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29 Sep 2023 at 01:56
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Bibliography on: Species Concept


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RJR: Recommended Bibliography 29 Sep 2023 at 01:56 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"[tiab:~6] OR "species concepts"[tiab] OR "species problem") NOT "invasive species" ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2023-09-28

Cortese-Krott MM (2023)

The Reactive Species Interactome in Red Blood Cells: Oxidants, Antioxidants, and Molecular Targets.

Antioxidants (Basel, Switzerland), 12(9): pii:antiox12091736.

Beyond their established role as oxygen carriers, red blood cells have recently been found to contribute to systemic NO and sulfide metabolism and act as potent circulating antioxidant cells. Emerging evidence indicates that reactive species derived from the metabolism of O2, NO, and H2S can interact with each other, potentially influencing common biological targets. These interactions have been encompassed in the concept of the reactive species interactome. This review explores the potential application of the concept of reactive species interactome to understand the redox physiology of RBCs. It specifically examines how reactive species are generated and detoxified, their interactions with each other, and their targets. Hemoglobin is a key player in the reactive species interactome within RBCs, given its abundance and fundamental role in O2/CO2 exchange, NO transport/metabolism, and sulfur species binding/production. Future research should focus on understanding how modulation of the reactive species interactome may regulate RBC biology, physiology, and their systemic effects.

RevDate: 2023-09-27

Jiménez-Gaona Y, Vivanco-Galván O, Cruz D, et al (2023)

Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in Tulasnella (Basidiomycota).

Journal of fungi (Basel, Switzerland), 9(9): pii:jof9090894.

BACKGROUND: The delimitation of species of Tulasnella has been extensively studied, mainly at the morphological (sexual and asexual states) and molecular levels-showing ambiguity between them. An integrative species concept that includes characteristics such as molecular, ecology, morphology, and other information is crucial for species delimitation in complex groups such as Tulasnella.

OBJECTIVES: The aim of this study is to test evolutionary relationships using a combination of alignment-based and alignment-free distance matrices as an alternative molecular tool to traditional methods, and to consider the secondary structures and CBCs from ITS2 (internal transcribed spacer) sequences for species delimitation in Tulasnella.

METHODOLOGY: Three phylogenetic approaches were plotted: (i) alignment-based, (ii) alignment-free, and (iii) a combination of both distance matrices using the DISTATIS and pvclust libraries from an R package. Finally, the secondary structure consensus was modeled by Mfold, and a CBC analysis was obtained to complement the species delimitation using 4Sale.

RESULTS AND CONCLUSIONS: The phylogenetic tree results showed delimited monophyletic clades in Tulasnella spp., where all 142 Tulasnella sequences were divided into two main clades A and B and assigned to seven species (T. asymmetrica, T. andina, T. eichleriana ECU6, T. eichleriana ECU4 T. pinicola, T. violea), supported by bootstrap values from 72% to 100%. From the 2D secondary structure alignment, three types of consensus models with helices and loops were obtained. Thus, T. albida belongs to type I; T. eichleriana, T. tomaculum, and T. violea belong to type II; and T. asymmetrica, T. andina, T. pinicola, and T. spp. (GER) belong to type III; each type contains four to six domains, with nine CBCs among these that corroborate different species.

RevDate: 2023-09-25

Wang Z, Kim W, Wang YW, et al (2023)

The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics.

Frontiers in fungal biology, 4:1214537.

Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.

RevDate: 2023-09-20

Biswas R, Batista Da Rocha C, Bennick RA, et al (2023)

Water-Soluble Fullerene Monoderivatives for Biomedical Applications.

ChemMedChem [Epub ahead of print].

Monoderivatives of fullerenes functionalized with hydrophilic groups make them water soluble, while preserving the hydrophobic fullerene cage. This class of molecules have intriguing biomedical applications, including drug delivery, photodynamic therapy (PDT), antiviral and antimicrobial activity and reactive oxygen species (ROS)-scavenging abilities. In this Concept we discuss the synthesis and biomedical applications of water-soluble fullerene monoderivatives and their biological behavior based on their structures.

RevDate: 2023-09-18

Pollmann M, Kuhn D, König C, et al (2023)

New species based on the biological species concept within the complex of Lariophagus distinguendus (Hymenoptera, Chalcidoidea, Pteromalidae), a parasitoid of household pests.

Ecology and evolution, 13(9):e10524.

The pteromalid parasitoid Lariophagus distinguendus (Foerster) belongs to the Hymenoptera, a megadiverse insect order with high cryptic diversity. It attacks stored product pest beetles in human storage facilities. Recently, it has been shown to consist of two separate species. To further study its cryptic diversity, strains were collected to compare their relatedness using barcoding and nuclear genes. Nuclear genes identified two clusters which agree with the known two species, whereas the barcode fragment determined an additional third Clade. Total reproductive isolation (RI) according to the biological species concept (BSC) was investigated in crossing experiments within and between clusters using representative strains. Sexual isolation exists between all studied pairs, increasing from slight to strong with genetic distance. Postzygotic barriers mostly affected hybrid males, pointing to Haldane's rule. Hybrid females were only affected by unidirectional Spiroplasma-induced cytoplasmic incompatibility and behavioural sterility, each in one specific strain combination. RI was virtually absent between strains separated by up to 2.8% COI difference, but strong or complete in three pairs from one Clade each, separated by at least 7.2%. Apparently, each of these clusters represents one separate species according to the BSC, highlighting cryptic diversity in direct vicinity to humans. In addition, these results challenge the recent 'turbo-taxonomy' practice of using 2% COI differences to delimitate species, especially within parasitic Hymenoptera. The gradual increase in number and strength of reproductive barriers between strains with increasing genetic distance also sheds light on the emergence of barriers during the speciation process in L. distinguendus.

RevDate: 2023-09-14

Fowers BJ, Novak LF, Kiknadze NC, et al (2023)

Is the concept of personality capacious enough to incorporate virtues?.

Frontiers in psychology, 14:1232637.

We will consider four answers to the question about whether the concept of personality is capacious enough to incorporate virtues. The simplest is that the concept of personality encompasses all individual variations in persons. It follows from this answer that virtues would, as individual differences, be incorporated into personality. Unfortunately, definitions of personality do not always invoke such capaciousness, and, in practice, most scholars limit their work to the Big Five or HEXACO models, which do not incorporate virtues. The second answer is that the concept of personality incorporates all trait or dimension level variations across persons, with some exceptions, such as intelligence, attachment style, and psychopathy. Following this definition, virtues, as traits, would be incorporated into such a broad definition of personality. Unfortunately, the boundaries for inclusion and exclusion into personality are fuzzy in this case, and there is no extant definition of personality that solves this problem. The third answer is that personality traits and virtue traits are similar, but distinct concepts. This article presents conceptual and empirical arguments for this similarity in seeing traits as a higher order concept that includes the species of personality and the species of virtue. The fourth answer is that personality and virtue are unrelated. This answer is dismissed because there are many studies that indicate that they are correlated, and few advocate such a clear differentiation. The conclusion is that, pending conceptual and empirical results indicating otherwise, the genus-species relationship seems most fitting where traits are a genus, and personality and virtue are each a species within that genus.

RevDate: 2023-09-11

Thomas GWC, Hughes JJ, Kumon T, et al (2023)

The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats.

bioRxiv : the preprint server for biology pii:2023.08.28.555178.

A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.

RevDate: 2023-09-08

Mercogliano R, D Dongo (2023)

Fish welfare during slaughter: the European Council Regulation 1099/09 application.

Italian journal of food safety, 12(3):10926.

The Treaty of Lisbon states that animals are sentient beings. Fish species show physiological differences from terrestrial animals and are slaughtered and killed in a very different context. Many existing commercial killing methods expose fish to extensive suffering over a prolonged period of time, and some of the slaughtering practices they experience can cause pain and distress. This study highlights the limited feasibility of European Council Regulation 1099/09 requirements on welfare when killing cephalopods and crustaceans. Sentience is the animal's capacity to have positive (comfort, excitement) and negative (pain, anxiety, distress, or harm) feelings. Considerable evidence is now showing that the major commercial fish species, including cephalopods and crustaceans, possess complex neurological substrates supporting pain sensitivity and conscious experiences. In the legislation applied to scientific procedures, the concept of sentience in these species is important. Therefore, it would be appropriate to acknowledge current scientific evidence and establish reference criteria for fish welfare. For the welfare of fish species during slaughter, European Council Regulation 1099/09 applicability is limited. Fish welfare during slaughter is more than just an ethical problem. According to the One-Health approach, food safety should also include the concept of sentience for fish welfare. Pending studies that dispel all doubt, the precautionary principle of European Council Regulation 178/04 remains valid and should be applied to fish welfare.

RevDate: 2023-09-07

Ansari L, Asgari B, Zare R, et al (2023)

Penicillium rhizophilum, a novel species in the section Exilicaulis isolated from the rhizosphere of sugarcane in Southwest Iran.

International journal of systematic and evolutionary microbiology, 73(9):.

During a survey of species diversity of Penicillium and Talaromyces in sugarcane (Saccharum officinarum) rhizosphere in the Khuzestan province of Iran [1], 195 strains were examined, from which 187 belonged to Penicillium (11 species) and eight to Talaromyces (one species). In the present study, three strains of Penicillium belonging to section Exilicaulis series Restricta, identified as P. restrictum by Ansari et al. [1], were subjected to a phylogenetic study. The multilocus phylogeny of partial β-tubulin, calmodulin and RNA polymerase II second largest subunit genes enabled the recognition of one new phylogenetic species that is here formally described as Penicillium rhizophilum sp. nov. This species is phylogenetically distinct in series Restricta, but it does not show significant morphological differences from other species previously classified in the series. Therefore, we here placed bias on the phylogenetic species concept. The holotype of Penicillium rhizophilum sp. nov. is IRAN 18169F and the ex-type culture is LA30[T] (=IRAN 4042C[T]=CBS 149737[T]).

RevDate: 2023-08-31

Sen A, Ansari A, Swain A, et al (2023)

Probing the Origins of Puzzling Reactivity in Fe/Mn-Oxo/Hydroxo Species toward C-H Bonds: A DFT and Ab Initio Perspective.

Inorganic chemistry [Epub ahead of print].

Activation of C-H bonds using an earth-abundant metal catalyst is one of the top challenges of chemistry, where high-valent Mn/Fe-oxo(hydroxo) biomimic species play an important role. There are several open questions related to the comparative oxidative abilities of these species, and a unifying concept that could accommodate various factors influencing reactivity is lacking. To shed light on these open questions, here, we have used a combination of density functional theory (DFT) (B3LYP-D3/def2-TZVP) and ab initio (CASSCF/NEVPT2) calculations to study a series of high-valent metal-oxo species [M[n+]H3buea(O/OH)] (M = Mn and Fe, n = II to V; H3buea = tris[(N'-tert-butylureaylato)-N-ethylene)]aminato towards the activation of dihydroanthracene (DHA). The H-bonding network in the ligand architecture influences the ground state-excited state gap and brings several excited states of the same spin multiplicity closer in energy, which triggers reactivity via one of those excited states, reducing the kinetic barriers for the C-H bond activation and rationalizing several puzzling reactivity trends observed in various high-valent Mn/Fe-oxo(hydroxo) species.

RevDate: 2023-08-28

Génin F, Rambeloarivony H, Silvestro D, et al (2023)

Ontogeny and phylogeny of mating behaviour: social heteroch rony in primates.

Theoretical biology forum, 116(1-2):15-50.

Based on the Recognition Concept of species, the specific-mate contact model posits that mating systems develop as combinations of two fundamental courtship strategies that we interpret here in terms of behavioural heterochrony: territorial mate-attraction evolved as an effect of peramorphosis whereas group-living mate-seeking evolved as an effect of paedomorphosis. We tested this hypothesis on primates in a phylogenetic and paleo-climatic context. Our results suggest that primate promiscuity (both males and females are mate-seekers) evolved with group-living from ancestral pair-living monogamy (both males and females are mate-attractors) in the Palaeogene, as the result of a slowdown in growth (neoteny) caused by increased environmental predictability. A secondary return to territorial monogamy probably evolved as the result of accelerated growth driven by seasonality (acceleration). Polygamy evolved in the Neogene during periods of forest fragmentation and environmental unpredictability. Small monogamous ancestors evolved seasonal polyandry (female attraction) as an effect of truncated development (progenesis). Large promiscuous, neotenic ancestors evolved non-seasonal polygyny (male attraction) as an effect of prolonged development (hypermorphosis) in males. We conclude that social heterochrony offers alternative explanations for the coevolution of life history and mating be-haviour; and we discuss the implications of our model for human social evolution.

RevDate: 2023-08-26

Xesfyngi Y, Georgoutsou-Spyridonos M, Tripathy A, et al (2023)

A High-Performance Antibacterial Nanostructured ZnO Microfluidic Device for Controlled Bacterial Lysis and DNA Release.

Antibiotics (Basel, Switzerland), 12(8): pii:antibiotics12081276.

In this work, the antibacterial properties of nanostructured zinc oxide (ZnO) surfaces are explored by incorporating them as walls in a simple-to-fabricate microchannel device. Bacterial cell lysis is demonstrated and quantified in such a device, which functions due to the action of its nanostructured ZnO surfaces in contact with the working fluid. To shed light on the mechanism responsible for lysis, E. coli bacteria were incubated in zinc and nanostructured ZnO substrates, as well as the here-investigated ZnO-based microfluidic devices. The unprecedented killing efficiency of E. coli in nanostructured ZnO microchannels, effective after a 15 min incubation, paves the way for the implementation of such microfluidic chips in the disinfection of bacteria-containing solutions. In addition, the DNA release was confirmed by off-chip PCR and UV absorption measurements. The results indicate that the present nanostructured ZnO-based microfluidic chip can, under light, achieve partial inactivation of the released bacterial DNA via reactive oxygen species-mediated oxidative damage. The present device concept can find broader applications in cases where the presence of DNA in a sample is not desirable. Furthermore, the present microchannel device enables, in the dark, efficient release of bacterial DNA for downstream genomic DNA analysis. The demonstrated potential of this antibacterial device for tailored dual functionality in light/dark conditions is the main novel contribution of the present work.

RevDate: 2023-08-26

Jabin G, Joshi BD, Wang MS, et al (2023)

Mid-Pleistocene Transitions Forced Himalayan ibex to Evolve Independently after Split into an Allopatric Refugium.

Biology, 12(8): pii:biology12081097.

Pleistocene glaciations had profound impact on the spatial distribution and genetic makeup of species in temperate ecosystems. While the glacial period trapped several species into glacial refugia and caused abrupt decline in large populations, the interglacial period facilitated population growth and range expansion leading to allopatric speciation. Here, we analyzed 40 genomes of four species of ibex and found that Himalayan ibex in the Pamir Mountains evolved independently after splitting from its main range about 0.1 mya following the Pleistocene species pump concept. Demographic trajectories showed Himalayan ibex experienced two historic bottlenecks, one each c. 0.8-0.5 mya and c. 50-30 kya, with an intermediate large population expansion c. 0.2-0.16 mya coinciding with Mid-Pleistocene Transitions. We substantiate with multi-dimensional evidence that Himalayan ibex is an evolutionary distinct phylogenetic species of Siberian ibex which need to be prioritized as Capra himalayensis for taxonomic revision and conservation planning at a regional and global scale.

RevDate: 2023-08-16

Carrasco RA, KM Breen (2023)

Allostasis in Neuroendocrine Systems Controlling Reproduction.

Endocrinology pii:7243365 [Epub ahead of print].

Allostasis provides a supporting role to the homeostatic control of biological variables in mammalian species. While the concept of homeostasis is related to the control of variables within a set point or range that are essential to life, allostasis refers to systems that facilitate adaptation to challenges that the organism faces and the new requirements for survival. Essential for such adaptation is the role played by the brain in eliciting neural and neuroendocrine responses. Reproductive function is fundamental for the survival of species but is costly in energetic terms and requires a synchrony with an ever-changing environment. Thus, in many species reproductive function is blocked or delayed over immediate challenges. This review will cover the physiological systems and neuroendocrine pathways that supply allostatic control over reproductive neuroendocrine systems. Light, hypoxia, temperature, nutrition, psychosocial, and immune mediators influence the neuroendocrine control of reproductive functions through pathways that are confluent at the paraventricular nucleus; however, understanding of the integrative responses to these stimuli has not been clarified. Likely, the ultimate consequence of these allostatic mechanisms is the modification of kisspeptin and gonadotropin-releasing hormone neuronal activity, thus compromising reproduction function in the short term, while preserving species survivability.

RevDate: 2023-08-08

Weiss AS, Niedermeier LS, von Strempel A, et al (2023)

Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community.

Nature communications, 14(1):4780.

A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.

RevDate: 2023-08-01

Wang XC, Zhuang WY, RL Zhao (2023)

Species Diversity of Helvella lacunosa Clade (Pezizales, Ascomycota) in China and Description of Sixteen New Species.

Journal of fungi (Basel, Switzerland), 9(7):.

Helvella lacunosa and its allies are widely distributed in the Northern Hemisphere and perform important functions in ecosystems. A comprehensive study on 101 collections of Helvella lacunosa, including those deposited in four Chinese fungaria or collected recently from 10 provinces, was conducted based on morphological and molecular characteristics. Phylogenies of "Helvella lacunosa clade" inferred from Hsp90, ITS, LSU, and TEF were reconstructed with 49 lineages recognized, of which 25 lineages occurred in China, and each represented an individual species. Sixteen new species were determined with detailed descriptions and illustrations. Two new Chinese records were reported. Species concepts and their distinctions in macro- and micro-features were discussed.

