of global warming were also predicted. Our results support the recognition of two species in the complex, N. sylvatica and N. biflora, following the phylogenetic species concept. We found no genetic evidence supporting recognitions of intraspecific taxa. However, we propose subsp. ursina and subsp. biflora within N. biflora due to their distinction in habits, distributions, and habitats. Our results further support movements of trees in eastern North America in response to climatic changes. Finally, our study demonstrates that RAD-seq data and a combination of population genomics and SDM are valuable in resolving relationship and biogeographic history of closely related species that are taxonomically difficult.

RevDate: 2018-11-14
CmpDate: 2018-07-24

Klishko OK, Lopes-Lima M, Bogan AE, et al (2018)

Morphological and molecular analyses of Anodontinae species (Bivalvia, Unionidae) of Lake Baikal and Transbaikalia.

PloS one, 13(4):e0194944.

The diversity and taxonomy of anodontine species in Lake Baikal and Transbaikalia region has been contentious since it is based on a typological species concept, the so called "Comparatory Method". Using this method, six Comparatory anodontine species have been described for the study area as belonging to the genus Colletopterum. This genus was separated from Anodonta based on shell characteristics and further split into two subgenera, i.e. Colletopterum sensu stricto and Colletopterum (Piscinaliana). However, many authors do not recognize this separation maintaining all Colletopterum forms within Anodonta. The current study clarifies the taxonomy and systematics of Anodontinae in this region, using a combination of molecular, morphological and anatomical data. All previously recognized Comparatory forms are here recognized as a single species, i.e. Anodonta anatina.

RevDate: 2018-10-04
CmpDate: 2018-09-26

Lherminier P (2018)

[Informative predation: Towards a new species concept].

Comptes rendus biologies, 341(4):209-218.