RevDate: 2023-07-26

Huang GJ, Li CW, Lee PY, et al (2023)

Electronic Preresonance Stimulated Raman Scattering Spectromicroscopy Using Multiple-Plate Continuum.

The journal of physical chemistry. B [Epub ahead of print].

Stimulated Raman scattering (SRS) spectromicroscopy is a powerful technique that enables label-free detection of chemical bonds with high specificity. However, the low Raman cross section due to typical far-electronic resonance excitation seriously restricts the sensitivity and undermines its application to bio-imaging. To address this bottleneck, the electronic preresonance (EPR) SRS technique has been developed to enhance the Raman signals by shifting the excitation frequency toward the molecular absorption. A fundamental weakness of the previous demonstration is the lack of dual-wavelength tunability, making EPR-SRS only applicable to a limited number of species in the proof-of-concept experiment. Here, we demonstrate the EPR-SRS spectromicroscopy using a multiple-plate continuum (MPC) light source able to examine a single vibration mode with independently adjustable pump and Stokes wavelengths. In our experiments, the C═C vibration mode of Alexa 635 is interrogated by continuously scanning the pump-to-absorption frequency detuning throughout the entire EPR region enabled by MPC. The results exhibit 150-fold SRS signal enhancement and good agreement with the Albrecht A-term preresonance model. Signal enhancement is also observed in EPR-SRS images of the whole Drosophila brain stained with Alexa 635. With the improved sensitivity and potential to implement hyperspectral measurement, we envision that MPC-EPR-SRS spectromicroscopy can bring the Raman techniques closer to a routine in bio-imaging.

RevDate: 2023-07-24

Cobo-Simón M, Hart R, H Ochman (2023)

Gene flow and species boundaries of the genus Salmonella.

mSystems [Epub ahead of print].

The genus Salmonella comprises two species, Salmonella bongori and Salmonella enterica, which are infectious to a wide variety of animal hosts. The diversity within S. enterica has been further partitioned into 6-10 subspecies based on such features as host range, geography, and most recently, genetic relatedness and phylogenetic affiliation. Although Salmonella pathogenicity is attributable to large numbers of acquired virulence factors, the extent of homologous exchange in the species at large is apparently constrained such that the species and subspecies form distinct clusters of strains. To explore the extent of gene flow within and among subspecies, and to ultimately define true biological species, we evaluated patterns of recombination in over 1,000 genomes currently assigned to the genus. Those Salmonella subspecies containing sufficient numbers of sequenced genomes to allow meaningful analysis-i.e., subsp. enterica and diarizonae-were found to be reproductively isolated from one another and from all other subspecies. Based on the configuration of genomic sequence divergence among subspecies, it is expected that each of the other Salmonella subspecies will also represent a biological species. Our findings argue against the application of prescribed nucleotide-identity thresholds to delineate bacterial species and contend that the Biological Species Concept should not be disregarded for bacteria, even those, like Salmonella, that demonstrate complex patterns of species and subspecies divergence. IMPORTANCE The Biological Species Concept (BSC), which defines species boundaries based on the capacity for gene exchange, is widely used to classify sexually reproducing eukaryotes but is generally thought to be inapplicable to bacteria due to their completely asexual mode of reproduction. We show that the genus Salmonella, whose thousands of described serovars were formerly considered to be strictly clonal, undergoes sufficient levels of homologous recombination to be assigned to species according to the BSC. Aside from the two recognized species, Salmonella enterica and Salmonella bongori, several (and likely all) of the subspecies within S. enterica are reproductively isolated from one another and should each be considered a separate biological species. These findings demonstrate that species barriers in bacteria can form despite high levels of nucleotide identity and that commonly applied thresholds of genomic sequence identity are not reliable indicators of bacterial species status.

RevDate: 2023-07-30

Tong S, Samet JM, Steffen W, et al (2023)

Solidarity for the Anthropocene.

Environmental research, 235:116716 pii:S0013-9351(23)01520-7 [Epub ahead of print].

Social solidarity is essential to large-scale collective action, but the need for solidarity has received little attention from scholars of Earth Systems, sustainability and public health. Now, the need for solidarity requires recognition. We have entered a new planetary epoch - the Anthropocene - in which human-induced global changes are occurring at an unprecedented scale. There are multiple health crises facing humanity - widening inequity, climate change, biodiversity loss, diminishing resources, persistent poverty, armed conflict, large-scale migration, and others. These global challenges are so far-reaching, and call for such extensive, large-scale action, that solidarity is a sine qua non for tackling these challenges. However, the heightened need for solidarity has received little attention in the context of the Anthropocene and, in particular, how it can be created and nurtured has been overlooked. In this commentary, we explore the concept of solidarity from inter-species, intra-generational and inter-generational perspectives. We also propose strategies to enhance solidarity in the Anthropocene.

RevDate: 2023-07-21
CmpDate: 2023-07-21

Lisboa TP, de Faria LV, de Oliveira WBV, et al (2023)

Cost-effective protocol to produce 3D-printed electrochemical devices using a 3D pen and lab-made filaments to ciprofloxacin sensing.

Mikrochimica acta, 190(8):310.

A novel conductive filament based on graphite (Gr) dispersed in polylactic acid polymer matrix (PLA) is described to produce 3D-electrochemical devices (Gr/PLA). This conductive filament was used to additively manufacture electrochemical sensors using the 3D pen. Thermogravimetric analysis confirmed that Gr was successfully incorporated into PLA, achieving a composite material (40:60% w/w, Gr and PLA, respectively), while Raman and scanning electron microscopy revealed the presence of defects and a high porosity on the electrode surface, which contributes to improved electrochemical performance. The 3D-printed Gr/PLA electrode provided a more favorable charge transfer (335 Ω) than the conventional glassy carbon (1277 Ω) and 3D-printed Proto-pasta® (3750 Ω) electrodes. As a proof of concept, the ciprofloxacin antibiotic, a species of multiple interest, was selected as a model molecule. Thus, a square wave voltammetry (SWV) method was proposed in the potential range + 0.9 to + 1.3 V (vs Ag|AgCl|KCl(sat)), which provided a wide linear working range (2 to 32 µmol L[-1]), 1.79 µmol L[-1] limit of detection (LOD), suitable precision (RSD < 7.9%), and recovery values from 94 to 109% when applied to pharmaceutical and milk samples. Additionally, the sensor is free from the interference of other antibiotics routinely employed in veterinary practices. This device is disposable, cost-effective, feasibly produced in financially limited laboratories, and consequently promising for evaluation of other antibiotic species in routine applications.

RevDate: 2023-08-06
CmpDate: 2023-08-03

Graves JL (Jr) (2023)

Favored Races in the Struggle for Life: Racism and the Speciation Concept.

Cold Spring Harbor perspectives in biology, 15(8): pii:cshperspect.a041454.

Evolutionary speciation, whether it be cladistic or phyletic, has always been associated with race concepts. Biological races are conceived as definable stages of divergence from a common ancestor. However, the species concept in Western science began within a special creationist framework. The sixteenth century European voyages of discovery resulted in special creationist schemes explaining the origin of the new peoples encountered. These were designed to provide the moral justification for their colonization and enslavement. By the seventeenth century, European naturalists were beginning to seriously question the meaning of the variation within the animals and plants they observed within the context of God's role in creation. By the middle of the nineteenth century, "the species question" was the most important intellectual enterprise within biology. Here I discuss how notions of speciation influenced and were influenced by conceptions of race within Homo sapiens.

RevDate: 2023-07-18

Bhat AH, Machado RAR, Abolafia J, et al (2023)

Multigene Sequence-Based and Phenotypic Characterization Reveals the Occurrence of a Novel Entomopathogenic Nematode Species, Steinernema anantnagense n. sp.

Journal of nematology, 55(1):20230029.

Three entomopathogenic nematode populations were isolated from agricultural fields in the Anantnag district of Jammu and Kashmir (India). Sequences of multiple gene regions and phenotypic features show that they are conspecific and represent a novel species. Molecular and morphological features provided evidence for placing the new species into the "Kushidai" clade. Within this clade, analysis of sequence data of the internal transcribed spacer (ITS) gene, the D2D3 region of the 28S rRNA gene, the mitochondrial cytochrome oxidase I (mtCOI) gene, and the mitochondrial 12S (mt12S) gene depicted the novel species as a distinctive entity closely related to Steinernema akhursti, S. kushidai, and S. populi. Phylogenetic analyses also show that the new species is a sister species to S. akhursti, and these two species are closely related to S. kushidai and S. populi. Additionally, the new species does not mate or produce fertile progeny with any of the closely related species, reinforcing its uniqueness from a biological species concept standpoint. The new species is further characterized by the third-stage infective juveniles with almost straight bodies (0.7-0.8 mm length), poorly developed stoma and pharynx, and conoid-elongate tail (49-66 µm) with hyaline posterior part. Adult females are characterized by short and conoid tails bearing a short mucron in the first generation and long conoid tails with thin mucron in the second generation. Adult males have ventrally curved spicules in both generations. Moreover, the first-generation male has rounded manubrium, fusiform gubernaculum, conoid and slightly ventrally curved tails with minute mucron, and the second generation has rhomboid manubrium anteriorly ventrad bent, and tails with long and robust mucron. The morphological, morphometrical, molecular, and phylogenetic analyses support the new species status of this nematode, which is hereby described as Steinernema anantnagense n. sp. The bacterial symbiont associated with S. anantnagense n. sp. represents a novel species, closely related to Xenorhabdus japonica. These findings shed light on the diversity of entomopathogenic nematodes and their symbiotic bacteria, providing valuable information for future studies in this field.

RevDate: 2023-07-16

Poorter L, Amissah L, Bongers F, et al (2023)

Successional theories.

Biological reviews of the Cambridge Philosophical Society [Epub ahead of print].

Succession is a fundamental concept in ecology because it indicates how species populations, communities, and ecosystems change over time on new substrate or after a disturbance. A mechanistic understanding of succession is needed to predict how ecosystems will respond to land-use change and to design effective ecosystem restoration strategies. Yet, despite a century of conceptual advances a comprehensive successional theory is lacking. Here we provide an overview of 19 successional theories ('models') and their key points, group them based on conceptual similarity, explain conceptual development in successional ideas and provide suggestions how to move forward. Four groups of models can be recognised. The first group (patch & plants) focuses on plants at the patch level and consists of three subgroups that originated in the early 20th century. One subgroup focuses on the processes (dispersal, establishment, and performance) that operate sequentially during succession. Another subgroup emphasises individualistic species responses during succession, and how this is driven by species traits. A last subgroup focuses on how vegetation structure and underlying demographic processes change during succession. A second group of models (ecosystems) provides a more holistic view of succession by considering the ecosystem, its biota, interactions, diversity, and ecosystem structure and processes. The third group (landscape) considers a larger spatial scale and includes the effect of the surrounding landscape matrix on succession as the distance to neighbouring vegetation patches determines the potential for seed dispersal, and the quality of the neighbouring patches determines the abundance and composition of seed sources and biotic dispersal vectors. A fourth group (socio-ecological systems) includes the human component by focusing on socio-ecological systems where management practices have long-lasting legacies on successional pathways and where regrowing vegetations deliver a range of ecosystem services to local and global stakeholders. The four groups of models differ in spatial scale (patch, landscape) or organisational level (plant species, ecosystem, socio-ecological system), increase in scale and scope, and reflect the increasingly broader perspective on succession over time. They coincide approximately with four periods that reflect the prevailing view of succession of that time, although all views still coexist. The four successional views are: succession of plants (from 1910 onwards) where succession was seen through the lens of species replacement; succession of communities and ecosystems (from 1965 onwards) when there was a more holistic view of succession; succession in landscapes (from 2000 onwards) when it was realised that the structure and composition of landscapes strongly impact successional pathways, and increased remote-sensing technology allowed for a better quantification of the landscape context; and succession with people (from 2015 onwards) when it was realised that people and societal drivers have strong effects on successional pathways, that ecosystem processes and services are important for human well-being, and that restoration is most successful when it is done by and for local people. Our review suggests that the hierarchical successional framework of Pickett is the best starting point to move forward as this framework already includes several factors, and because it is flexible, enabling application to different systems. The framework focuses mainly on species replacement and could be improved by focusing on succession occurring at different hierarchical scales (population, community, ecosystem, socio-ecological system), and by integrating it with more recent developments and other successional models: by considering different spatial scales (landscape, region), temporal scales (ecosystem processes occurring over centuries, and evolution), and by taking the effects of the surrounding landscape (landscape integrity and composition, the disperser community) and societal factors (previous and current land-use intensity) into account. Such a new, comprehensive framework could be tested using a combination of empirical research, experiments, process-based modelling and novel tools. Applying the framework to seres across broadscale environmental and disturbance gradients allows a better insight into what successional processes matter and under what conditions.

RevDate: 2023-07-12

Cannon CH, M Lerdau (2023)

Conservation should not make 'perfect' an enemy of 'good'.

RevDate: 2023-07-07
CmpDate: 2023-07-06

Flütsch S, Wiestner F, Butticaz L, et al (2023)

Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp.

BMC genomics, 24(1):375.

BACKGROUND: Vibrio spp. are a diverse group of ecologically important marine bacteria responsible for several foodborne outbreaks of gastroenteritis around the world. Their detection and characterization are moving away from conventional culture-based methods towards next generation sequencing (NGS)-based approaches. However, genomic methods are relative in nature and suffer from technical biases arising from library preparation and sequencing. Here, we introduce a quantitative NGS-based method that enables the quantitation of Vibrio spp. at the limit of quantification (LOQ) through artificial DNA standards and their absolute quantification via digital PCR (dPCR).

RESULTS: We developed six DNA standards, called Vibrio-Sequins, together with optimized TaqMan assays for their quantification in individually sequenced DNA libraries via dPCR. To enable Vibrio-Sequin quantification, we validated three duplex dPCR methods to quantify the six targets. LOQs were ranging from 20 to 120 cp/µl for the six standards, whereas the limit of detection (LOD) was ~ 10 cp/µl for all six assays. Subsequently, a quantitative genomics approach was applied to quantify Vibrio-DNA in a pooled DNA mixture derived from several Vibrio species in a proof-of-concept study, demonstrating the increased power of our quantitative genomic pipeline through the coupling of NGS and dPCR.

CONCLUSIONS: We significantly advance existing quantitative (meta)genomic methods by ensuring metrological traceability of NGS-based DNA quantification. Our method represents a useful tool for future metagenomic studies aiming at quantifying microbial DNA in an absolute manner. The inclusion of dPCR into sequencing-based methods supports the development of statistical approaches for the estimation of measurement uncertainties (MU) for NGS, which is still in its infancy.

RevDate: 2023-07-12

Johnson A, Miller EA, Weber B, et al (2023)

Evidence of host specificity in Lactobacillus johnsonii genomes and its influence on probiotic potential in poultry.

Poultry science, 102(9):102858 [Epub ahead of print].

To date, the selection of candidate strains for probiotic development in production animals has been largely based upon screens for desired phenotypic traits. However, increasing evidence indicates that the use of host-specific strains may be important, because coevolution with the animal host better prepares a bacterial strain to colonize and succeed in its respective host animal species. This concept was applied to Lactobacillus johnsonii in commercial poultry production because of its previous correlation with enhanced bird performance. Using 204 naturally isolated chicken- and turkey-source L. johnsonii, we demonstrate that there is a strong phylogenetic signal for coevolution with the animal host. These isolates differ phenotypically, even within host source, and these differences can be correlated with certain L. johnsonii phylogenetic clades. In commercial turkey poults, turkey-specific strains with strong in vitro phenotypes performed better early in life than strains lacking those phenotypes. A follow-up performance trial in broiler chickens demonstrated that chicken-specific strains result in better overall bird performance than nonchicken-specific strains. Collectively, this work provides evidence for the impact of host adaptation on a probiotic strain's potential. Furthermore, this top-down approach is useful for screening larger numbers of isolates for probiotic candidates.

RevDate: 2023-07-01

Han SL, Wang MM, Ma ZY, et al (2023)

Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus.

Studies in mycology, 104:87-148.

Fusarium species are important cereal pathogens that cause severe production losses to major cereal crops such as maize, rice, and wheat. However, the causal agents of Fusarium diseases on cereals have not been well documented because of the difficulty in species identification and the debates surrounding generic and species concepts. In this study, we used a citizen science initiative to investigate diseased cereal crops (maize, rice, wheat) from 250 locations, covering the major cereal-growing regions in China. A total of 2 020 Fusarium strains were isolated from 315 diseased samples. Employing multi-locus phylogeny and morphological features, the above strains were identified to 43 species, including eight novel species that are described in this paper. A world checklist of cereal-associated Fusarium species is provided, with 39 and 52 new records updated for the world and China, respectively. Notably, 56 % of samples collected in this study were observed to have co-infections of more than one Fusarium species, and the detailed associations are discussed. Following Koch's postulates, 18 species were first confirmed as pathogens of maize stalk rot in this study. Furthermore, a high-confidence species tree was constructed in this study based on 1 001 homologous loci of 228 assembled genomes (40 genomes were sequenced and provided in this study), which supported the "narrow" generic concept of Fusarium (= Gibberella). This study represents one of the most comprehensive surveys of cereal Fusarium diseases to date. It significantly improves our understanding of the global diversity and distribution of cereal-associated Fusarium species, as well as largely clarifies the phylogenetic relationships within the genus. Taxonomic novelties: New species: Fusarium erosum S.L. Han, M.M. Wang & L. Cai, Fusarium fecundum S.L. Han, M.M. Wang & L. Cai, Fusarium jinanense S.L. Han, M.M. Wang & L. Cai, Fusarium mianyangense S.L. Han, M.M. Wang & L. Cai, Fusarium nothincarnatum S.L. Han, M.M. Wang & L. Cai, Fusarium planum S.L. Han, M.M. Wang & L. Cai, Fusarium sanyaense S.L. Han, M.M. Wang & L. Cai, Fusarium weifangense S.L. Han, M.M. Wang & L. Cai. Citation: Han SL, Wang MM, Ma ZY, Raza M, Zhao P, Liang JM, Gao M, Li YJ, Wang JW, Hu DM, Cai L (2023). Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. Studies in Mycology 104: 87-148. doi: 10.3114/sim.2022.104.02.

RevDate: 2023-07-01

Réblová M, Hernández-Restrepo M, Sklenář F, et al (2022)

Consolidation of Chloridium: new classification into eight sections with 37 species and reinstatement of the genera Gongromeriza and Psilobotrys.

Studies in mycology, 103:87-212.

Chloridium is a little-studied group of soil- and wood-inhabiting dematiaceous hyphomycetes that share a rare mode of phialidic conidiogenesis on multiple loci. The genus has historically been divided into three morphological sections, i.e. Chloridium, Gongromeriza, and Psilobotrys. Sexual morphs have been placed in the widely perceived genus Chaetosphaeria, but unlike their asexual counterparts, they show little or no morphological variation. Recent molecular studies have expanded the generic concept to include species defined by a new set of morphological characters, such as the collar-like hyphae, setae, discrete phialides, and penicillately branched conidiophores. The study is based on the consilience of molecular species delimitation methods, phylogenetic analyses, ancestral state reconstruction, morphological hypotheses, and global biogeographic analyses. The multilocus phylogeny demonstrated that the classic concept of Chloridium is polyphyletic, and the original sections are not congeneric. Therefore, we abolish the existing classification and propose to restore the generic status of Gongromeriza and Psilobotrys. We present a new generic concept and define Chloridium as a monophyletic, polythetic genus comprising 37 species distributed in eight sections. In addition, of the taxa earlier referred to Gongromeriza, two have been redisposed to the new genus Gongromerizella. Analysis of published metabarcoding data showed that Chloridium is a common soil fungus representing a significant (0.3 %) proportion of sequence reads in environmental samples deposited in the GlobalFungi database. The analysis also showed that they are typically associated with forest habitats, and their distribution is strongly influenced by climate, which is confirmed by our data on their ability to grow at different temperatures. We demonstrated that Chloridium forms species-specific ranges of distribution, which is rarely documented for microscopic soil fungi. Our study shows the feasibility of using the GlobalFungi database to study the biogeography and ecology of fungi. Taxonomic novelties: New genus: Gongromerizella Réblová; New sections: Chloridium section Cryptogonytrichum Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Gonytrichopsis Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Metachloridium Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Volubilia Réblová, Hern.-Restr., M. Kolařík & F. Sklenar; New species: Chloridium bellum Réblová & Hern.-Restr., Chloridium biforme Réblová & Hern.-Restr., Chloridium detriticola Réblová & Hern.-Restr., Chloridium gamsii Réblová & Hern.-Restr., Chloridium guttiferum Réblová & Hern.-Restr., Chloridium moratum Réblová & Hern.-Restr., Chloridium peruense Réblová & Hern.-Restr., Chloridium novae-zelandiae Réblová & Hern.-Restr., Chloridium elongatum Réblová & Hern.-Restr., Chloridium volubile Réblová & Hern.-Restr.; New varieties: Chloridium bellum var. luteum Réblová & Hern.-Restr., Chloridium detriticola var. effusum Réblová & Hern.-Restr., Chloridium chloridioides var. convolutum Réblová & Hern.-Restr.; New combinations: Chloridium section Gonytrichum (Nees & T. Nees) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Mesobotrys (Sacc.) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Pseudophialocephala (M.S. Calabon et al.) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium simile (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium chloridioides (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium subglobosum (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium fuscum (Corda) Réblová & Hern.-Restr., Chloridium ypsilosporum (Hol.-Jech.) Réblová & Hern.-Restr., Chloridium costaricense (G. Weber et al.) Réblová & Hern.-Restr., Chloridium cuneatum (N.G. Liu et al.) Réblová & Hern.-Restr., Fusichloridium cylindrosporum (W. Gams & Hol.-Jech.) Réblová, Gongromeriza myriocarpa (Fr.) Réblová, Gongromeriza pygmaea (P. Karst.) Réblová, Gongromerizella lignicola (F. Mangenot) Réblová, Gongromerizella pachytrachela (W. Gams & Hol.-Jech) Réblová, Gongromerizella pini (Crous & Akulov) Réblová; New name: Chloridium pellucidum Réblová & Hern.-Restr.; Epitypifications (basionyms): Chaetopsis fusca Corda, Gonytrichum caesium var. subglobosum W. Gams & Hol.-Jech.; Lectotypification (basionym): Gonytrichum caesium Nees & T. Nees. Citation: Réblová M, Hernández-Restrepo M, Sklenář F, Nekvindová J, Réblová K, Kolařík M (2022). Consolidation of Chloridium: new classification into eight sections with 37 species and reinstatement of the genera Gongromeriza and Psilobotrys. Studies in Mycology 103: 87-212. doi: 10.3114/sim.2022.103.04.

RevDate: 2023-06-17

Jiang Y, Wu R, Zhang W, et al (2023)

Construction of stable microbial consortia for effective biochemical synthesis.

Trends in biotechnology pii:S0167-7799(23)00155-5 [Epub ahead of print].

Microbial consortia can complete otherwise arduous tasks through the cooperation of multiple microbial species. This concept has been applied to produce commodity chemicals, natural products, and biofuels. However, metabolite incompatibility and growth competition can make the microbial composition unstable, and fluctuating microbial populations reduce the efficiency of chemical production. Thus, controlling the populations and regulating the complex interactions between different strains are challenges in constructing stable microbial consortia. This Review discusses advances in synthetic biology and metabolic engineering to control social interactions within microbial cocultures, including substrate separation, byproduct elimination, crossfeeding, and quorum-sensing circuit design. Additionally, this Review addresses interdisciplinary strategies to improve the stability of microbial consortia and provides design principles for microbial consortia to enhance chemical production.

RevDate: 2023-06-22
CmpDate: 2023-06-15

Gouvêa DY, I Brigandt (2023)

Against unifying homology concepts: Redirecting the debate.

Journal of morphology, 284(7):e21599.

The term "homology" is persistently polysemous, defying the expectation that extensive scientific research should yield semantic stability. A common response has been to seek a unification of various prominent definitions. This paper proposes an alternative strategy, based on the insight that scientific concepts function as tools for research: When analyzing various conceptualizations of homology, we should preserve those distinguishing features that support particular research goals. We illustrate the fruitfulness of our strategy by application to two cases. First, we revisit Lankester's celebrated evolutionary reappraisal of homology and argue that his analysis has been distorted by assimilation to modern agendas. His "homogeny" does not mean the same thing as modern evolutionary "homology," and his "homoplasy" is no mere antonym. Instead, Lankester uses both new terms to pose a question that remains strikingly relevant-how do mechanistic and historical causes of morphological resemblance interact? Second, we examine the puzzle of avian digit homology, which exemplifies disciplinary differences in homology conceptualization and assessment. Recent progress has been fueled by the development of new tools within the relevant disciplines (paleontology and developmental biology) and especially by increasing interdisciplinary cooperation. Conceptual unification has played very little role in this work, which instead seeks concrete evolutionary scenarios that integrate all the available evidence. Together these cases indicate the complex relationship between concepts and other tools in homology research.

RevDate: 2023-07-04
CmpDate: 2023-06-09

Kock A, Pheiffer W, Wepener V, et al (2023)

Using Confocal Microscopy and Pigment Analyses to Detect Adverse Insecticide Effects in non-target Freshwater Diatom species - a proof-of-concept Using Nitzschia palea.

Bulletin of environmental contamination and toxicology, 110(6):107.

The persistence of insecticides in aquatic environments is a cause of concern and to date hardly any studies have focused on the effects that DDT and deltamethrin have on non-target freshwater diatom communities. The application of diatoms in ecotoxicological studies is well acknowledged and therefore this study used laboratory bioassays to determine the effects that DDT and deltamethrin have on a monoculture of a diatom indicator species, Nitzschia palea. The insecticides affected the morphology of chloroplasts at all exposure concentrations. These effects were a maximum reduction in chlorophyll concentrations (4.8% and 2.3%), cell viability (51% and 42%), and increases in cell deformities (3.6% and 1.6%) following exposure to DDT and deltamethrin respectively. Based on the results we propose that methods, such as confocal microscopy, chlorophyll-α analysis and cell deformities are useful tools in assessing the effects of insecticides on diatoms.

RevDate: 2023-05-31

Cocquyt C, D Verschuren (2023)

Checklist of the diatoms (Bacillariophyta) from Lake Naivasha, Kenya, with some historical notes.

PhytoKeys, 224:101-174.

Lake Naivasha is one of only two large freshwater lakes in the Eastern Rift Valley of Kenya, East Africa. Together with its satellite lakes Crescent Island Crater, Oloidien and Sonachi, it comprises a great variety of pelagic and benthic habitats for aquatic biota, and its sediment record represents a unique archive of past climate change and long-term ecosystem dynamics in equatorial East Africa. This is particularly so because local paleoenvironmental reconstructions can be checked against historical data on the composition of aquatic fauna and flora collected in Lake Naivasha since the early 20[th] century. Some of the most prominent biological proxies for reconstructing past changes in lakes are diatoms (Bacillariophyta), a group of unicellular autotrophic eukaryotes of which the siliceous skeletons (valves) preserve well in lake sediments and are good indicators for, among others, climate-driven changes in salinity. However, diatom taxonomy and species concepts have changed a lot in recent decades, making it sometimes difficult for non-taxonomists to know which species are concerned in different published studies. This paper provides the currently accepted taxonomic names of the 310 specific and infraspecific diatom taxa reported from Lake Naivasha and its satellite lakes to date, together with their synonyms used in literature concerning these lakes as well as other, commonly used synonyms. Further, a short overview is given of the history of diatom research conducted on materials from Lake Naivasha and its satellite lakes. The present checklist may facilitate the identification and interpretation aspects of future diatom studies on the wider Lake Naivasha ecosystem and on other East African lakes that are less well studied.

RevDate: 2023-05-28

Amézquita A, Mazariegos-H LA, Cañaveral S, et al (2023)

Species richness under a vertebral stripe: integrative taxonomy uncovers three additional species of Pholidobolus lizards (Sauria, Squamata, Gymnophthalmidae) from the north-western Colombian Andes.

ZooKeys, 1141:119-148.

The systematic study of biodiversity underlies appropriate inference in most other fields of biological research, yet it remains hampered by disagreements on both theoretical and empirical issues such as the species concept and the operational diagnosis of a species. Both become particularly challenging in those lineages where morphological traits are evolutionarily constrained by their adaptive value. For instance, cryptic organisms often conserve or converge in their external appearance, which hinders the recognition of species boundaries. An integrative approach has been adopted to study microgeographic variation in the leaf-litter lizard Pholidobolusvertebralis and test three predictions derived from the evolutionary species concept. Molecular data provided unambiguous evidence of divergence among the three recovered new clades and a common evolutionary history for each of them. The broadly sympatric clades were indeed diagnosable from externally visible traits, such as head scales, adult size, and sexually dimorphic ventral colouration. Also, they barely overlapped on the phenotypic space that summarised 39 morphometric and meristic traits. These clades are described as three species and an available name is suggested for a recovered fourth clade. The geographic distribution of the new and proximate species suggests a role for elevation on evolutionary divergence; it also raises interesting questions on the speciation pattern of an otherwise underestimated cryptic lineage.

RevDate: 2023-05-25

Eilertsen HC, Strømholt J, Bergum JS, et al (2023)

Mass Cultivation of Microalgae: II. A Large Species Pulsing Blue Light Concept.

Biotech (Basel (Switzerland)), 12(2):.

If mass cultivation of photoautotrophic microalgae is to gain momentum and find its place in the new "green future", exceptional optimizations to reduce production costs must be implemented. Issues related to illumination should therefore constitute the main focus, since it is the availability of photons in time and space that drives synthesis of biomass. Further, artificial illumination (e.g., LEDs) is needed to transport enough photons into dense algae cultures contained in large photobioreactors. In the present research project, we employed short-term O2 production and 7-day batch cultivation experiments to evaluate the potential to reduce illumination light energy by applying blue flashing light to cultures of large and small diatoms. Our results show that large diatom cells allow more light penetration for growth compared to smaller cells. PAR (400-700 nm) scans yielded twice as much biovolume-specific absorbance for small biovolume (avg. 7070 μm[3]) than for large biovolume (avg. 18,703 μm[3]) cells. The dry weight (DW) to biovolume ratio was 17% lower for large than small cells, resulting in a DW specific absorbance that was 1.75 times higher for small cells compared to large cells. Blue 100 Hz square flashing light yielded the same biovolume production as blue linear light in both the O2 production and batch experiments at the same maximum light intensities. We therefore suggest that, in the future, more focus should be placed on researching optical issues in photobioreactors, and that cell size and flashing blue light should be central in this.

RevDate: 2023-05-23

Raclariu-Manolică AC, Mauvisseau Q, HJ de Boer (2023)

Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations.

Frontiers in pharmacology, 14:1179099.

Herbal medicines and preparations are widely used in healthcare systems globally, but concerns remain about their quality and safety. New herbal products are constantly being introduced to the market under varying regulatory frameworks, with no global consensus on their definition or characterization. These biologically active mixtures are sold through complex globalized value chains, which create concerns around contamination and profit-driven adulteration. Industry, academia, and regulatory bodies must collaborate to develop innovative strategies for the identification and authentication of botanicals and their preparations to ensure quality control. High-throughput sequencing (HTS) has significantly improved our understanding of the total species diversity within DNA mixtures. The standard concept of DNA barcoding has evolved over the last two decades to encompass genomic data more broadly. Recent research in DNA metabarcoding has focused on developing methods for quantifying herbal product ingredients, yielding meaningful results in a regulatory framework. Techniques, such as loop-mediated isothermal amplification (LAMP), DNA barcode-based Recombinase Polymerase Amplification (BAR-RPA), DNA barcoding coupled with High-Resolution Melting (Bar-HRM), and microfluidics-based methods, offer more affordable tests for the detection of target species. While target capture sequencing and genome skimming are considerably increasing the species identification resolution in challenging plant clades, ddPCR enables the quantification of DNA in samples and could be used to detect intended and unwanted ingredients in herbal medicines. Here, we explore the latest advances in emerging DNA-based technologies and the opportunities they provide as taxa detection tools for evaluating the safety and quality of dietary supplements and herbal medicines.

RevDate: 2023-06-19
CmpDate: 2023-06-19

Pacheco MA, AA Escalante (2023)

Origin and diversity of malaria parasites and other Haemosporida.

Trends in parasitology, 39(7):501-516.

Symbionts, including parasites, are ubiquitous in all world ecosystems. Understanding the diversity of symbiont species addresses diverse questions, from the origin of infectious diseases to inferring processes shaping regional biotas. Here, we review the current approaches to studying Haemosporida's species diversity and evolutionary history. Despite the solid knowledge of species linked to diseases, such as the agents of human malaria, studies on haemosporidian phylogeny, diversity, ecology, and evolution are still limited. The available data, however, indicate that Haemosporida is an extraordinarily diverse and cosmopolitan clade of symbionts. Furthermore, this clade seems to have originated with their vertebrate hosts, particularly birds, as part of complex community level processes that we are still characterizing.

RevDate: 2023-06-19
CmpDate: 2023-06-19

Li M, Li H, Zhang X, et al (2023)

Mechanistic Insight into Anion-Binding Catalytic Living Cationic Polymerization.

Angewandte Chemie (International ed. in English), 62(26):e202303237.

Exploiting non-covalent interactions to catalyze challenging ionic polymerizations is an ambitious goal but is in its infancy. We recently demonstrated non-covalent anion-binding catalysis as an effective methodology to enable living cationic polymerization (LCP) of vinyl ethers in an environmentally benign manner. Here, we further elucidate the structure-reactivity relationships of the elaborately designed seleno-cyclodiphosph(V)azanes catalysts and the roles of anion-binding interactions by a combined theoretical DFT study and experimental study. The investigation suggests that the distinct cis-cyclodiphosph(V)azane framework combined with "selenium effect" and electron-withdrawing 3,5-(CF3)2 -Phenyl substitution pattern in catalyst enables a critical contribution to accessing excellent stability, anion affinity and solubility under polymerization conditions. Thus, the catalyst could leverage anion-binding interactions to precisely control reversible and transient dormant-active species equilibrium, allowing it to dynamically bind, recognize and pre-organize propagating ionic species and monomer, thereby facilitating efficient chain propagation and minimizing irreversible chain transfer events under mild conditions. The more in-depth understanding of the mechanism for anion-binding catalytic LCP reported herein should help to guide future catalyst design and to extend this concept to broader polymerization systems where ionic species serve as crucial intermediates.

RevDate: 2023-05-17
CmpDate: 2023-05-17

Temraleeva AD, EA Portnaya (2023)

Morphological and Molecular Genetic Analyses of the Genus Vischeria (Eustigmatophyceae, Ochrophyta) in the Algal Collection of Soil Science Institute.

Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections, 508(1):20-31.