We distinguish two types of predations: the predation of matter-energy equals the food chain, and the informative predation is the capture of the information brought by the sexual partners. The cell or parent consumes energy and matter to grow, multiply and produce offspring. A fixed amount of resources is divided by the number of organisms, so individual growth and numerical multiplication are limited by depletion resources of the environment. Inversely, fertilization does not destroy information, but instead produces news. The information is multiplied by the number of partners and children, since each fertilization gives rise to a new genome following a combinatorial process that continues without exhaustion. The egg does not swallow the sperm to feed, but exchange good food for quality information. With the discovery of sex, that is, 1.5 Ga ago, life added soft predation to hard predation, i.e. information production within each species to matter-energy flow between species. Replicative and informative structures are subject to two competing biological constraints: replicative fidelity promotes proliferation, but limits adaptive evolution. On the contrary, the offspring of a couple obviously cannot be a copy of both partners, they are a new production, a re-production. Sexual recombination allows the exponential enrichment of the genetic diversity, thus promoting indefinite adaptive and evolutionary capacities. Evolutionary history illustrates this: the bacteria proliferate but have remained at the first purely nutritive stage in which most of the sensory functions, mobility, defense, and feeding have experienced almost no significant novelty in three billion years. Another world appeared with the sexual management of information. Sexual reproduction actually combines two functions: multiplicative by "vertical transfer" and informative by "horizontal transfer". This distinction is very common: polypus - medusa alternations, parasite multiplication cycles, the lytochal and deuterotochal parthenogenesis of aphids, and the innumerable para- and pseudo-sexual strategies of plants opportunistically combine the two modes of asexual replication and sexual combination. However, for the majority of animals and multicellular plants that produce many gametes, numerical proliferation by descendants and informative diversity by sexuality are mutually implicated, for example in the seed. The true discovery of eukaryotes may not be the "true nucleus", as their name implies, but an orderly informative function. The field of recombinations circumscribes a class of partners genetically compatible with each other, each simultaneously prey and predator of the DNA of the other. The mythical Maxwell demon capable of tracing entropy by sorting molecules according to their state does exist: each mate is the other's Maxwell's demon. While a sexless bacterium is simply divided into two cells, two sexual parents work together to produce a single offspring a time. Added to this are the burdens involved in meiosis and crossing-over, cellular diploidy, and mating. Sex produces an information gain that is paid for by a cost of energy-material, and this barter must be fair to survive. The domains of sexual intercourse are very diverse: uniparental reproduction, alternation of asexual proliferation and sexual information, self-fertilization, endogamy, exogamy, panmixis, diffuse or structured polymorphism, fertile or sterile hybridization, horizontal transfers. Each species is a recombination field between two domains, cloning and hybridization. Multiplicative descent and informative fertilization are organically distinct, but selectively associated: the information produced by the parents' sexuality favors the predation of matter-energy and therefore the proliferation of offspring, and this proliferation in turn favors the sexed producers of information. The equation specific to each species is: enough energy to proliferate, enough information to diversify. Alternatively, two other reproductive modes obtain or transmit less information at lower cost: not enough recombinations=repetitive clonal proliferation, and too many recombinations=disordered hybridization. But these marginal modes have poor prospects, as the model of the species is successfully attractive. Better discriminate to better inform. In bacteria, the exchanged and incorporated DNA segments are directly identified by the parity of the complementary strands, which determines simultaneously the similarity, the offspring, and the pairing. In eukaryotes, on the contrary, somatic growth and germinal information are segregated. During speciation, adaptive information is compacted, delocalized, codified and published to inform the species about its own state: the prezygotic relationship governs viable mating. Under the effect of sexual selection, the runaway and the reinforcement of the characters related to courtship testifies to their identifying function, which explains the paradox of the singularity and luxuriance of the sexual hypertrophies. The speciation discretizes a balanced recombination field and validates the informative relations. The species is without degree. Mates of a species recognize each other quickly and well because the logic of coding disengages from the ecological game of adaptations. The system of mate recognition has a function of cohesion and its regularity allows the adaptations of the less regular being, it is neither elitist nor normative, it is subjected neither to a level of aptitudes, nor to sexual performances, but permissive; it protects the variability and polymorphism. Two mutually irreducible relationships triggered the debate between the taxonomists who support the phyletic definition of the species by the descendance, and the proponents of the definition by interfertility. Such a taxonomic disagreement is not insurmountable, but the issue is deeper than taxonomic concepts, because these concepts relate to two different modes of evolution. According to the phyletic model, each species is a lineage passively isolated by external circumstances; on the contrary, in the sexual model each species is actively produced by an internal process of adjustment between replicative costs and informative gains. Each species develops a solution of the equation that matches material-energy expenditures with informative gains. A species concept based on a lasting relationship between these two quantities or on the limits of certain values or their equilibrium is therefore legitimate. It is this equilibrium that all couples resolve, without our formulation being as clearly as biology desires and as physics demands. Energy expenditures and informative gains in sexuality are almost impossible to measure, yet observation and experience allow an approximate ranking of the energy/information ratio. For example, endogamy is more economical, but less diversifying than exogamy, polymorphism increases information, the reinforcement of sexual isolation limits the rate of unproductive fertilization, between neighboring species hybridization allows certain genetic contributions, etc. A closed species evolves naturally towards another just as closed. On the contrary, the artificial transfer of DNA opens the species. The natural boundaries that isolate the species are easily trespassed as energy costs and constraints of sexual recognition are easily controlled; and the perspectives of manipulations are visible, whereas natural selection never anticipates and thus works blindly. Informative, artificially directed predation stimulates the evolution of species.

RevDate: 2018-11-14
CmpDate: 2018-08-13

Gutiérrez EE, GST Garbino (2018)

Species delimitation based on diagnosis and monophyly, and its importance for advancing mammalian taxonomy.

Zoological research, 39(5):301-308.