Four soil eustigmatophyte algal strains isolated from gray forest soils in Moscow and Tula regions of Russia and deposited in the Algal Collection of Soil Science Institute (ACSSI) were examined by morphological and molecular genetic methods. The strains were assigned to the genus Vischeria on evidence of 18S rRNA gene and ITS2 phylogeny. The strains were morphologically similar to V. magna. However, only one of them, ACSSI 026, clustered with the authentic strain SAG 2554, while the other strains formed a separate independent group. The taxonomy of the genus is problematic because its phylogenetic tree based on the 18S rRNA gene and ITS2 is unresolved, the variable regions V4-V5 and V8-V9 of the 18S rRNA gene are noninformative, and the compensatory base change (CBC) concept fails to work (the concept states that closely related species are distinct if even a single CBC occurs in conserved secondary structure regions of ITS2). The concept of species is presumably possible to develop for Eustigmatophyceae and the genus Vischeria in particular when a greater number of eustigmatophyte algal strains are isolated from various biotopes; plastid genes are used or the total plastid genome is deeply sequenced; and ultrastructural, physiological, and biochemical characteristics are studied in more detail.

RevDate: 2023-05-14

Iwamoto Y, Degawa Y, T Nakayama (2023)

Re-examination of a rare protosteloid amoeba Schizoplasmodiopsis micropunctata, and the revision of Tychosporium (Cavosteliida, Variosea, Amoebozoa).

Mycoscience, 64(2):63-68.

The genus Schizoplasmodiopsis is one of the most morphologically diverse groups among the class Variosea. Recent phylogenetic studies suggest that Schizoplasmodiopsis is polyphyletic, but there are few taxonomic studies of this genus. We established S. micropunctata strain YIP-40, observed in detail its of morphology and lifecycle, and conducted a phylogenetic analysis. The phylogenetic analysis revealed that S. micropunctata was sister to Tychosporium acutostipes. Scanning electron microscopy showed S. micropunctata had a non-deciduous hilum structure that is unique to Tychosporium. The morphology of amoebae, mitotic behavior, and prespore cells of S. micropunctata also supported the close relationship to Tychosporium. We propose to transfer S. micropunctata to Tychosporium and emend the generic concept of Tychosporium to include this species.

RevDate: 2023-05-08
CmpDate: 2023-05-08

Jeanroy F, Demontrond F, Vidal FX, et al (2023)

Deciphering dynamic combinatorial libraries of glycoclusters with miniaturized weak affinity chromatography coupled with mass spectrometry (nano-FAC-MS).

Analytica chimica acta, 1261:341227.

We report an original methodology based on affinity chromatography coupled with mass spectrometry to decipher the complexity of dynamic combinatorial libraries (DCLs) of glycoclusters. Such libraries are intended to boost the design of potential therapeutic anti-infectious agents targeting Pseudomonas aeruginosa, which is responsible for numerous diseases, mostly found in hospitals as major a cause of nosocomial infections. Dynamic combinatorial chemistry provides a rapid access to an equilibrating mixture of glycocluster candidates through the formation of reversible covalent bonds under thermodynamic control. Identifying each molecule in the complex mixture overcomes challenges due to the dynamic process. Selection of glycoclusters candidates was first realized on a model lectin (Concanavalin A, ConA). Home-made affinity nanocolumns, containing covalently immobilized ConA and have volumes in the microliter range, were used to separate DCLs of glycoclusters with respect to their specific lectin binding properties under buffered aqueous conditions. Miniaturization facilitates the inline coupling with MS detection in such purely aqueous and buffered conditions and reduces target protein consumption. Monolithic lectin-affinity columns prepared by immobilization of ConA were first characterized using a known ligand. The amount of active binding immobilized lectin is 61 ± 5 pmol on 8.5-cm length column. We demonstrated the ability of our approach to evaluate individual dissociation constants of species directly in the complex mixture. The concept was then successfully applied to the screening of DCLs of more complex glycoclusters to identify (by mass spectrometry) and rank the ligands (by relative breakthrough curve delay) according to their affinity for the immobilized lectin in a single experiment.

RevDate: 2023-05-07

Nascimento Brito V, Lana Alves J, Sírio Araújo K, et al (2023)

Endophytic Trichoderma species from rubber trees native to the Brazilian Amazon, including four new species.

Frontiers in microbiology, 14:1095199.

Fungi belonging to the genus Trichoderma have been widely recognized as efficient controllers of plant diseases. Although the majority of isolates currently deployed, thus far, have been isolated from soil, endophytic Trichoderma spp. is considered to be a promising option for application in biocontrol. In this study, 30 endophytic Trichoderma isolates-obtained from the leaves, stems, and roots of wild Hevea spp. in the Brazilian Amazon-were analyzed using specific DNA barcodes: sequences of internal transcribed spacers 1 and 2 of rDNA (ITS region), genes encoding translation elongation factor 1-α (TEF1-α), and the second largest subunit of RNA polymerase II (RPB2). The genealogical concordance phylogenetic species recognition (GCPSR) concept was used for species delimitation. A phylogenetic analysis showed the occurrence of Trichoderma species, such as T. erinaceum, T. ovalisporum, T. koningiopsis, T. sparsum, T. lentiforme, T. virens, and T. spirale. Molecular and morphological features resulted in the discovery of four new species, such as T. acreanum sp. nov., T. ararianum sp. nov., T. heveae sp. nov., and T. brasiliensis sp. nov. The BI and ML analyses shared a similar topology, providing high support to the final trees. The phylograms show three distinct subclades, namely, T. acreanum and T. ararianum being paraphyletic with T. koningiopsis; T. heveae with T. subviride; and T. brasiliensis with T. brevicompactum. This study adds to our knowledge of the diversity of endophytic Trichoderma species in Neotropical forests and reveals new potential biocontrol agents for the management of plant diseases.

RevDate: 2023-04-25

Ballego-Campos I, Bonifácio SKV, LCS Assis (2023)

A unified view of homology.

Cladistics : the international journal of the Willi Hennig Society [Epub ahead of print].

As it spread through time and into distinct areas of science-from comparative anatomy to evolutionary biology, cladistics, developmental and molecular biology-the homology concept has changed considerably, presenting various meanings. Despite many attempts at developing a comprehensive understanding of the concept, this context-sensitive notion of homology has been a subject of an ongoing debate. Inspired by that and following Kevin de Queiroz and Richard Mayden's view on species concept and delimitation, we presented in this article an attempt to systematize and advance the understanding of the homology problem. Our main goals were: (i) to present a comprehensive checklist of 'concepts of homology'; (ii) to identify which are really concepts with ontological definitions (theoretically rooted in structural correspondence and common ancestry), and which are, in fact, not concepts, but epistemological (empirical and methodological) criteria of homology delimitation; (iii) to provide a synonymy of the concepts and criteria of homology delimitation; (iv) to present a hierarchy of homology concepts within Hennig's hologenetic system; and (v) to endorse the adoption of a unified view of homology by treating homology as a correspondence of spatio-temporal properties (genetic, epigenetic, developmental and positional) at the level of the individual, species or monophyletic group. We found 59 'concepts of homology' in the literature, from which 34 were categorically treated as concepts, 17 as criteria of homology delimitation, Four were excluded from our treatment, and Müller's five concepts were rather treated as approaches to homology. Homology concepts and criteria were synonymized based on structural correspondence, replicability, common ancestry, genetic and epigenetic developmental causes, position and optimization. Regarding the synonymy, we conclusively recognized 21 different concepts of homology, and five empirical and four methodological criteria. Hierarchical ontological aspects of homology were systematized under Hennig's hologenetic system, based on the existence of ontogenetic, tokogenetic and phylogenetic levels of homology. The delimitation of tokogenetic and phylogenetic homologies depends on optimization criteria. The unified view of homology is discussed in the context of the ancestral angiosperm flower.

RevDate: 2023-04-25

Shibata S, Y Hirooka (2022)

Taxonomy and phylogeny of Exobasidium pentasporium causing witches' broom of Rhododendron species.

Mycoscience, 63(6):247-253.

Exobasidium pentasporium was first found on Rhododendron kaempferi in Nikko, Tochigi Prefecture, Japan and described only with a brief mentions and illustration of a specimen in 1896. This fungus causes a witches' broom disease of Rhododendron species. To stabilize the concept of this species, the specimen in the protologue was located, carefully examined, and illustrated. In addition, the name was epitypified based on a newly collected topotype specimen. A phylogenetic tree using ITS and LSU sequences showed that our isolates of E. pentasporium grouped with other Exobasidium species on Rhododendron forming a monophyletic clade with strong statistical support and were unrelated to E. nobeyamense, another causal agent of witches' broom disease on Rhododendron species.

RevDate: 2023-06-27
CmpDate: 2023-06-20

Liberles DA (2023)

A Genomic Conceptualization of Species.

Journal of molecular evolution, 91(4):379-381.

Species concepts have been defined through a number of lenses, but are almost entirely empirical in nature. Fundamentally linked to various existing species concepts, an interpretation of genomic data through a species classification filter based upon a theoretical genotype-phenotype map with a monophyly requirement is discussed.

RevDate: 2023-04-24
CmpDate: 2023-04-18

Bangal P, H Sridhar (2023)

Revisiting the 'nuclear species' concept: do we really know what we think we know?.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 378(1878):20220108.

The idea of 'nuclear species' has received a lot of attention in mixed-species flock research. Our impression of this literature is that referenced statements tend to cite the same papers in support of a small set of ideas, and often there is a mismatch between what papers contain and what they're cited for. Motivated by these impressions, we built and quantitatively examined a database of referenced statements about nuclearity in flocks. This confirmed our impression quantitatively, but more strikingly, a single paper stood out in its influence on ideas around nuclearity in flocks. Moynihan's 1962 monograph on mixed-species flocks in Panama, 'The organization and probable evolution of some mixed-species flocks of neotropical birds' published in Smithsonian Miscellaneous Collections, was cited twice as much as the next most-cited paper and was the most-cited paper for 10 out of 15 most-discussed ideas related to nuclearity. Further, a number of other highly cited papers are strongly influenced by Moynihan's ideas, i.e. its influence is much greater than what a count of citations conveys. We also found that Moynihan was mis-cited frequently. We juxtapose what we found from the citation analysis with what the paper actually contains to better understand the nature of support that Moynihan provides, and discuss the implications of our findings for what we know about and how we research nuclearity in flocks. This article is part of the theme issue 'Mixed-species groups and aggregations: shaping ecological and behavioural patterns and processes'.

RevDate: 2023-05-27
CmpDate: 2023-04-17

De León ME, Wilson HS, Jospin G, et al (2023)

Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives.

Microbial genomics, 9(4):.

Violacein is a water-insoluble violet pigment produced by various Gram-negative bacteria. The compound and the bacteria that produce it have been gaining attention due to the antimicrobial and proposed antitumour properties of violacein and the possibility that strains producing it may have broad industrial uses. Bacteria that produce violacein have been isolated from diverse environments including fresh and ocean waters, glaciers, tropical soils, trees, fish and the skin of amphibians. We report here the isolation and characterization of six violacein-producing bacterial strains and three non-violacein-producing close relatives, each isolated from either an aquatic environment or moist food materials in northern California, USA. For each isolate, we characterized traditional phenotypes, generated and analysed draft genome sequences, and carried out multiple types of taxonomic, phylogenetic and phylogenomic analyses. Based on these analyses we assign putative identifications to the nine isolates, which include representatives of the genera Chromobacterium, Aquitalea, Iodobacter, Duganella, Massilia and Janthinobacterium. In addition, we discuss the utility of various metrics for taxonomic assignment in these groups including average nucleotide identity, whole genome phylogenetic analysis and extent of recent homologous recombination using the software program PopCOGenT.

RevDate: 2023-08-06

Winsor MP (2023)

Darwin's dark matter: utter extinction.

Annals of science [Epub ahead of print].

Species that died without leaving descendants Darwin called 'utterly extinct'. They far outnumber the ancestors of all living things, so they resemble the dark matter of modern cosmology, which far outweighs visible matter. He realized in 1837 that their absence is what creates the groups in a natural classification. In his Notebook B he combined the idea that species multiply with the idea that ancestors' relatives must mostly be extinct. The fossil Megatherium was utterly extinct. The iconic branching 'I think' diagram shows extinction causing the origin of genera by eliminating intermediate species. Darwin's concept of taxonomic ranks, starting with the genus, was informed by his interaction with taxonomists. Based on his familiarity with demography, Darwin reasoned that the survival of transitional forms was unlikely, which helped him decide to focus at the species level. When drafting his theory in the 1840s, he left out these speculative ideas, but they emerged again in the 1850s when he realized his theory needed a cause for branches to diverge. His ecological answer worked at the species level, but his Principle of Divergence was unconvincing at higher taxonomic levels. In the Origin, Darwin repeatedly insisted on the importance of utter extinction.

RevDate: 2023-04-14
CmpDate: 2023-04-14

Yan M, Bao J, Luo M, et al (2022)

Phylogenetic analyses and species delimitation of Aconurella Ribaut (Hemiptera: Cicadellidae: Deltocephalinae: Chiasmini) in China based on molecular data.

Zootaxa, 5205(3):281-296.

The grassland leafhopper genus Aconurella is widespread in the Old World. Species of this genus are difficult to identify by traditional morphological characters but the morphology-based species classification in this genus has not previously been tested using molecular data. This study analysed DNA sequence data from two mitochondrial genes (COI, 16S) and one nuclear gene (ITS2) to infer the phylogenetic relationships and status of five previously recognized Aconurella species and compare the performance of different molecular species-delimitation methods using single and multiple loci. The analysis divided the included haplotypes into five well-supported subclades, most corresponding to existing morphology-based species concepts. However, different molecular species delimitation methods (jMOTU, ABGD, bPTP, GMYC and BPP) yielded somewhat different results, suggesting the presence of between 4 and 8 species, sometimes lumping the haplotypes of Aconurella diplachnis and Aconurella sibirica into a single species or recognizing multiple putative species within Aconurella prolixa. Considering the different results yielded by various methods employing single loci, the BPP method, which combines data from multiple loci, may be more reliable for delimiting species of Aconurella. Our results suggest that the morphological characters previously used to identify these species are reliable and adequately reflect boundaries between genetically distinct taxa.

RevDate: 2023-04-14
CmpDate: 2023-04-14

Uluar O, Yahyaoğlu Ö, B Çiplak (2022)

Anatolian endemic genus Bolua (Orthoptera: Tettigoniidae: Tettigoniinae): genetic and phenotypic data indicate inconsistent diversity and evolutionary patterns.

Zootaxa, 5195(3):224-240.

Anatolia harbours diverse and unique biodiversity. Nearly half of the genera and more than 80% of the species belonging to the tettigoniid subfamily Tettigoniinae are endemic to Anatolia. Although the Anatolian Tettigoniinae have been well studied, proper documentation of Tettigoniinae biodiversity requires studies using contemporary approaches and techniques. We attempted to study the taxonomy, phylogeny, and phylogeography of the Bolua, a monotypic genus endemic to northwest Anatolia. Species delimitation tests applied to three mitochondrial and two nuclear gene segments indicated three putative species in the genus. Analyses suggested inversely related genetic and phenotypic divergence. By integrating these results, we reached the following conclusions. (i) The plausible taxonomic composition recognizes three species in the genus; the type species Bolua turkiyae and two new species B. balikesirensis sp. n. and B. bursaensis sp. n., (ii) the radiation steps in Bolua correspond to the starting of the Pliocene, Mid Pleistocene Transition (MPT) and end of cold periods of Günz and Riss glacial. By considering intra generic divergence steps and habitat preference plus the distribution pattern of the species, ecological speciation seems to be the mode of generic radiation, (iii) possibly due to habitat conservatism, the isolated relict populations on highlands evolved under similar selection pressures, and this led to a conserved phenotype, consequently morphologically poorly diverged species, though genetic divergence is deep and (iv) although morphological diagnoses is poor, genetic divergence between species is deep, and each species fulfils the criteria of several species concepts.

RevDate: 2023-04-14
CmpDate: 2023-04-14

Abo-Shnaf R, Castilho RC, Marticorena JLM, et al (2023)

A new genus and three new species of mites, with a revised concept of the family Ameroseiidae (Acari: Mesostigmata: Ascoidea).

Zootaxa, 5231(3):249-272.

This paper describes a new genus and three new species of mites found in litter and soil samples from Brazil and Egypt. Endopodoseius Abo-Shnaf & Moraes n. gen., Endopodoseius erikae Abo-Shnaf & Marticorena n. sp., Endopodoseius zaheri Abo-Shnaf & Moraes n. sp. and Endopodoseius edmilsoni Abo-Shnaf & Castilho n. sp. are considered to belong to the Superfamily Ascoidea and the Family Ameroseiidae. The concept of the family is expanded to include species with one or more of the following character states-the podonotal and opisthonotal shields partially or totally separate; poroid iv1 absent; dorsal idiosomal setae J1, J5 and R1 present; genital seta st5 inserted outside the epigynal shield; opisthogaster with 7-10 pairs of setae; and femur II with 11 setae.

RevDate: 2023-04-14
CmpDate: 2023-04-14

Tishechkin DY (2023)

An enigma of Handianus Ribaut, 1942 (Hemiptera: Cicadellidae: Deltocephalinae: Athysanini): identical host preferences and male calling signals in two morphologically distinctive sympatric species.

Zootaxa, 5239(4):585-592.

Handianus eurotiae and H. fartilis distinctly differ in the forewing venation and the male genitalia shape, but have strongly overlapping ranges, do not differ in ecological preferences, feed on the same host plant, Krascheninnikovia ceratoides, and produce almost identical male calling signals. They were never found in the same biotope, although the mechanism of such vicariation is not clear. According to Mayr's biological species concept, such taxa are good species, but Paterson's species recognition concept is inapplicable in this case. Similar examples in Orthoptera and Auchenorrhyncha are considered.