A recently proposed taxonomic classification of extant ungulates sparked a series of publications that criticize the Phylogenetic Species Concept (PSC) claiming it to be a particularly poor species concept. These opinions reiteratively stated that (1) the two fundamental elements of the "PSC", i.e., monophyly and diagnosability, do not offer objective criteria as to where the line between species should be drawn; and (2) that extirpation of populations can lead to artificial diagnosability and spurious recognitions of species. This sudden eruption of criticism against the PSC is misleading. Problems attributed to the PSC are common to most approaches and concepts that modern systematists employ to establish species boundaries. The controversial taxonomic propositions that sparked criticism against the PSC are indeed highly problematic, not because of the species concept upon which they are based, but because no evidence (whatsoever) has become public to support a substantial portion of the proposed classification. We herein discuss these topics using examples from mammals. Numerous areas of biological research rest upon taxonomic accuracy (including conservation biology and biomedical research); hence, it is necessary to clarify what are (and what are not) the real sources of taxonomic inaccuracy.

RevDate: 2019-12-11
CmpDate: 2018-05-08

Hubka V, Nováková A, Jurjević Ž, et al (2018)

Polyphasic data support the splitting of Aspergillus candidus into two species; proposal of Aspergillus dobrogensis sp. nov.

International journal of systematic and evolutionary microbiology, 68(4):995-1011.

Aspergillus candidus is a species frequently isolated from stored grain, food, indoor environments, soil and occasionally also from clinical material. Recent bioprospecting studies highlighted the potential of using A. candidus and its relatives in various industrial sectors as a result of their significant production of enzymes and bioactive compounds. A high genetic variability was observed among A. candidus isolates originating from various European countries and the USA, that were mostly isolated from indoor environments, caves and clinical material. The A. candidus sensu lato isolates were characterized by DNA sequencing of four genetic loci, and agreement between molecular species delimitation results, morphological characters and exometabolite spectra were studied. Classical phylogenetic methods (maximum likelihood, Bayesian inference) and species delimitation methods based on the multispecies coalescent model supported recognition of up to three species in A. candidus sensu lato. After evaluation of phenotypic data, a broader species concept was adopted, and only one new species, Aspergillus dobrogensis, was proposed. This species is represented by 22 strains originating from seven countries (ex-type strain CCF 4651T=NRRL 62821T=IBT 32697T=CBS 143370T) and its differentiation from A. candidus is relevant for bioprospecting studies because these species have different exometabolite profiles. Evaluation of the antifungal susceptibility of section Candidi members to six antifungals using the reference EUCAST method showed that all species have low minimum inhibitory concentrations for all tested antifungals. These results suggest applicability of a wide spectrum of antifungal agents for treatment of infections caused by species from section Candidi.

RevDate: 2019-11-20

Johnson LA, D Gowen (2017)

Ex uno, multis: taxonomic revision in Navarretia divaricata (Polemoniaceae) and the recognition of four additional cryptic or near-cryptic species.


Navarretia divaricata, endemic to western North America and most recently considered a single species with two subspecies, was re-examined in light of field work, DNA sequences, comparative morphology, and a review of herbarium specimens including types. From these studies, we lectotypify the material on which N. divaricata is based, elevate N. divaricata subsp. vividior, which is an allotetraploid, to species rank (as N. vividiorcomb. et stat. nov.), and recognize three additional species: N. modocensissp. nov., N. aeroidessp. nov., and N. torreyellasp. nov.Navarretia modocensis, the diploid paternal progenitor of N. vividior, is morphologically cryptic with respect to its allotetraploid offspring and difficult to distinguish on herbarium sheets. Navarretia aeroides, the diploid maternal progenitor of N. vividior, is nearly cryptic, but more easily distinguished from both N. modocensis and N. vividior by its smaller, more glandular inflorescences. Navarretia torreyella is readily distinguished from all of these species, but has been generally mistaken for N. divaricata subsp. vividior given its colored corolla tube and rare co-occurrence with the other vividior-like species. Conservation assessments, an identification key, and table of comparative morphological features are provided for each species, emended descriptions for N. divaricata and N. vividior, and a discussion of the syntypes for Gilia divaricata Torr. ex A.Gray.

RevDate: 2018-11-13
CmpDate: 2018-02-27

Petkevičiūtė R, Stunžėnas V, G Stanevičiūtė (2018)

Comments on species divergence in the genus Sphaerium (Bivalvia) and phylogenetic affinities of Sphaerium nucleus and S. corneum var. mamillanum based on karyotypes and sequences of 16S and ITS1 rDNA.

PloS one, 13(1):e0191427.

Chromosome, 16S and ITS1 rDNA sequence analyses were used to obtain reliable diagnostic characters and to clarify phylogenetic relationships of sphaeriid bivalves of the genus Sphaerium. The species studied were found to be diploid, with modal number 2n = 28 in S. nucleus and 2n = 30 in S. corneum var. mamillanum. Small, biarmed, C- negative B chromosomes were found in all studied populations of both species. Karyological and molecular markers revealed no differences between S. corneum s. str. and S. corneum var. mamillanum. No intraspecific differences were found in the basic karyotype of S. nucleus. Molecular analyses, however, uncovered three genetically distinct ITS1 lineages: one comprised of samples from Lithuania, Slovakia, and Russia, another from Czech, and a third from Ukraine. Additionally to known 16S haplotype from Ukraine, three new 16S haplotypes of S. nucleus were detected: one in the samples from Lithuania and Russia, one in Slovakian and one in Czech population. In the ITS1 phylogenetic tree, all branches of S. nucleus clustered in one clade. In the 16S phylogenetic tree, however, the haplotype of Czech S. nucleus formed a separate branch, distant from three other haplotypes of S. nucleus. Molecular results indicate that in the context of the Evolutionary Species Concept the S. nucleus morphospecies may represent a complex of separate taxa, however referring on the Biological Species Concept the genetic lineages could represent the intraspecific variability.

RevDate: 2019-02-19
CmpDate: 2019-02-18

Fišer C, Robinson CT, F Malard (2018)

Cryptic species as a window into the paradigm shift of the species concept.

Molecular ecology, 27(3):613-635.

The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.

RevDate: 2019-12-27
CmpDate: 2018-12-27

Sepúlveda VE, Márquez R, Turissini DA, et al (2017)

Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum.

mBio, 8(6):.

Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least four species that are genetically isolated and rarely interbreed. Therefore, we propose a taxonomic rearrangement of the genus.IMPORTANCE The evolutionary processes that give rise to new pathogen lineages are critical to our understanding of how they adapt to new environments and how frequently they exchange genes with each other. The fungal pathogen Histoplasma capsulatum provides opportunities to precisely test hypotheses about the origin of new genetic variation. We find that H. capsulatum is composed of at least four different cryptic species that differ genetically and also in virulence. These results have implications for the epidemiology of histoplasmosis because not all Histoplasma species are equivalent in their geographic range and ability to cause disease.

RevDate: 2019-11-20

Wallin H, Kvamme T, J Bergsten (2017)

To be or not to be a subspecies: description of Saperda populnea lapponica ssp. n. (Coleoptera, Cerambycidae) developing in downy willow (Salix lapponum L.).


A new subspecies of the European cerambycid Saperda populnea (Linnaeus, 1758) is described: Saperda populnea lapponicassp. n. based on specimens from Scandinavia. The male genitalia characters were examined and found to provide support for this separation, as well as differences in morphology, geographical distribution and bionomy. The preferred host tree for the nominate subspecies S. populnea populnea is Populus tremula L., whereas S. populnea lapponicassp. n. is considered to be monophagous on Salix lapponum L. DNA sequence data of mitochondrial cytochrome oxidase subunit I (COI) was generated from Scandinavian specimens of S. populnea populnea and specimens representing S. populnea lapponicassp. n. The two subspecies were not reciprocally monophyletic and genetic distances in COI were small. All synonyms of S. populnea populnea have been considered, and species similar to S. populnea populnea have been examined, and not found to be related to S. populnea lapponicassp. n. A male lectotype has been designated for each of the two following synonyms: Cerambyx decempunctatus De Geer, 1775, and Saperda salicis Zetterstedt, 1818. The synonymised species from Asia, S. balsamifera (Motshulsky, 1860), is elevated to subspecies: S. populnea balsamiferastat. n. We end with a discussion on the definition of subspecies under the unified species concept.