RevDate: 2023-04-18
CmpDate: 2023-04-18

Bartlett JS, CL Lambkin (2022)

Australian Opilonini (Coleoptera: Cleridae: Clerinae) part I: A revised taxonomy for Australian Opilo Latreille including descriptions of new genera and species.

Zootaxa, 5220(1):1-81.

The species- and genus-level taxonomy of Australian species assigned to Opilo Latreille is assessed and revised in the context of a morphological species concept. Australian species are deemed not congeneric with Opilo mollis (Linnaeus), the type species of Opilo Latreille. Species are grouped into genera by degree of difference observed in states of the tegmen, median lobe, antennal scape, basitarsi, hindwing, elytral striae and pronotal disc. Examination of 1,259 specimens resulted in recognition of 6 genera and 44 species, 36 of which are new to science. The following new genera are proposed: Ancyropilus gen. nov.; Culcipternulus gen. nov.; Infectostriatus gen. nov.; Monilonotum gen. nov.; Notopilo gen. nov.; Platynotum gen. nov.. Three infraspecific taxa described as 'varieties', viz, Opilo congruus var. abdominalis Schenkling, 1901, Notoxus congruus var. femoralis Westwood, 1849 and Opilo pascoei var. doddi Schenkling, 1906, are elevated to species status, with Opilo abdominalis (occupied by Opilo abdominalis Fairmaire, 1891) requiring a replacement name. The 44 species recognised in this revision are: Ancyropilus brigalowae sp. nov.; Ancyropilus emmotti sp. nov.; Ancyropilus exossuarius sp. nov.; Ancyropilus hornensis sp. nov.; Ancyropilus labris sp. nov.; Ancyropilus monteithi sp. nov.; Ancyropilus noonbahensis sp. nov.; Ancyropilus packsaddlensis sp. nov.; Ancyropilus simplex sp. nov.; Ancyropilus tricolor sp. nov.; Culcipternulus mareebensis sp. nov.; Infectostriatus absentis sp. nov.; Infectostriatus differens sp. nov.; Monilonotum bunyense sp. nov.; Monilonotum doddi (Schenkling, 1906) stat. rev., comb. nov. (transferred from Opilo); Monilonotum eburneocincta (Gorham, 1878) comb. nov. (transferred from Opilo); Monilonotum pascoei (Gorham, 1876) comb. nov. (transferred from Opilo); Monilonotum rufiventre (Gerstmeier, 1990) comb. nov. (transferred from Olesterus); Monilonotum sundholmi sp. nov.; Notopilo beswickensis sp. nov.; Notopilo brevistriatus sp. nov.; Notopilo calicis sp. nov.; Notopilo cambageicola sp. nov.; Notopilo confusus sp. nov.; Notopilo congruus (Newman) comb. nov. (transferred from Opilo); Notopilo elstoni sp. nov.; Notopilo eremosus sp. nov.; Notopilo gerstmeieri sp. nov.; Notopilo interfabulatus sp. nov.; Notopilo katherinensis sp. nov.; Notopilo lawnhillensis sp. nov.; Notopilo magnus sp. nov.; Notopilo obesus sp. nov.; Notopilo reduncus stat, rev., nom. nov. (replacement name for Opilo abdominalis Schenkling, 1901); Notopilo tanybasilaris sp. nov.; Notopilo tompricensis sp. nov.; Notopilo variipes (Chevrolat) comb. nov. (transferred from Opilo); Notopilo xanthoimprocerus sp. nov.; Notopilo xanthoprolatus sp. nov.; Platynotum bulli sp. nov.; Platynotum culgoense sp. nov.; Platynotum femorale (Westwood) stat. rev., comb. nov. (transferred from Opilo); Platynotum foveosetosa sp. nov.; Platynotum gracile sp. nov.. The available names Opilus congruus Newman, 1842 and Opilus femoralis Westwood, 1849, are respectively corrected to Opilo congruus Newman, 1842 and Opilo femoralis Westwood, 1849 in accordance with Article of the Code (ICZN 1999). Lectotypes are designated for Opilo abdominalis Schenkling, 1901, Opilo congruus Newman, 1842, Opilo femoralis Westwood, 1849, Opilo variipes Chevrolat, Opilo doddi Schenkling, 1906 and Opilo pascoei Gorham, 1876.

RevDate: 2023-04-14
CmpDate: 2023-04-14

Huo QB, Zhao MY, DU YZ, et al (2023)

The intraspecific morphological variability of Styloperla Wu, 1935 (Plecoptera: Styloperlidae).

Zootaxa, 5249(1):125-137.

Intraspecific morphological variability of four Styloperla Wu, 1935 species are described and discussed in this paper. The males of each species have variable specializations present at their basal cercal process, including the variable number of branches or differing degrees of curvature at the apical spines. A generalization on the species definition of Plecoptera, especially a new concept of conspecificity is also provided herein.

RevDate: 2023-04-12
CmpDate: 2023-04-10

Hanganu-Opatz IL, Klausberger T, Sigurdsson T, et al (2023)

Resolving the prefrontal mechanisms of adaptive cognitive behaviors: A cross-species perspective.

Neuron, 111(7):1020-1036.

The prefrontal cortex (PFC) enables a staggering variety of complex behaviors, such as planning actions, solving problems, and adapting to new situations according to external information and internal states. These higher-order abilities, collectively defined as adaptive cognitive behavior, require cellular ensembles that coordinate the tradeoff between the stability and flexibility of neural representations. While the mechanisms underlying the function of cellular ensembles are still unclear, recent experimental and theoretical studies suggest that temporal coordination dynamically binds prefrontal neurons into functional ensembles. A so far largely separate stream of research has investigated the prefrontal efferent and afferent connectivity. These two research streams have recently converged on the hypothesis that prefrontal connectivity patterns influence ensemble formation and the function of neurons within ensembles. Here, we propose a unitary concept that, leveraging a cross-species definition of prefrontal regions, explains how prefrontal ensembles adaptively regulate and efficiently coordinate multiple processes in distinct cognitive behaviors.

RevDate: 2023-04-11
CmpDate: 2023-04-11

van der Wal FJ, Achterberg RP, van der Goot JA, et al (2023)

Proof of concept for multiplex detection of antibodies against Chlamydia species in chicken serum using a bead-based suspension array with peptides as antigens.

Veterinary research, 54(1):31.

The available differentiating tests for Chlamydia are based on detection of genetic material and only give information about the actual infection status, but reveal nothing of past infections. As the use of serological methods increases the window of detection, the goal of this study was to investigate if it is possible to develop a differentiating serological test for antibodies against Chlamydia species in chicken sera. Focus was on C. psittaci, C. gallinacea, and two closely related species, i.e. C. abortus and C. avium. To enable differentiating serology, a bead-based Luminex suspension array was constructed, using peptides as antigens, derived from known immunoreactive Chlamydia proteins. For the majority of these peptides, species-specific seroreactivity in mammalian sera has been reported in literature. The suspension array correctly identified antibodies against various Chlamydia species in sera from experimentally infected mice, and was also able to differentiate between antibodies against C. psittaci and C. gallinacea in sera from experimentally infected chickens. In field sera, signals were difficult to interpret as insufficient sera from experimentally infected chickens were available for evaluating the seroreactivity of all peptides. Nevertheless, results of the suspension array with field sera are supported by published data on the occurrence of C. gallinacea in Dutch layers, thereby demonstrating the proof of concept of multiplex serology for Chlamydial species in poultry.

RevDate: 2023-04-24
CmpDate: 2023-04-06

Caicoya AL, Schaffer A, Holland R, et al (2023)

Innovation across 13 ungulate species: problem solvers are less integrated in the social group and less neophobic.

Proceedings. Biological sciences, 290(1996):20222384.

Innovation is the ability to solve new problems or find novel solutions to familiar problems, and it is known to provide animals with crucial fitness benefits. Although this ability has been extensively studied in some taxa, the factors that predict innovation within and across species are still largely unclear. In this study, we used a novel foraging task to test 111 individuals belonging to 13 ungulate species-a still understudied taxon. To solve the task, individuals had to open transparent and opaque cups with food rewards, by removing their cover. We assessed whether individual factors (neophobia, social integration, sex, age, rank) and socio-ecological factors (dietary breadth, fission-fusion dynamics, domestication, group size) predicted participation and performance in the task. Using a phylogenetic approach, we showed that success was higher for less neophobic and socially less integrated individuals. Moreover, less neophobic individuals, individuals of domesticated species and having higher fission-fusion dynamics were more likely to participate in the task. These results are in line with recent literature suggesting a central role of sociality and personality traits to successfully deal with novel challenges, and confirm ungulates as a promising taxon to test evolutionary theories with a comparative approach.

RevDate: 2023-06-05
CmpDate: 2023-03-31

Qiu L, Dong J, Li X, et al (2023)

Defining honeybee subspecies in an evolutionary context warrants strategized conservation.

Zoological research, 44(3):483-493.

Despite the urgent need for conservation consideration, strategic action plans for the preservation of the Asian honeybee, Apis cerana Fabricius, 1793, remain lacking. Both the convergent and divergent adaptations of this widespread insect have led to confusing phenotypical traits and inconsistent infraspecific taxonomy. Unclear subspecies boundaries pose a significant challenge to honeybee conservation efforts, as it is difficult to effectively prioritize conservation targets without a clear understanding of subspecies identities. Here, we investigated genome variations in 362 worker bees representing almost all populations of mainland A. cerana to understand how evolution has shaped its population structure. Whole-genome single nucleotide polymorphisms (SNPs) based on nuclear sequences revealed eight putative subspecies, with all seven peripheral subspecies exhibiting mutually exclusive monophyly and distinct genetic divergence from the widespread central subspecies. Our results demonstrated that most classic morphological traits, including body size, were related to the climatic variables of the local habitats and did not reflect the true evolutionary history of the organism. Thus, such morphological traits were not suitable for subspecific delineation. Conversely, wing vein characters showed relative independence to the environment and supported the subspecies boundaries inferred from nuclear genomes. Mitochondrial phylogeny further indicated that the present subspecies structure was a result of multiple waves of population divergence from a common ancestor. Based on our findings, we propose that criteria for subspecies delineation should be based on evolutionary independence, trait distinction, and geographic isolation. We formally defined and described eight subspecies of mainland A. cerana. Elucidation of the evolutionary history and subspecies boundaries enables a customized conservation strategy for both widespread and endemic honeybee conservation units, guiding colony introduction and breeding.

RevDate: 2023-03-31

Du Z, Li Y, Wang XC, et al (2023)

Re-Examination of the Holotype of Ganoderma sichuanense (Ganodermataceae, Polyporales) and a Clarification of the Identity of Chinese Cultivated Lingzhi.

Journal of fungi (Basel, Switzerland), 9(3):.

The widely cultivated Chinese Lingzhi is a famous fungus with significant medicinal and economic value, which has commonly been misidentified as Ganoderma lucidum for a long period of time. The scientific binomial of the fungus is always a hotly debated question that revolves around G. lingzhi and G. sichuanense. To interpret the species concept of the taxon, six specific primers for G. sichuanense and one universal primer were designed. Through directed and nested PCRs, we obtained nine ITS sequences from the holotype (HMAS 42798) of G. sichuanense. By genome sequencing, the ITS sequence of the first cultivated Lingzhi (HMAS 25103) was assembled. Based on a phylogenetic study of the genus Ganoderma, the correct name for widely cultivated Ganoderma species in China was confirmed as G. sichuanense, and G. lingzhi should be a later synonym.

RevDate: 2023-03-31

Żabicka J, Kirschey T, Migdałek G, et al (2023)

Genetic Variation versus Morphological Variability in European Peatland Violets (Viola epipsila-V. palustris Group).

Biology, 12(3):.

In Europe, the V. epipsila-V. palustris group comprises V. epipsila Ledeb., V. palustris L., V. pubifolia (Kuta) G. H. Loos (=V. palustris subsp. pubifolia Kuta), interspecific hybrids, and putative introgressants. The genetic affinity of V. pubifolia to V. palustris, and their shared origin via hybridization followed by polyploidization, were confirmed using inter simple sequence repeat (ISSR) markers, restriction site-associated DNA sequencing (RAD-Seq), and a low-copy nuclear gene, GPI, which encodes glucose-6-phosphate isomerase. The other taxa of subsect. Stolonosae were not identified as putative parents of V. pubifolia by GPI. Our analyses indicated that V. pubifolia can be included in the morphological and genetic variation of V. palustris. The ISSR, RAD-Seq, and genome size value separated well V. palustris from V. epipsila and hybrids. The results also reopen the discussion on intraspecific variation in the context of taxa ranks and species concepts. The reduced tolerance of V. epipsila in Europe to changing environmental conditions might result from low genetic differentiation and heterozygosity, as well as the increased number of interspecific hybrids (V. epipsila × V. palustris), and eventually can possibly lead to its extinction. The disappearance of populations/individuals of this species may indicate anthropogenic changes occurring in peatlands.

RevDate: 2023-03-21

Milner DS, Galindo LJ, Irwin NAT, et al (2023)

Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes.

Annual review of microbiology [Epub ahead of print].

Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the functional factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire. Expected final online publication date for the Annual Review of Microbiology, Volume 77 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

RevDate: 2023-03-15

Konashev MB (2023)

The Russian Backdrop to Dobzhansky's Genetics and the Origin of Species.

Journal of the history of biology [Epub ahead of print].

Theodosius Dobzhansky was one of the principal 'founding fathers' of the modern 'synthetic theory of evolution' and the 'biological species' concept, first set forth in his classic book, Genetics and the Origin of Species (1937). Much of the discussion of Dobzhansky's work by historians has focused on English-accessible sources, and has emphasized the roles of the Morgan School, and figures such as Sewall Wright, and Leslie C. Dunn. This article uses Dobzhansky's Russian articles that are unknown to English-speaking readers, and his late 1920s to early 1930s correspondence with colleagues and friends in the Soviet Union, to clarify some of the Russian influences on Dobzhansky's evolving evolutionary views, particularly the development of his views on species and speciation. For Dobzhansky, as for Darwin, the problem of species and speciation was crucial for his theoretical explanation of evolution.

RevDate: 2023-03-28

Bai S, Han X, D Feng (2023)

Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil.

Frontiers in plant science, 14:1139744.

High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.

RevDate: 2023-03-07

Wang MZ, Fan XK, Zhang YH, et al (2023)

Phylogenomics and integrative taxonomy reveal two new species of Amana (Liliaceae).

Plant diversity, 45(1):54-68.

Until now the genus Amana (Liliaceae), known as 'East Asian tulips', has contained just seven species. In this study, a phylogenomic and integrative taxonomic approach was used to reveal two new species, Amana nanyueensis from Central China and A. tianmuensis from East China. A. nanyueensis resembles Amana edulis in possessing a densely villous-woolly bulb tunic and two opposite bracts, but differs in its leaves and anthers. Amana tianmuensis resembles Amana erythronioides in possessing three verticillate bracts and yellow anthers, but differs in aspects of its leaves and bulbs. These four species are clearly separated from each other in principal components analysis based on morphology. Phylogenomic analyses based on plastid CDS further support the species delimitation of A. nanyueensis and A. tianmuensis and suggests they are closely related to A. edulis. Cytological analysis shows that A. nanyueensis and A. tianmuensis are both diploid (2n = 2x = 24), different from A. edulis, which is either diploid (northern populations) or tetraploid (southern populations, 2n = 4x = 48). The pollen morphology of A. nanyueensis is similar to other Amana species (single-groove germination aperture), but A. tianmuensis is quite different because of the presence of a sulcus membrane, which creates the illusion of double grooves. Ecological niche modelling also revealed a niche differentiation between A. edulis, A. nanyueensis and A. tianmuensis.

RevDate: 2023-03-07

Anderson BD, JE Bisanz (2023)

Challenges and opportunities of strain diversity in gut microbiome research.

Frontiers in microbiology, 14:1117122.

Just because two things are related does not mean they are the same. In analyzing microbiome data, we are often limited to species-level analyses, and even with the ability to resolve strains, we lack comprehensive databases and understanding of the importance of strain-level variation outside of a limited number of model organisms. The bacterial genome is highly plastic with gene gain and loss occurring at rates comparable or higher than de novo mutations. As such, the conserved portion of the genome is often a fraction of the pangenome which gives rise to significant phenotypic variation, particularly in traits which are important in host microbe interactions. In this review, we discuss the mechanisms that give rise to strain variation and methods that can be used to study it. We identify that while strain diversity can act as a major barrier in interpreting and generalizing microbiome data, it can also be a powerful tool for mechanistic research. We then highlight recent examples demonstrating the importance of strain variation in colonization, virulence, and xenobiotic metabolism. Moving past taxonomy and the species concept will be crucial for future mechanistic research to understand microbiome structure and function.

RevDate: 2023-02-28

Zuo J, Zhu E, Yin W, et al (2023)

Long-term spatiotemporal and highly specific imaging of the plasma membrane of diverse plant cells using a near-infrared AIE probe.

Chemical science, 14(8):2139-2148.