RevDate: 2018-12-02
CmpDate: 2018-03-09

Segatto ALA, Reck-Kortmann M, Turchetto C, et al (2017)

Multiple markers, niche modelling, and bioregions analyses to evaluate the genetic diversity of a plant species complex.

BMC evolutionary biology, 17(1):234.

BACKGROUND: The classification of closely related plants is not straightforward. These morphologically similar taxa frequently maintain their inter-hybridization potential and share ancestral polymorphisms as a consequence of their recent divergence. Under the biological species concept, they may thus not be considered separate species. The Petunia integrifolia complex is especially interesting because, in addition to the features mentioned above, its taxa share a pollinator, and their geographical ranges show multiple overlaps. Here, we combined plastid genome sequences, nuclear microsatellites, AFLP markers, ecological niche modelling, and bioregions analysis to investigate the genetic variability between the different taxa of the P. integrifolia complex in a comprehensive sample covering the entire geographical range of the complex.

RESULTS: Results from molecular markers did not fully align with the current taxonomic classification. Niche modelling and bioregions analyses revealed that taxa were associated with different ecological constraints, indicating that the habitat plays an important role in preserving species boundaries. For three taxa, our analyses showed a mostly conserved, non-overlapping geographical distribution over time. However, for two taxa, niche modelling found an overlapping distribution over time; these taxa were also associated with the same bioregions.

CONCLUSIONS: cpDNA markers were better able to discriminate between Petunia taxa than SSRs and AFLPs. Overall, our results suggest that the P. integrifolia complex represents a continuum of individuals from distant and historically isolated populations, which share some morphological traits, but are established in four different evolutionary lineages.

RevDate: 2018-12-18
CmpDate: 2018-12-18

Ruiz-García M, Pinedo-Castro M, JM Shostell (2018)

Small spotted bodies with multiple specific mitochondrial DNAs: existence of diverse and differentiated tigrina lineages or species (Leopardus spp: Felidae, Mammalia) throughout Latin America.

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis, 29(7):993-1014.

We analysed two sets of mitochondrial (mt) DNA data from tigrinas (traditionally, Leopardus tigrinus) we sampled in Costa Rica, Venezuela, Colombia, Ecuador, Peru, Bolivia, northwestern and northeastern Argentina and southern Brazil. Additionally, the analysis included some GenBank sequences from southern, central and northeastern Brazil. The first mt set (mt ATP8+mt 16S rRNA with 41 tigrina) revealed the existence of seven different tigrina-like haplogroups. They could represent, at least, 4-6 different tigrina species following the Phylogenetic Species Concept (PSC). In the second mt set (mitogenomics with 18 tigrinas), we detected six different tigrina-like haplogroups. They could represent 4-5 different tigrina species - including a possible full new species, which has gone previously unnoticed to the world of science both morphologic and molecularly. Coat patterns of several of these different tigrinas support the molecular differences. We also detected intense hybridization in many Andean tigrina with margays (Leopardus wiedii) and ocelots (Leopardus pardalis) as well as hybridization of one Bolivian tigrina with Leopardus geoffroyi. Similar hybridization was found for many of the southern Brazilian tigrina (Leopardus guttulus). All of the temporal split estimates for these tigrina haplogroups, together with those of the Leopardus species recognized to date, began in the late Pliocene but mostly occurred during the Pleistocene. In agreement with the existence of multiple species within the traditional L. tigrinus species, we detected strong and significant spatial structure in the two mt data sets. There were clear circular clines. A major part of the analyses detected more genetic resemblance between the Central American + trans Andean Colombian and Ecuadorian tigrina (L. oncilla) with the most geographically distant tigrina from central and southern Brazil (L. guttulus; pure individuals not hybridized with L. geoffroyi). In comparison, the Andean tigrina taxa had intermediate geographical origins but were highly genetically differentiated both from the Central American + trans Andean Colombian-Ecuadorian tigrina and from the central and southern Brazilian tigrina.

RevDate: 2018-12-18
CmpDate: 2018-12-18

Shadwick JDL, Silberman JD, FW Spiegel (2018)

Variation in the SSUrDNA of the Genus Protostelium Leads to a New Phylogenetic Understanding of the Genus and of the Species Concept for Protostelium mycophaga (Protosteliida, Amoebozoa).

The Journal of eukaryotic microbiology, 65(3):331-344.

Members of the genus Protostelium (including P. mycophaga, P. nocturnum, and P. okumukumu) are protosteloid amoebae commonly found in terrestrial habitats on dead plant matter. They, along with the closely allied nominal genus Planoprotostelium, containing the single species Pl. aurantium, all have an amoeboid trophic stage with acutely pointed subpseudopodia and orange lipid droplets in the granuloplasm. These amoebae form stalked fruiting bodies topped with a single, usually deciduous spore. The species are identified based on their fruiting body morphologies except for Pl. aurantium which looks similar to P. mycophaga in fruiting morphology, but has amoebae that can make flagella in liquid medium. We built phylogenetic trees using nuclear small subunit ribosomal DNA sequences of 35 isolates from the genera Protostelium and Planoprotostelium and found that (1) the nonflagellated P. nocturnum and P. okumukumu branch basally in the genus Protostelium, (2) the flagellate, Pl. aurantium falls within the genus Protostelium in a monophyletic clade with the nominal variety, P. mycophaga var. crassipes, (3) the cultures initially identified as Protostelium mycophaga can be divided into at least three morphologically recognizable taxa, P. aurantium n. comb., P. apiculatum n. sp., and P. m. rodmani n. subsp., as well as a paraphyletic assemblage that includes the remainder of the P. mycophaga morphotype. These findings have implications for understanding the ecology, evolution, and diversity of these amoeboid organisms and for using these amoebae as models for other amoeboid groups.

RevDate: 2019-11-20

Gama R, Aguirre-Gutiérrez J, M Stech (2017)

Ecological niche comparison and molecular phylogeny segregate the invasive moss species Campylopus introflexus (Leucobryaceae, Bryophyta) from its closest relatives.

Ecology and evolution, 7(19):8017-8031.

The delimitation of the invasive moss species Campylopus introflexus from its closest relative, Campylopus pilifer, has been long debated based on morphology. Previous molecular phylogenetic reconstructions based on the nuclear ribosomal internal transcribed spacers (ITS) 1 and 2 showed that C. pilifer is split into an Old World and a New World lineage, but remained partly inconclusive concerning the relationships between these two clades and C. introflexus. Analyses of an extended ITS dataset displayed statistically supported incongruence between ITS1 and ITS2. ITS1 separates the New World clade of C. pilifer from a clade comprising C. introflexus and the Old World C. pilifer. Ancestral state reconstruction showed that this topology is morphologically supported by differences in the height of the dorsal costal lamellae in leaf cross-section (despite some overlap). ITS2, in contrast, supports the current morphological species concept, i.e., separating C. introflexus from C. pilifer, which is morphologically supported by the orientation of the hyaline hair point at leaf apex as well as costal lamellae height. Re-analysis of published and newly generated plastid atpB-rbcL spacer sequences supported the three ITS lineages. Ecological niche modeling proved a useful approach and showed that all three molecular lineages occupy distinct environmental spaces that are similar, but undoubtedly not equivalent. In line with the ITS1 topology, the C. pilifer lineage from the New World occupies the most distinct environmental niche, whereas the niches of Old World C. pilifer and C. introflexus are very similar. Taking the inferences from ecological niche comparisons, phylogenetics, and morphology together, we conclude that all three molecular lineages represent different taxa that should be recognized as independent species, viz. C. introflexus, C. pilifer (Old World clade), and the reinstated C. lamellatus Mont. (New World clade).

RevDate: 2018-11-13
CmpDate: 2018-05-18

Hoetzinger M, MW Hahn (2017)

Genomic divergence and cohesion in a species of pelagic freshwater bacteria.

BMC genomics, 18(1):794.