Fluorescent probes are valuable tools to visualize plasma membranes intuitively and clearly and their related physiological processes in a spatiotemporal manner. However, most existing probes have only realized the specific staining of the plasma membranes of animal/human cells within a very short time period, while almost no fluorescent probes have been developed for the long-term imaging of the plasma membranes of plant cells. Herein, we designed an AIE-active probe with NIR emission to achieve four-dimensional spatiotemporal imaging of the plasma membranes of plant cells based on a collaboration approach involving multiple strategies, demonstrated long-term real-time monitoring of morphological changes of plasma membranes for the first time, and further proved its wide applicability to plant cells of different types and diverse plant species. In the design concept, three effective strategies including the similarity and intermiscibility principle, antipermeability strategy and strong electrostatic interactions were combined to allow the probe to specifically target and anchor the plasma membrane for an ultralong amount of time on the premise of guaranteeing its sufficiently high aqueous solubility. The designed APMem-1 can quickly penetrate cell walls to specifically stain the plasma membranes of all plant cells in a very short time with advanced features (ultrafast staining, wash-free, and desirable biocompatibility) and the probe shows excellent plasma membrane specificity without staining other areas of the cell in comparison to commercial FM dyes. The longest imaging time of APMem-1 can be up to 10 h with comparable performance in both imaging contrast and imaging integrity. The validation experiments on different types of plant cells and diverse plants convincingly proved the universality of APMem-1. The development of plasma membrane probes with four-dimensional spatial and ultralong-term imaging ability provides a valuable tool to monitor the dynamic processes of plasma membrane-related events in an intuitive and real-time manner.

RevDate: 2023-05-19
CmpDate: 2023-05-15

Kious BM (2023)

Suffering and the dilemmas of pediatric care: a response to Tyler Tate.

Theoretical medicine and bioethics, 44(3):249-258.

In a recent article, Tyler Tate argues that the suffering of children - especially children with severe cognitive impairments - should be regarded as the antithesis of flourishing, where flourishing is relative to one's individual characteristics and essentially involves receiving care from others. Although initially persuasive, Tate's theory is ambiguous in several ways, leading to significant conceptual problems. By identifying flourishing with receiving care, Tate raises questions about the importance of care that he does not address, giving rise to a bootstrapping problem. By making flourishing relative to an individual's circumstances, Tate is forced to confront questions about exactly how relative it can be, suggesting the possibility that, on his view, to flourish is simply to be however one is. In an attempt to surmount these problems, I offer a revision and restatement of Tate's view that defines the relationship between individualized flourishing and the more conventional, species-relative concept, and describe more clearly the role that care should play with respect to flourishing - one that is instrumental and not merely constitutive. Even this restated view, however, fails to answer difficult questions about how one should respond to the medical needs of some children, highlighting the fact that a conceptual analysis of suffering may do little, in the end, to untangle ethical dilemmas in the care of severely ill children.

RevDate: 2023-02-17

Korshunova T, Lundin K, Malmberg K, et al (2023)

Narrowly defined taxa on a global scale: The phylogeny and taxonomy of the genera Catriona and Tenellia (Nudibranchia, Trinchesiidae) favours fine-scale taxonomic differentiation and dissolution of the "lumpers & splitters" dilemma.

Evolutionary applications, 16(2):428-460.

By applying morphological and molecular data on two genera of the nudibranch molluscs it is shown that the tension between taxonomic practice and evolutionary processes persists. A review of the related genera Catriona and Tenellia is used to demonstrate that the fine-scale taxonomic differentiation is an important tool in the integration of morphological and molecular data. This is highlighted by the hidden species problem and provides strong argument that the genus must be kept as a maximally narrowly-defined entity. Otherwise, we are forced to compare a highly disparate species under the putatively lumped name "Tenellia". We demonstrate this in the present study by applying a suite of delimitation methods and describing a new species of Tenellia from the Baltic Sea. The new species possesses fine-scale morphological distinguishing features, which were not investigated before. The true, narrowly defined genus Tenellia represents a peculiar taxon with a clearly expressed paedomorphic characters and predominantly brackish-water habitats. The phylogenetically related genus Catriona, of which three new species are described here, clearly demonstrates different features. A lumping decision to call many morphologically and evolutionary different taxa as "Tenellia" will downgrade the taxonomic and phylogenetic resolution of the entire family Trinchesiidae to just a single genus. The dissolution of the dilemma of "lumpers & splitters", which still significantly affects taxonomy, will further help to make systematics a true evolutionary discipline.

RevDate: 2023-04-06
CmpDate: 2023-04-04

Sherratt E, B Kraatz (2023)

Multilevel analysis of integration and disparity in the mammalian skull.

Evolution; international journal of organic evolution, 77(4):1006-1018.

Biological variation is often considered in a scalable hierarchy, e.g., within the individual, within the populations, above the species level. Morphological integration, the concept of covariation among constituent parts of an organism, is also hierarchical; the degree to which these "modules" covary is a matter of the scale of the study as well as underlying processes driving the covariation. Multilevel analyses of trait covariation are a valuable tool to infer the origins and historical persistence of morphological diversity. Here, we investigate concordance in patterns of integration and modularity across three biological levels of variation: within a species, within two genera-level radiations, and among species at the family level. We demonstrate this approach using the skull of mammalian family Leporidae (rabbits and hares), which is morphologically diverse and has a rare-among-mammals functional signal of locomotion adaptation. We tested three alternative hypotheses of modularity; from the most supported we investigated disparity and integration of each module to infer which is most responsible for patterns of cranial variation across these levels, and whether variation is partitioned consistently across levels. We found a common pattern of modularity underlies leporid cranial diversity, though there is inconsistency across levels in each module's disparity and integration. The face module contributes the most to disparity at all levels, which we propose is facilitating evolutionary diversity in this clade. Therefore, the distinctive facial tilt of leporids is an adaptation to locomotory behavior facilitated by a modular system that allows lineages to respond differently to selection pressures.

RevDate: 2023-02-13

Fraiture MA, D'aes J, Guiderdoni E, et al (2023)

Targeted High-Throughput Sequencing Enables the Detection of Single Nucleotide Variations in CRISPR/Cas9 Gene-Edited Organisms.

Foods (Basel, Switzerland), 12(3):.

Similar to genetically modified organisms (GMOs) produced by classical genetic engineering, gene-edited (GE) organisms and their derived food/feed products commercialized on the European Union market fall within the scope of European Union Directive 2001/18/EC. Consequently, their control in the food/feed chain by GMO enforcement laboratories is required by the competent authorities to guarantee food/feed safety and traceability (2003/1829/EC; 2003/1830/EC). However, their detection is potentially challenging at both the analytical and interpretation levels since this requires methodological approaches that can target and detect a specific single nucleotide variation (SNV) introduced into a GE organism. In this study, we propose a targeted high-throughput sequencing approach, including (i) a prior PCR-based enrichment step to amplify regions of interest, (ii) a sequencing step, and (iii) a data analysis methodology to identify SNVs of interest. To investigate if the performance of this targeted high-throughput sequencing approach is compatible with the performance criteria used in the GMO detection field, several samples containing different percentages of a GE rice line carrying a single adenosine insertion in OsMADS26 were prepared and analyzed. The SNV of interest in samples containing the GE rice line could successfully be detected, both at high and low percentages. No impact related to food processing or to the presence of other crop species was observed. The present proof-of-concept study has allowed us to deliver the first experimental-based evidence indicating that the proposed targeted high-throughput sequencing approach may constitute, in the future, a specific and sensitive tool to support the safety and traceability of the food/feed chain regarding GE plants carrying SNVs.

RevDate: 2023-02-11

Sharkey MJ, Tucker EM, Baker A, et al (2022)

More discussion of minimalist species descriptions and clarifying some misconceptions contained in Meier et al. 2021.

ZooKeys, 1110:135-149.

This is a response to a preprint version of "A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science", https://www.biorxiv.org/content/10.1101/2021.04.28.441626v2. Meier et al. strongly criticized Sharkey et al.'s publication in which 403 new species were deliberately minimally described, based primarily on COI barcode sequence data. Here we respond to these criticisms. The following points are made: 1) Sharkey et al. did not equate BINs with species, as demonstrated in several examples in which multiple species were found to be in single BINs. 2) We reiterate that BINs were used as a preliminary sorting tool, just as preliminary morphological identification commonly sorts specimens based on color and size into unit trays; despite BINs and species concepts matching well over 90% of species, this matching does not equate to equality. 3) Consensus barcodes were used only to provide a diagnosis to conform to the rules of the International Code of Zoological Nomenclature just as consensus morphological diagnoses are. The barcode of a holotype is definitive and simply part of its cellular morphology. 4) Minimalist revisions will facilitate and accelerate future taxonomic research, not hinder it. 5) We refute the claim that the BOLD sequences of Plesiocoelusvanachterbergi are pseudogenes and demonstrate that they simply represent a frameshift mutation. 6) We reassert our observation that morphological evidence alone is insufficient to recognize species within species-rich higher taxa and that its usefulness lies in character states that are congruent with molecular data. 7) We show that in the cases in which COI barcodes code for the same amino acids in different putative species, data from morphology, host specificity, and other ecological traits reaffirm their utility as indicators of genetically distinct lineages.

RevDate: 2023-02-11

Brunke AJ (2022)

A world generic revision of Quediini (Coleoptera, Staphylinidae, Staphylininae), part 1. Early diverging Nearctic lineages.

ZooKeys, 1134:129-170.

Several phylogenetically isolated, early diverging lineages of rove beetle tribe Quediini, all endemic to the western Nearctic, have recently been revealed by phylogenomic systematics. These three lineages, currently treated as either Quedius (Raphirus) or Q. (Paraquedius) warrant recognition at the genus level in the ongoing effort to achieve reciprocal monophyly of genera in Quediini. The three lineages were each morphologically studied in detail, with the following results: Paraquedius Casey, stat. res. is re-elevated to genus rank, Quediellus Casey, stat. res. is resurrected from synonymy and redefined, and Iratiquedius gen. nov. is described for the species of the Amabilis and Prostans groups. A morphological diagnosis is provided for each genus at both the global and regional (Nearctic) level. Species level revisions, with keys, are provided for Iratiquedius, Paraquedius, and Quediellus with the following results: Iratiquediusuncifer sp. nov. and Paraquediusmarginicollis sp. nov. are described, Quediellusnanulus Casey is treated as syn. nov. of Quediellusdebilis (Horn), and I.amabilis (Smetana), I.mutator (Smetana), and P.puncticeps (Horn) are substantially redefined. Where possible, CO1 barcode sequence data are integrated with the morphological species concepts used herein and their clusters were found to be congruent.

RevDate: 2023-02-11

Boza Espinoza TE, M Kessler (2022)

A monograph of the genus Polylepis (Rosaceae).

PhytoKeys, 203:1-274.

We present a monograph of the high Andean tree genus Polylepis (Rosaceae), based on a species concept considering morphological, climatic and biogeographic distinctness as indicators of evolutionary independence. In total, we recognize 45 species of Polylepis, grouped in five sections. Polylepissect.Sericeae is represented by 15 species in four subsections, P.sect.Reticulatae by seven species, P.sect.Subsericantes by three species, P.sect.Australes by two species and P.sect.Incanaee by three subsections with 18 species. We describe seven new species, one from Colombia (P.frontinensis), one from Ecuador (P.simpsoniae) and five from Peru (P.acomayensis, P.fjeldsaoi, P.occidentalis, P.pilosissima and P.sacra). Three species from Peru (P.albicans, P.pallidistigma and P.serrata) are re-instated as valid species. Two taxa from Bolivia (P.incanoides and P.nana) are elevated from subspecies to species rank. The morphology, habitat, distribution, ecology and conservation status of each species are documented. We also provide an identification key to the species of the genus and general introductions on taxonomic history, morphology, evolution, ecology and conservation.

RevDate: 2023-02-11

Sklenář F, Glässnerová K, Jurjević Ž, et al (2022)

Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability.

Studies in mycology, 102:53-93.

Aspergillus series Versicolores members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin (CaM) genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (benA, CaM, RPB2, Mcm7, Tsr1). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series Versicolores to four species, namely A. versicolor, A. creber, A. sydowii and A. subversicolor, and the remaining species are synonymized with either A. versicolor or A. creber. The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between A. versicolor and A. creber. Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied Aspergillus species complexes and other fungal genera. Citation: Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson RA, Visagie CM, Yilmaz N, Gené J, Cano J, Chen AJ, Nováková A, Yaguchi T, Kolařík M, Hubka V (2022). Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Studies in Mycology 102 : 53-93. doi: 10.3114/sim.2022.102.02.

RevDate: 2023-04-03
CmpDate: 2023-02-02

Rivi V, Benatti C, Rigillo G, et al (2023)

Invertebrates as models of learning and memory: investigating neural and molecular mechanisms.

The Journal of experimental biology, 226(3):.

In this Commentary, we shed light on the use of invertebrates as model organisms for understanding the causal and conserved mechanisms of learning and memory. We provide a condensed chronicle of the contribution offered by mollusks to the studies on how and where the nervous system encodes and stores memory and describe the rich cognitive capabilities of some insect species, including attention and concept learning. We also discuss the use of planarians for investigating the dynamics of memory during brain regeneration and highlight the role of stressful stimuli in forming memories. Furthermore, we focus on the increasing evidence that invertebrates display some forms of emotions, which provides new opportunities for unveiling the neural and molecular mechanisms underlying the complex interaction between stress, emotions and cognition. In doing so, we highlight experimental challenges and suggest future directions that we expect the field to take in the coming years, particularly regarding what we, as humans, need to know for preventing and/or delaying memory loss. This article has an associated ECR Spotlight interview with Veronica Rivi.

RevDate: 2023-02-02

Manoj KM (2023)

Murburn posttranslational modifications of proteins: Cellular redox processes and murzyme-mediated metabolo-proteomics.

Journal of cellular physiology [Epub ahead of print].

Murburn concept constitutes the thesis that diffusible reactive species or DRS are obligatorily involved in routine metabolic and physiological activities. Murzymes are defined as biomolecules/proteins that generate/modulate/sustain/utilize DRS. Murburn posttranslational modifications (PTMs) result because murburn/murzyme functionalism is integral to cellular existence. Cells must incorporate the inherently stochastic nature of operations mediated by DRS. Due to the earlier/inertial stigmatic perception that DRS are mere agents of chaos, several such outcomes were either understood as deterministic modulations sponsored by house-keeping enzymes or deemed as unregulated nonenzymatic events resulting out of "oxidative stress". In the current review, I dispel the myths around DRS-functions, and undertake systematic parsing and analyses of murburn modifications of proteins. Although it is impossible to demarcate all PTMs into the classical or murburn modalities, telltale signs of the latter are evident from the relative inaccessibility of the locus, non-specificities and mechanistic details. It is pointed out that while many murburn PTMs may be harmless, some others could have deleterious or beneficial physiological implications. Some details of reversible/irreversible modifications of amino acid residues and cofactors that may be subjected to phosphorylation, halogenation, glycosylation, alkylation/acetylation, hydroxylation/oxidation, etc. are listed, along with citations of select proteins where such modifications have been reported. The contexts of these modifications and their significance in (patho)physiology/aging and therapy are also presented. With more balanced explorations and statistically verified data, a definitive understanding of normal versus pathological contexts of murburn modifications would be obtainable in the future.

RevDate: 2023-02-02

Chang JT, Chao CT, Nakamura K, et al (2022)

Corrigendum: Divergence with gene flow and contrasting population size blur the species boundary in Cycas Sect. Asiorientales, as inferred from morphology and RAD-seq data.

Frontiers in plant science, 13:1081728.

[This corrects the article DOI: 10.3389/fpls.2022.824158.].

RevDate: 2023-06-07
CmpDate: 2023-02-07

Le Bras Z, Bouchet S, LHE Winkel (2023)

Sensitive and High-Throughput Analysis of Volatile Organic Species of S, Se, Br, and I at Trace Levels in Water and Atmospheric Samples by Thermal Desorption Coupled to Gas Chromatography and Inductively Coupled Plasma Mass Spectrometry.

Analytical chemistry, 95(5):2967-2974.

Emissions of volatile organic sulfur (S), selenium (Se), bromine (Br), and iodine (I) species from aquatic ecosystems represent an important source of these elements into the atmosphere. Available methods to measure these species are either not sensitive enough or not automated, which hinder a full understanding of species distribution and production mechanisms. Here, we present a sensitive and high-throughput method for the simultaneous and comprehensive quantification of S, Se, Br, and I volatile organic species in atmospheric and aqueous samples using a preconcentration step onto sorbent tubes and subsequent analysis by thermal desorption coupled to gas chromatography and inductively coupled plasma mass spectrometry (TD-GC-ICP-MS). Selected commercially available sorbent tubes, consisting of mixed porous polymer and graphitized black carbon, offered the highest trapping capacity and lowest loss of species when stored at -20 °C for 28 days after sampling. After optimization of the TD-GC-ICP-MS method, absolute detection limits were better than 3.8 pg, 9.1 fg, 313 fg, and 50 fg, respectively, for S, Se, Br, and I species. As a proof of concept, the concentrations of target species were determined in aqueous and continuously collected atmospheric samples during a cruise in the Baltic and North Seas. Moreover, unknown S, Br, and I volatile species were detected in both aqueous and atmospheric samples demonstrating the full potential of the method.

RevDate: 2023-03-17
CmpDate: 2023-01-27

Chen SW, Zheng ZY, Mahfut FB, et al (2023)

Leveraging an advanced simulated moving bed approach to achieve 3-component separation for enhanced impurity removal in a non-affinity cation exchange capture step.

PloS one, 18(1):e0280760.

One of the key challenges in downstream bioprocessing is to obtain products of high purity in a productive fashion through the effective removal of process and product related impurities. While a classical simulated moving bed (SMB) system operation can typically achieve a 2-component separation between the weakly bound impurities and target species, here we present an advanced SMB approach that can achieve a 3-component separation, including the removal of the strongly bound impurities from the target species. As a proof-of-concept, we demonstrate the enhanced removal of strongly bound host cell proteins (HCP) from the target monoclonal antibody (mAb) through the utilisation of the advanced SMB approach in a non-affinity cation exchange (CEX) capture step. In this way, 1 less polishing step was required to achieve the therapeutic requirements of < 100 ppm HCP and the overall process recovery was increased by ~ 6% compared to the corresponding process that utilised a batch CEX operation. The non-affinity CEX capture platform technology established through the utilisation of the advanced SMB approach presented here can potentially be further applied to address the downstream processing challenges presented by other challenging biotherapeutic modalities to yield a final target product with improved purity and recovery.