BACKGROUND: In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwaters with low habitat connectivity - i.e. elevated geographic barriers to gene flow - is unclear. To investigate further we studied genomic trends within the globally abundant PnecC cluster (genus Polynucleobacter, Betaproteobacteria) and analyzed homologous recombination within the affiliated species P. asymbioticus.

RESULTS: Comparisons among 20 PnecC genomes revealed a clearly discontinuous distribution of nucleotide sequence similarities. Among the nine conspecific individuals (P. asymbioticus) all average nucleotide identity (ANI) values were greater than 97%, whereas all other comparisons exhibited ANI values lower than 85%. The reconstruction of recombination and mutation events for the P. asymbioticus core genomes yielded an r/m ratio of 7.4, which is clearly above estimated thresholds for recombination to act as a cohesive force. Hotspots of recombination were found to be located in the flanking regions of genomic islands. Even between geographically separated habitats a high flux of recombination was evident. While a biogeographic population structure was suggested from MLST data targeting rather conserved loci, such a structure was barely visible when whole genome data was considered. However, both MLST and whole genome data showed evidence of differentiation between two lineages of P. asymbioticus. The ratios of non-synonymous to synonymous substitution rates as well as growth rates in transplantation experiments suggested that this divergence was not selectively neutral.

CONCLUSIONS: The high extent of homologous recombination among P. asymbioticus bacteria can act as a cohesive force that effectively counteracts genetic divergence. At least on a regional scale, homologous recombination can act across geographically separated ecosystems and therefore plays an important role in the evolution and consistency of bacterial freshwater species. A species model akin to the biological species concept may be applicable for P. asymbioticus. Nonetheless, two genetically distinct lineages have emerged and further research may clarify if their divergence has been initiated by reinforced geographical barriers or has been evolving in sympatry.

RevDate: 2018-09-04
CmpDate: 2018-09-04

Borg Dahl M, Brejnrod AD, Unterseher M, et al (2018)

Genetic barcoding of dark-spored myxomycetes (Amoebozoa)-Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies.

Molecular ecology resources, 18(2):306-318.

Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.

RevDate: 2018-07-09
CmpDate: 2018-05-29

Rooney-Latham S, Lutz M, Blomquist CL, et al (2017)

Entyloma helianthi: identification and characterization of the causal agent of sunflower white leaf smut.

Mycologia, 109(3):520-528.

White leaf smut is a minor foliar disease of sunflower (Helianthus annuus) in the United States. The disease occurs primarily in greenhouse-grown sunflowers in California and causes leaf spot, defoliation, and a reduction in yield and crop value. Historically, many Entyloma specimens with similar morphological characters, but infecting diverse plant genera including Helianthus, were called Entyloma polysporum. Recent comparative morphological and molecular work has shown that Entyloma species infect hosts within a single genus or species, suggesting that the sunflower Entyloma species may not be E. polysporum. In 2015, sunflower leaf smut material was collected from ornamental sunflowers in a greenhouse in Santa Barbara County, California. Morphologically, this species differed from E. polysporum in having smaller, more regular-shaped teliospores and prominently developed conidiophores with cylindrical conidia. The rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS]) region of the sunflower leaf smut was phylogenetically distinct from all previously sequenced Entyloma species and found only on H. annuus. This study confirms that the sunflower leaf smut pathogen represents a novel species, Entyloma helianthi. Possible misidentification of the anamorphic stage of Entyloma helianthi as another leaf spot pathogen, Ramularia helianthi, is also discussed.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

Order from Amazon

This is a must read book for anyone with an interest in invasion biology. The full title of the book lays out the author's premise — The New Wild: Why Invasive Species Will Be Nature's Salvation. Not only is species movement not bad for ecosystems, it is the way that ecosystems respond to perturbation — it is the way ecosystems heal. Even if you are one of those who is absolutely convinced that invasive species are actually "a blight, pollution, an epidemic, or a cancer on nature", you should read this book to clarify your own thinking. True scientific understanding never comes from just interacting with those with whom you already agree. R. Robbins

963 Red Tail Lane
Bellingham, WA 98226


E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

RJR Picks from Around the Web (updated 11 MAY 2018 )