RevDate: 2023-02-01

Bateman RM, PJ Rudall (2023)

Morphological Continua Make Poor Species: Genus-Wide Morphometric Survey of the European Bee Orchids (Ophrys L.).

Biology, 12(1):.

Despite (or perhaps because of) intensive multidisciplinary research, opinions on the optimal number of species recognised within the Eurasian orchid genus Ophrys range from nine to at least 400. The lower figure of nine macrospecies is based primarily on seeking small but reliable discontinuities in DNA 'barcode' regions, an approach subsequently reinforced and finessed via high-throughput sequencing studies. The upper figure of ca. 400 microspecies reflects the morphological authoritarianism of traditional taxonomy combined with belief in extreme pollinator specificity caused by reliance on pollination through pseudo-copulation, enacted by bees and wasps. Groupings of microspecies that are less inclusive than macrospecies are termed mesospecies. Herein, we present multivariate morphometric analyses based on 51 characters scored for 457 individual plants that together span the full morphological and molecular diversity within the genus Ophrys, encompassing 113 named microspecies that collectively represent all 29 mesospecies and all nine macrospecies. We critique our preferred morphometric approach of accumulating heterogeneous data and analysing them primarily using principal coordinates, noting that our conclusions would have been strengthened by even greater sampling and the inclusion of data describing pseudo-pheromone cocktails. Morphological variation within Ophrys proved to be exceptionally multidimensional, lacking strong directional trends. Multivariate clustering of plants according to prior taxonomy was typically weak, irrespective of whether it was assessed at the level of macrospecies, mesospecies or microspecies; considerable morphological overlap was evident even between subsets of the molecularly differentiable macrospecies. Characters supporting genuine taxonomic distinctions were often sufficiently subtle that they were masked by greater and more positively correlated variation that reflected strong contrasts in flower size, tepal colour or, less often, plant size. Individual macrospecies appear to represent morphological continua, within which taxonomic divisions are likely to prove arbitrary if based exclusively on morphological criteria and adequately sampled across their geographic range. It remains unclear how much of the mosaic of subtle character variation among the microspecies reflects genetic versus epigenetic or non-genetic influences and what proportion of any contrasts observed in gene frequencies can be attributed to the adaptive microevolution that is widely considered to dictate speciation in the genus. Moreover, supplementing weak morphological criteria with extrinsic criteria, typically by imposing constraints on geographic location and/or supposed pollinator preference, assumes rather than demonstrates the presence of even the weakest of species boundaries. Overall, it is clear that entities in Ophrys below the level of macrospecies have insufficiently structured variation, either phenotypic or genotypic, to be resolved into discrete, self-circumscribing ("natural") entities that can legitimately be equated with species as delimited within other less specialised plant genera. Our search for a non-arbitrary (meso)species concept competent to circumscribe an intermediate number of species has so far proven unsuccessful.

RevDate: 2023-02-28
CmpDate: 2023-02-07

Dai C, P Feng (2023)

Multiple concordant cytonuclear divergences and potential hybrid speciation within a species complex in Asia.

Molecular phylogenetics and evolution, 180:107709.

Various environmental factors impact the distribution, population structure, demography and evolutionary trajectory of a bird species, leading to genetic and morphological divergences between populations across its distribution. The Paradoxornis webbianus species complex is found throughout much of East Asia, where its geographically distinct populations exhibit dramatic morphological variation. This has resulted in a hotly debated taxonomy. This study intended to identify genetic divergence patterns and their underlying contributing factors for this species complex. We collected 243 birds, whose data was combined with those available in GenBank to perform phylogeographic analyses using one mitochondrial and six nuclear loci. Six mitochondrial clades were observed in the species complex, while individual-based Bayesian clustering using nuclear markers showed multiple congruent breaks. Overall, the six molecular lineages could be recognized as independent species under the lineage species concept in view of genetic divergence, clade-specific morphological changes and distribution: P. webbianus, P. w. bulomachus, P. alphonsianus, P. a. ganluoensis, P. brunneus brunneus and P. b. ricketti. The estimated divergence times range from 0.46 to 3.36 million years ago, suggesting it was likely impacted by paleoclimatic changes. Interestingly, P. alphonsianus carries two divergent mitochondrial lineages shared with P. webbianus and P. a. ganluoensis, respectively, and analyses based on nuclear loci found a similar pattern. We discussed the various hypotheses for this pattern and argued that P. alphonsianus was likely the result of hybridization between P. webbianus and P. a. ganluoensis. Further data on genome, transcriptome and breeding ecology are needed to address the hypothesis of hybrid speciation and its underlying mechanisms.

RevDate: 2023-04-27
CmpDate: 2023-01-20

Kim JG, Cho K, Yoon SM, et al (2023)

Taxonomic review of the genus Stenocaris Sars (Copepoda, Harpacticoida, Cylindropsyllidae), with (re)descriptions of two Stenocaris species from the Far East.

PeerJ, 11:e14623.

The taxonomic concept of the genus Stenocaris Sars, 1909 is uncertain because none of the synapomorphies for the species of Stenocaris are defined. Detailed comparison of previous records of Stenocaris minor (T. Scott, 1892) from different localities reveals that this species represents a species complex composed of two species, S. minor s. str. and S. minor sensu Cottarelli & Venanzetti, 1989. Because the latter species has fundamental differences in the nature of the fifth leg in females and the sexual dimorphism of the second leg in males, we propose a new species for S. minor sensu Cottarelli & Venanzetti, 1989, S. figaroloensis sp. nov. We also suggest that S. minor sensu Apostolov, 1971, S. minor sensu Marinov, 1971, and S. minor sensu Apostolov & Marinov, 1988 from the Black Sea and S. minor sensu Wilson, 1932 from North America should be relegated to species inquirenda in the genus. Taxonomic review of the morphology of all Stenocaris species indicated that the generic concept must be restricted to accommodate S. minor s. str., S. gracilis Sars, 1909, S. intermedia Itô, 1972, S. figaroloensis sp. nov., and the South Korean new species, S. marcida sp. nov., based on the synapomorphic condition of the confluent fifth leg in males. As a result of our analysis, two Stenocaris species, S. baltica Arlt, 1983 and S. pygmaea Noodt, 1955, are transferred to the genus Vermicaris Kornev & Chertoprud, 2008 as V. baltica (Arlt, 1983) comb. nov. and V. pygmaea (Noodt, 1955) comb. nov. based on the synapomorphic characters of a reduced condition of the second and fifth legs. Additionally, S. arenicola Wilson, 1932 and S. kliei (Kunz, 1938) are allocated to a new genus, Huysicaris gen. nov., mainly characterized by obvious caudal rami with a recurved dorsal spinous process and convex inner margins, as H. arenicola (Wilson, 1932) comb. nov. and H. kliei (Kunz, 1938) comb. nov. A marine interstitial harpacticoid collected from the subtidal substrate off Dok-do Island in the East Sea of South Korea is proposed as S. marcida sp. nov. and the distribution of S. intermedia, originally known from its type locality in Japanese waters only, is extended to the East Sea of Korea and Russia. We provide their detailed descriptions and illustrations and discuss the morphological characters supporting their identities.

RevDate: 2023-02-01
CmpDate: 2023-01-25

Bolnick DI, Hund AK, Nosil P, et al (2023)

A multivariate view of the speciation continuum.

Evolution; international journal of organic evolution, 77(1):318-328.

The concept of a "speciation continuum" has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.

RevDate: 2023-02-14
CmpDate: 2023-01-12

Cobo-Simón M, Hart R, H Ochman (2023)

Escherichia Coli: What Is and Which Are?.

Molecular biology and evolution, 40(1):.

Escherichia coli have served as important model organisms for over a century-used to elucidate key aspects of genetics, evolution, molecular biology, and pathogenesis. However, defining which strains actually belong to this species is erratic and unstable due to shifts in the characters and criteria used to distinguish bacterial species. Additionally, many isolates designated as E. coli are genetically more closely related to strains of Shigella than to other E. coli, creating a situation in which the entire genus of Shigella and its four species are encompassed within the single species E. coli. We evaluated all complete genomes assigned to E. coli and its closest relatives according to the biological species concept (BSC), using evidence of reproductive isolation and gene flow (i.e., homologous recombination in the case of asexual bacteria) to ascertain species boundaries. The BSC establishes a uniform, consistent, and objective principle that allows species-level classification across all domains of life and does not rely on either phenotypic or genotypic similarity to a defined type-specimen for species membership. Analyzing a total of 1,887 sequenced genomes and comparing our results to other genome-based classification methods, we found few barriers to gene flow among the strains, clades, phylogroups, or species within E. coli and Shigella. Due to the utility in recognizing which strains constitute a true biological species, we designate genomes that form a genetic cohesive group as members of E. coliBIO.

RevDate: 2022-12-27

Carrillo-Bilbao G, Navarro JC, Martin-Solano S, et al (2022)

First Molecular Identification of Trypanosomes and Absence of Babesia sp. DNA in Faeces of Non-Human Primates in the Ecuadorian Amazon.

Pathogens (Basel, Switzerland), 11(12):.

Trypanosomes are a group of pathogens distributed in the continents of Africa, America, Asia and Europe, and they affect all vertebrates including the neotropical primate group. Information about the trypanosome's diversity, phylogeny, ecology and pathology in non-human primates (NHPs) from the neotropical region is scarce. The objective of the study was to identify Trypanosoma and Babesia molecularly in NHPs under the phylogenetic species concept. We extracted DNA from a total of 76 faecal samples collected between 2019 and 2021, from a total of 11 non-human primate species of which 46 are from captive NHPs and 30 are free-living NHPs in the Western Amazon region of Ecuador. We did not detect DNA of Babesia sp. by polymerase chain reaction test in any of the faecal samples. However, the nested-PCR-based method revealed Trypanosoma parasites by ITS gene amplification in two faecal samples; one for the species Leontocebus lagonotus (from the captive population) and a second one for Cebus albifrons (from the free-ranging population). Maximum parsimony and likelihood methods with the Kimura2+G+I model inferred the evolutionary history of the two records, which showed an evolutionary relationship with the genus Trypanosoma. Two sequences are monophyletic with Trypanosoma. However, the number of sequences available in GenBank for their species identification is limited. The two samples present different molecular identifications and evolutionary origins in the tree topology. We are most likely referring to two different species, and two different localities of infection. We suggest that health management protocols should be implemented to prevent the transmission of blood-borne pathogens such as Trypanosoma sp. among captive populations. In addition, these protocols also protect the personnel of wildlife rehabilitation centers working in close proximity to NHPs and vice versa.

RevDate: 2023-04-03
CmpDate: 2023-02-02

Deepak V, Gower DJ, N Cooper (2023)

Diet and habit explain head-shape convergences in natricine snakes.

Journal of evolutionary biology, 36(2):399-411.

The concept of ecomorphs, whereby species with similar ecologies have similar phenotypes regardless of their phylogenetic relatedness, is often central to discussions regarding the relationship between ecology and phenotype. However, some aspects of the concept have been questioned, and sometimes species have been grouped as ecomorphs based on phenotypic similarity without demonstrating ecological similarity. Within snakes, similar head shapes have convergently evolved in species living in comparable environments and/or with similar diets. Therefore, ecomorphs could exist in some snake lineages, but this assertion has rarely been tested for a wide-ranging group within a single framework. Natricine snakes (Natricinae) are ecomorphologically diverse and currently distributed in Asia, Africa, Europe and north-central America. They are primarily semiaquatic or ground-dwelling terrestrial snakes, but some are aquatic, burrowing or aquatic and burrowing in habit and may be generalist or specialist in diet. Thus, natricines present an interesting system to test whether snakes from different major habit categories represent ecomorphs. We quantify morphological similarity and disparity in head shape among 191 of the ca. 250 currently recognized natricine species and apply phylogenetic comparative methods to test for convergence. Natricine head shape is largely correlated with habit, but in some burrowers is better explained by dietary specialism. Convergence in head shape is especially strong for aquatic burrowing, semiaquatic and terrestrial ecomorphs and less strong for aquatic and burrowing ecomorphs. The ecomorph concept is useful for understanding natricine diversity and evolution, though would benefit from further refinement, especially for aquatic and burrowing taxa.

RevDate: 2023-02-01
CmpDate: 2023-01-18

Manoj KM, Gideon DA, Bazhin NM, et al (2023)

Na,K-ATPase: A murzyme facilitating thermodynamic equilibriums at the membrane-interface.

Journal of cellular physiology, 238(1):109-136.

The redox metabolic paradigm of murburn concept advocates that diffusible reactive species (DRS, particularly oxygen-centric radicals) are mainstays of physiology, and not mere pathological manifestations. The murburn purview of cellular function also integrates the essential principles of bioenergetics, thermogenesis, homeostasis, electrophysiology, and coherence. In this context, any enzyme that generates/modulates/utilizes/sustains DRS functionality is called a murzyme. We have demonstrated that several water-soluble (peroxidases, lactate dehydrogenase, hemogoblin, etc.) and membrane-embedded (Complexes I-V in mitochondria, Photosystems I/II in chloroplasts, rhodopsin/transducin in rod cells, etc.) proteins serve as murzymes. The membrane protein of Na,K-ATPase (NKA, also known as sodium-potassium pump) is the focus of this article, owing to its centrality in neuro-cardio-musculo electrophysiology. Herein, via a series of critical queries starting from the geometric/spatio-temporal considerations of diffusion/mass transfer of solutes in cells to an update on structural/distributional features of NKA in diverse cellular systems, and from various mechanistic aspects of ion-transport (thermodynamics, osmoregulation, evolutionary dictates, etc.) to assays/explanations of inhibitory principles like cardiotonic steroids (CTS), we first highlight some unresolved problems in the field. Thereafter, we propose and apply a minimalist murburn model of trans-membrane ion-differentiation by NKA to address the physiological inhibitory effects of trans-dermal peptide, lithium ion, volatile anesthetics, confirmed interfacial DRS + proton modulators like nitrophenolics and unsaturated fatty acid, and the diverse classes of molecules like CTS, arginine, oximes, etc. These explanations find a pan-systemic connectivity with the inhibitions/uncouplings of other membrane proteins in cells.

RevDate: 2022-12-13
CmpDate: 2022-12-07

Tester PA, Litaker RW, Soler-Onís E, et al (2022)

Using artificial substrates to quantify Gambierdiscus and other toxic benthic dinoflagellates for monitoring purposes.

Harmful algae, 120:102351.

Collecting methods generally used to determine cell abundances of toxic benthic dinoflagellates (BHAB) use cells dislodged from either macrophytes or artificial substrates. This article compares the advantages of the macrophyte and artificial substrate methods and discusses which method is more appropriate for use in monitoring programs that focus on toxic BHAB species identification and quantification. The concept of benthic dinoflagellate "preference" for specific macrophytes was also reviewed. Examination of data from 75 field studies showed macrophytes with higher surface area per unit biomass harbored higher concentrations of Gambierdiscus cells. There was no definitive evidence that cells were actively selecting one macrophyte over another. This observation supports the use of artificial substrates (AS) as a means of assessing cell abundances in complex habitats because cell counts are normalized to a standardized surface area, not macrophyte biomass. The artificial substrate method represents the most robust approach, currently available, for collecting toxic, benthic dinoflagellates for a cell-based early warning system.

RevDate: 2022-12-06

Hohenwallner K, Troppmair N, Panzenboeck L, et al (2022)

Decoding Distinct Ganglioside Patterns of Native and Differentiated Mesenchymal Stem Cells by a Novel Glycolipidomics Profiling Strategy.

JACS Au, 2(11):2466-2480.

Gangliosides are an indispensable glycolipid class concentrated on cell surfaces with a critical role in stem cell differentiation. Nonetheless, owing to the lack of suitable methods for scalable analysis covering the full scope of ganglioside molecular diversity, their mechanistic properties in signaling and differentiation remain undiscovered to a large extent. This work introduces a sensitive and comprehensive ganglioside assay based on liquid chromatography, high-resolution mass spectrometry, and multistage fragmentation. Complemented by an open-source data evaluation workflow, we provide automated in-depth lipid species-level and molecular species-level annotation based on decision rule sets for all major ganglioside classes. Compared to conventional state-of-the-art methods, the presented ganglioside assay offers (1) increased sensitivity, (2) superior structural elucidation, and (3) the possibility to detect novel ganglioside species. A major reason for the highly improved sensitivity is the optimized spectral readout based on the unique capability of two parallelizable mass analyzers for multistage fragmentation. We demonstrated the high-throughput universal capability of our novel analytical strategy by identifying 254 ganglioside species. As a proof of concept, 137 unique gangliosides were annotated in native and differentiated human mesenchymal stem cells including 78 potential cell-state-specific markers and 38 previously unreported gangliosides. A general increase of the ganglioside numbers upon differentiation was observed as well as cell-state-specific clustering based on the ganglioside species patterns. The combination of the developed glycolipidomics assay with the extended automated annotation tool enables comprehensive in-depth ganglioside characterization as shown on biological samples of interest. Our results suggest ganglioside patterns as a promising quality control tool for stem cells and their differentiation products. Additionally, we believe that our analytical workflow paves the way for probing glycolipid-based biochemical processes shedding light on the enigmatic processes of gangliosides and glycolipids in general.

RevDate: 2022-12-06
CmpDate: 2022-12-06

Alcántara-Salinas G, Hunn ES, Ibáñez-Bravo ME, et al (2022)

Bird conservation status and cultural values in Indigenous Mexican communities: towards a bioculturally informed conservation policy.

Journal of ethnobiology and ethnomedicine, 18(1):69.

BACKGROUND: We summarize comparative ethnoornithological data for ten Mexican Indigenous communities, an initial step towards a comprehensive archive of the avian diversity conserved within Mexico's Indigenous territories. We do so by counting highlighted species listed for bird conservation status on widely recognized "red lists" and their cultural value to build biocultural policies in Mexico for their conservation.

METHODS: Indigenous bird names for each study site were determined to allow calculation of the "Scientific Species Recognition Ratio" (SSRR) for high cultural value birds obtained across communities. This demonstrated patterns of cultural prominence. A matrix of 1275 bird versus seven biocultural values was analysed using a correspondence analysis (InfoStat/L-v2020) to illustrate patterns of concordance between bird conservation status and cultural values.

RESULTS: This paper contributes to quantitative and qualitative data on the role of ethnoornithology and ethnobiology in biocultural conservation. The areas studied provide refugia for almost 70% of the Mexican avifauna within a fraction of 1% of the national territory, that is 769 bird species recorded for all communities. The global correspondence of regions of biological and linguistic megadiversity is well established, while linguistic diversity is widely accepted as a good proxy for general cultural diversity. Our correspondence analysis explained 81.55% of the variation, indicating a strong relation between cultural importance and bird conservation status. We propose three main categories to establish a bioculturally informed public policy in Mexico for the conservation of what we described as high, medium, and bioculturally prominent bird species all include cultural value in any material or symbolic aspect. High are those species appearing on any threatened list, but also considered in any endemic status, while medium include threatened listed species. The last category included species not necessarily listed on any threat list, but with a wide range of social and cultural uses. We suggest that the concept might be extended to other species of biocultural importance.

CONCLUSIONS: We argue that bird conservation policies should be biocultural, that is they should recognize birds of cultural value on a par with bird species "of special interest" because they are most critical for biodiversity conservation. The desire of local people to protect their traditional community lands and livelihoods can be an effective biodiversity conservation strategy, which should be recognized in national biocultural policies.

RevDate: 2023-01-05
CmpDate: 2022-12-21

Stagg O, Morris K, Townsend LT, et al (2022)

Sulfidation and Reoxidation of U(VI)-Incorporated Goethite: Implications for U Retention during Sub-Surface Redox Cycling.

Environmental science & technology, 56(24):17643-17652.

Over 60 years of nuclear activity have resulted in a global legacy of contaminated land and radioactive waste. Uranium (U) is a significant component of this legacy and is present in radioactive wastes and at many contaminated sites. U-incorporated iron (oxyhydr)oxides may provide a long-term barrier to U migration in the environment. However, reductive dissolution of iron (oxyhydr)oxides can occur on reaction with aqueous sulfide (sulfidation), a common environmental species, due to the microbial reduction of sulfate. In this work, U(VI)-goethite was initially reacted with aqueous sulfide, followed by a reoxidation reaction, to further understand the long-term fate of U species under fluctuating environmental conditions. Over the first day of sulfidation, a transient release of aqueous U was observed, likely due to intermediate uranyl(VI)-persulfide species. Despite this, overall U was retained in the solid phase, with the formation of nanocrystalline U(IV)O2 in the sulfidized system along with a persistent U(V) component. On reoxidation, U was associated with an iron (oxyhydr)oxide phase either as an adsorbed uranyl (approximately 65%) or an incorporated U (35%) species. These findings support the overarching concept of iron (oxyhydr)oxides acting as a barrier to U migration in the environment, even under fluctuating redox conditions.

RevDate: 2023-03-29
CmpDate: 2023-01-05

Stork S, Jalinsky J, M Neiman (2022)

Evidence for stronger discrimination between conspecific and heterospecific mating partners in sexual vs. asexual female freshwater snails.

PeerJ, 10:e14470.

Once-useful traits that no longer contribute to fitness tend to decay over time. Here, we address whether the expression of mating-related traits that increase the fitness of sexually reproducing individuals but are likely less useful or even costly to asexual counterparts seems to exhibit decay in the latter. Potamopyrgus antipodarum is a New Zealand freshwater snail characterized by repeated transitions from sexual to asexual reproduction. The frequent coexistence of sexual and asexual lineages makes P. antipodarum an excellent model for the study of mating-related trait loss. Under the presumption (inherent in the Biological Species Concept) that failure to discriminate between conspecific and heterospecific mating partners represents a poor mate choice, we used a mating choice assay including sexual and asexual P. antipodarum females and conspecific (presumed better choice) vs. heterospecific (presumed worse choice) males to evaluate the loss of behavioral traits related to sexual reproduction. We found that sexual females engaged in mating behaviors with conspecific mating partners more frequently and for a greater duration than with heterospecific mating partners. By contrast, asexual females mated at similar frequency and duration as sexual females, but did not mate more often or for longer duration with conspecific vs. heterospecific males. While further confirmation will require inclusion of a more diverse array of sexual and asexual lineages, these results are consistent with a scenario where selection acting to maintain effective mate discrimination in asexual P. antipodarum is weak or ineffective relative to sexual females and, thus, where asexual reproduction is associated with the evolutionary decay of mating-related traits in this system.

RevDate: 2022-11-19

Bergmann A, Burchardt LS, Wimmer B, et al (2022)

The soundscape of swarming: Proof of concept for a noninvasive acoustic species identification of swarming Myotis bats.

Ecology and evolution, 12(11):e9439.

Bats emit echolocation calls to orientate in their predominantly dark environment. Recording of species-specific calls can facilitate species identification, especially when mist netting is not feasible. However, some taxa, such as Myotis bats can be hard to distinguish acoustically. In crowded situations where calls of many individuals overlap, the subtle differences between species are additionally attenuated. Here, we sought to noninvasively study the phenology of Myotis bats during autumn swarming at a prominent hibernaculum. To do so, we recorded sequences of overlapping echolocation calls (N = 564) during nights of high swarming activity and extracted spectral parameters (peak frequency, start frequency, spectral centroid) and linear frequency cepstral coefficients (LFCCs), which additionally encompass the timbre (vocal "color") of calls. We used this parameter combination in a stepwise discriminant function analysis (DFA) to classify the call sequences to species level. A set of previously identified call sequences of single flying Myotis daubentonii and Myotis nattereri, the most common species at our study site, functioned as a training set for the DFA. 90.2% of the call sequences could be assigned to either M. daubentonii or M. nattereri, indicating the predominantly swarming species at the time of recording. We verified our results by correctly classifying the second set of previously identified call sequences with an accuracy of 100%. In addition, our acoustic species classification corresponds well to the existing knowledge on swarming phenology at the hibernaculum. Moreover, we successfully classified call sequences from a different hibernaculum to species level and verified our classification results by capturing swarming bats while we recorded them. Our findings provide a proof of concept for a new noninvasive acoustic monitoring technique that analyses "swarming soundscapes" by combining classical acoustic parameters and LFCCs, instead of analyzing single calls. Our approach for species identification is especially beneficial in situations with multiple calling individuals, such as autumn swarming.

RevDate: 2023-04-19
CmpDate: 2023-01-20

Hu J, Vandenkoornhuyse P, Khalfallah F, et al (2023)

Ecological corridors homogenize plant root endospheric mycobiota.

The New phytologist, 237(4):1347-1362.

Ecological corridors promote species coexistence in fragmented habitats where dispersal limits species fluxes. The corridor concept was developed and investigated with macroorganisms in mind, while microorganisms, the invisible majority of biodiversity, were disregarded. We analyzed the effect of corridors on the dynamics of endospheric fungal assemblages associated with plant roots at the scale of 1 m over 2 years (i.e. at five time points) by combining an experimental corridor-mesocosm with high-throughput amplicon sequencing. We showed that plant root endospheric mycobiota were sensitive to corridor effects when the corridors were set up at a small spatial scale. The endospheric mycobiota of connected plants had higher species richness, lower beta-diversity, and more deterministic assembly than the mycobiota of isolated plants. These effects became more pronounced with the development of host plants. Biotic corridors composed of host plants may thus play a key role in the spatial dynamics of microbial communities and may influence microbial diversity and related ecological functions.

RevDate: 2022-11-04

Portillo JTDM, Barbo FE, RJ Sawaya (2022)

Climatic niche breadths of the Atlantic Forest snakes do not increase with increasing latitude.

Current zoology, 68(5):535-540.

The climatic niche is a central concept for understanding species distribution, with current and past climate interpreted as strong drivers of present and historical-geographical ranges. Our aim is to understand whether Atlantic Forest snakes follow the general geographical pattern of increasing species climatic niche breadths with increasing latitude. We also tested if there is a tradeoff between temperature and precipitation niche breadths of species in order to understand if species with larger breadths of one niche dimension have stronger dispersal constraints by the other due to narrower niche breadths. Niche breadths were calculated by the subtraction of maximal and minimal values of temperature and precipitation across species ranges. We implemented Phylogenetic Generalized Least Squares to measure the relationship between temperature and precipitation niche breadths and latitude. We also tested phylogenetic signals by Lambda statistics to analyze the degree of phylogenetic niche conservatism to both niche dimensions. Temperature niche breadths were not related to latitude. Precipitation niche breadths decreased with increasing latitude and presented a high phylogenetic signal, that is, significant phylogenetic niche conservatism. We rejected the tradeoff hypotheses of temperature and precipitation niche breadths. Our results also indicate that precipitation should be an important ecological constraint affecting the geographical distribution of snake lineages across the South American Atlantic Forest. We then provide a general view of how phylogenetic niche conservatism could impact the patterns of latitudinal variation of climatic niches across this biodiversity hotspot.

RevDate: 2023-04-10
CmpDate: 2023-02-24

Berns GS (2023)

Deciphering the dog brain with fMRI.

Trends in neurosciences, 46(3):173-175.

fMRI has been increasingly used to study brain function in domestic dogs trained to lie still in MRI scanners. These studies highlight both similarities and differences between dogs and humans when presented with the same stimuli, raising intriguing questions about the concept of functional homologies in a coevolved species that shares the human environment.

RevDate: 2022-10-30

Peçanha PM, Peçanha-Pietrobom PM, Grão-Velloso TR, et al (2022)

Paracoccidioidomycosis: What We Know and What Is New in Epidemiology, Diagnosis, and Treatment.

Journal of fungi (Basel, Switzerland), 8(10):.

Paracoccidioidomycosis (PCM) is a systemic mycosis endemic to Latin America caused by thermodimorphic fungi of the genus Paracoccidioides. In the last two decades, enhanced understanding of the phylogenetic species concept and molecular variations has led to changes in this genus' taxonomic classification. Although the impact of the new species on clinical presentation and treatment remains unclear, they can influence diagnosis when serological methods are employed. Further, although the infection is usually acquired in rural areas, the symptoms may manifest years or decades later when the patient might be living in the city or even in another country outside the endemic region. Brazil accounts for 80% of PCM cases worldwide, and its incidence is rising in the northern part of the country (Amazon region), owing to new settlements and deforestation, whereas it is decreasing in the south, owing to agriculture mechanization and urbanization. Clusters of the acute/subacute form are also emerging in areas with major human intervention and climate change. Advances in diagnostic methods (molecular and immunological techniques and biomarkers) remain scarce, and even the reference center's diagnostics are based mainly on direct microscopic examination. Classical imaging findings in the lungs include interstitial bilateral infiltrates, and eventually, enlargement or calcification of adrenals and intraparenchymal central nervous system lesions are also present. Besides itraconazole, cotrimoxazole, and amphotericin B, new azoles may be an alternative when the previous ones are not tolerated, although few studies have investigated their use in treating PCM.

RevDate: 2022-10-30

Ali F, Khan N, O Rahmonov (2022)

Ecosystem Services and Linkages of Naturally Managed Monotheca buxifolia (Falc.) A. DC. Forests with Local Communities across Contiguous Mountainous Ranges in Pakistan.

Biology, 11(10):.

The local community of the Suleiman and Hindukush mountain systems in Pakistan has largely depended on the natural resources of the environment since ancient times. The ecosystem of these regions is under huge pressure due to a lack of awareness and the uncontrolled interference of communal, commercial, security, political, and ecological conditions. The present study was designed to illuminate the link between mountain society and the consumption of the benefits from Monotheca phytocoenoses using the ecosystem services concept from the sphere of the socio-ecological system to cultural relations. The use of this approach is very important due to the visible role and dominant status of Monotheca vegetation within the ecological system of the region. M. buxifolia is strongly connected with both local and cultural traditions and is counted as a key species, particularly for high-mountain inhabitants. We report that Monotheca phytocoenoses provide several services including shelter, food, fodder, medicines, and wood, etc., to the indigenous community and is highly valued in the local culture because of the poor economic condition of the society. The concept of this cultural keystone species is crucial for understanding ecosystem services and must be considered for the protection and conservation of these habitats. The results of field and social studies have shown that the stable maintenance of Monotheca phytocoenosis forests ensures the existence of key species as the most important providers of ecosystem services, e.g., provisioning, regulation, maintenance and cultural services, indicating the close relations between society and the protection of mountain areas. According to the results obtained, the mountains community of the studied area believes that tree species like M. buxifolia, F. palmata, O. ferruginea, P. granatum, A. modesta, J. regia, etc., are the key components contributing to the function of both the mountain ecosystem and communities' well-being. This approach will be extremely useful for ensuring an inclusive management of the socio-ecological system of the Hindukush and Suleiman Mountain ranges of Pakistan.

RevDate: 2022-11-23
CmpDate: 2022-11-23

Lamattina D, OD Salomón (2023)

Triatoma infestans, to be or not to be autogenic?.

Acta tropica, 237:106727.

Autogeny, the ability to develop eggs without a meal in the adult stage, has been described in several groups of arthropods, especially hematophagous Diptera Nematocera. In obligate hematophagous hemimetabolous insects that feed on blood in all their instars, such as Triatominae, this concept gives rise to species with apparently facultative autogeny, such as Triatoma infestans. Generalized linear models were applied to explain egg production by the predictor variables molting weight as a proxy of nymphal accumulated reserves and digested blood weight as an indicator of adult reserve in fasted, incompletely fed and engorged at repletion females. The relationship between these indicators of nutritional status and egg development turned out to be a continuous function in which, with molting weights greater than 254 mg, the insects are autogenic, but for the first batch of eggs with molting weights between 132 and 253 mg, they require one adult meal of at least 202 mg, and with molting weights less than 131 mg at least two meals are required. Both molting weight and blood intake could determine oocyte production in an additive manner, thus the concept of autogeny as a switch on-off phenomenon is not directly applicable to Triatominae. Nevertheless, autogenic ability would allow Triatominae with relatively long cycles to accelerate population growth under favorable or low competition conditions during colonization or recovery after a control intervention.

RevDate: 2023-02-10
CmpDate: 2022-12-27

Wang S, Qian YQ, Zhao RP, et al (2023)

Graph-based pan-genomes: increased opportunities in plant genomics.

Journal of experimental botany, 74(1):24-39.

Due to the development of sequencing technology and the great reduction in sequencing costs, an increasing number of plant genomes have been assembled, and numerous genomes have revealed large amounts of variations. However, a single reference genome does not allow the exploration of species diversity, and therefore the concept of pan-genome was developed. A pan-genome is a collection of all sequences available for a species, including a large number of consensus sequences, large structural variations, and small variations including single nucleotide polymorphisms and insertions/deletions. A simple linear pan-genome does not allow these structural variations to be intuitively characterized, so graph-based pan-genomes have been developed. These pan-genomes store sequence and structural variation information in the form of nodes and paths to store and display species variation information in a more intuitive manner. The key role of graph-based pan-genomes is to expand the coordinate system of the linear reference genome to accommodate more regions of genetic diversity. Here, we review the origin and development of graph-based pan-genomes, explore their application in plant research, and further highlight the application of graph-based pan-genomes for future plant breeding.

RevDate: 2022-10-19

Rocchini D, Santos MJ, Ustin SL, et al (2022)

The Spectral Species Concept in Living Color.

Journal of geophysical research. Biogeosciences, 127(9):e2022JG007026.

Biodiversity monitoring is an almost inconceivable challenge at the scale of the entire Earth. The current (and soon to be flown) generation of spaceborne and airborne optical sensors (i.e., imaging spectrometers) can collect detailed information at unprecedented spatial, temporal, and spectral resolutions. These new data streams are preceded by a revolution in modeling and analytics that can utilize the richness of these datasets to measure a wide range of plant traits, community composition, and ecosystem functions. At the heart of this framework for monitoring plant biodiversity is the idea of remotely identifying species by making use of the 'spectral species' concept. In theory, the spectral species concept can be defined as a species characterized by a unique spectral signature and thus remotely detectable within pixel units of a spectral image. In reality, depending on spatial resolution, pixels may contain several species which renders species-specific assignment of spectral information more challenging. The aim of this paper is to review the spectral species concept and relate it to underlying ecological principles, while also discussing the complexities, challenges and opportunities to apply this concept given current and future scientific advances in remote sensing.


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.

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The complex idea of “species” has evolved over time, yet its meaning is far from resolved. This comprehensive work takes a fresh look at an idea central to the field of biology by tracing its history from antiquity to today. John S. Wilkins explores the essentialist view, a staple of logic from Plato and Aristotle through the Middle Ages to fairly recent times, and considers the idea of species in natural history―a concept often connected to reproduction. Tracing “generative conceptions” of species back through Darwin to Epicurus, Wilkins provides a new perspective on the relationship between philosophical and biological approaches to this concept. He also reviews the array of current definitions. Species is a benchmark exploration and clarification of a concept fundamental to the past, present, and future of the natural sciences.

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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 )