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Bibliography on: Current Literature — Recent Full Contents

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

RJR: Recommended Bibliography 04 Feb 2019 at 16:56 Created: 

Current Literature — Recent Full Contents

Current Literature: Full, recent table-of-contents listings for a few selected journals.

Created with PubMed® Query: 2018[PDAT] AND ( 0003-0147[issn] or 0006-3568[issn] or 0006-8977[issn] or 0012-1606[issn] or 0014-3820[issn] or 0022-0930[issn] or 0022-2844[issn] or 0025-9241[issn] or 0028-0836[issn] or 0031-8248[issn] or 0033-5770[issn] or 0039-3681[issn] or 0047-2484[issn] or 0066-4154[issn] or 0066-4162[issn] or 0066-4197[issn] or 0066-4227[issn] or 0068-6735[issn] or 0071-3260[issn] or 0085-0748[issn] or 0090-4996[issn] or 0095-134x[issn] or 0165-0157[issn] or 0168-6445[issn] or 0168-6496[issn] or 0168-9525[issn] or 0169-3867[issn] or 0169-5347[issn] or 0169-6149[issn] or 0269-7653[issn] or 0343-8651[issn] or 0346-8313[issn] or 0378-2697[issn] or 0393-9375[issn] or 0394-9370[issn] or 0737-4038[issn] or 0743-4634[issn] or 0923-2508[issn] or 0947-5745[issn] or 0949-944x[issn] or 0960-8788[issn] or 0962-8436[issn] or 0966-842x[issn] or 0967-3849[issn] or 0972-7736[issn] or 0972-8422[issn] or 1010-061x[issn] or 1055-7903[issn] or 1060-1538[issn] or 1061-4036[issn] or 1064-7554[issn] or 1081-0706[issn] or 1090-5138[issn] or 1091-6490[issn] or 1095-9203[issn] or 1121-7138[issn] or 1176-9343[issn] or 1369-5274[issn] or 1369-8486[issn] or 1399-560x[issn] or 1433-8319[issn] or 1439-6092[issn] or 1462-2912[issn] or 1464-7931[issn] or 1466-5026[issn] or 1471-0056[issn] or 1471-2091[issn] or 1471-2105[issn] or 1471-2121[issn] or 1471-213x[issn] or 1471-2148[issn] or 1471-2156[issn] or 1471-2164[issn] or 1471-2180[issn] or 1471-2199[issn] or 1471-2229[issn] or 1471-4922[issn] or 1472-6785[issn] or 1474-7049[issn] or 1520-541x[issn] or 1522-0613[issn] or 1527-8204[issn] or 1543-5008[issn] or 1543-592x[issn] or 1552-4884[issn] or 1552-5007[issn] or 1661-5425[issn] or 1674-4918[issn] or 1740-1526[issn] or 1741-7007[issn] or 1752-0509[issn] or 1752-4571[issn] or 1753-6561[issn] or 1756-0500[issn] or 1758-2229[issn] or 1759-6653[issn] or 1933-5377[issn] or 1935-7877[issn] or 1936-6426[issn] or 1941-1405[issn] or 1943-0264[issn] or 1944-3277[issn] or 2036-2641[issn] or 2041-210x[issn] or 2045-7758[issn] or 2049-2618[issn] or 2050-6201[issn] or 2058-5276[issn] or 2090-8032[issn] or 2163-9434[issn] or 2165-3402[issn] or 2210-6502[issn] or 2296-701x[issn] or 2326-8298[issn] or 2329-9002[issn] or 2333-9683[issn] or 2397-334x[issn] or freeble ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-02-01

Nesse RM (2019)

Tinbergen's four questions: Two proximate, two evolutionary.

Evolution, medicine, and public health, 2019(1):2 pii:eoy035.

RevDate: 2019-02-01

Nesse RM (2019)

The smoke detector principle: Signal detection and optimal defense regulation.

Evolution, medicine, and public health, 2019(1):1 pii:eoy034.

RevDate: 2019-02-01

Brady SP, Monosson E, Matson C, et al (2019)

Fundamental and applied pursuits in evolutionary toxicology are mutually beneficial: A reply to Hahn (2018).

Evolutionary applications, 12(2):353 pii:EVA12710.

RevDate: 2019-02-01

Hahn ME (2019)

Evolutionary concepts can benefit both fundamental research and applied research in toxicology (A comment on Brady et al. 2017).

Evolutionary applications, 12(2):350-352 pii:EVA12695.

RevDate: 2019-02-01

Kim J, Ni G, Kim T, et al (2019)

Phylogeography of the highly invasive sugar beet nematode, Heterodera schachtii (Schmidt, 1871), based on microsatellites.

Evolutionary applications, 12(2):324-336 pii:EVA12719.

Plant-parasitic nematodes (PPNs) threaten crop production worldwide. Yet few studies have examined their intraspecific genetic diversity or patterns of invasion, critical data for managing the spread of these cryptic pests. The sugar beet nematode Heterodera schachtii, a global invader that parasitizes over 200 plant species, represents a model for addressing important questions about the invasion genetics of PPNs. Here, a phylogeographic study using 15 microsatellite markers was conducted on 231 H. schachtii individuals sampled from four continents, and invasion history was reconstructed through an approximate Bayesian computation approach, with emphasis on the origin of newly discovered populations in Korea. Multiple analyses confirmed the existence of cryptic lineages within this species, with the Korean populations comprising one group (group 1) and the populations from Europe, Australia, North America, and western Asia comprising another (group 2). No multilocus genotypes were shared between the two groups, and large genetic distance was inferred between them. Population subdivision was also revealed among the populations of group 2 in both population comparison and STRUCTURE analyses, mostly due to different divergent times between invasive and source populations. The Korean populations showed substantial genetic homogeneity and likely originated from a single invasion event. However, none of the other studied populations were implicated as the source. Further studies with additional populations are needed to better describe the distribution of the potential source population for the East Asian lineage.

RevDate: 2019-02-01

Lippens C, Guivier E, Reece SE, et al (2019)

Early Plasmodium-induced inflammation does not accelerate aging in mice.

Evolutionary applications, 12(2):314-323 pii:EVA12718.

Aging is associated with a decline of performance leading to reduced reproductive output and survival. While the antagonistic pleiotropy theory of aging has attracted considerable attention, the molecular/physiological functions underlying the early-life benefits/late-life costs paradigm remain elusive. We tested the hypothesis that while early activation of the inflammatory response confers benefits in terms of protection against infection, it also incurs costs in terms of reduced reproductive output at old age and shortened longevity. We infected mice with the malaria parasite Plasmodium yoelii and increased the inflammatory response using an anti-IL-10 receptor antibody treatment. We quantified the benefits and costs of the inflammatory response during the acute phase of the infection and at old age. In agreement with the antagonistic pleiotropy hypothesis, the inflammatory response provided an early-life benefit, since infected mice that were treated with anti-IL-10 receptor antibodies had reduced parasite density and anemia. However, at old age, mice in all treatment groups had similar levels of C-reactive protein, reproductive output, survival rate, and lifespan. Overall, our results do not support the hypothesis that the benefits of a robust response to malaria infection in early life incur longer term fitness costs.

RevDate: 2019-02-01

Raynes Y, DM Weinreich (2019)

Genomic clustering of fitness-affecting mutations favors the evolution of chromosomal instability.

Evolutionary applications, 12(2):301-313 pii:EVA12717.

Most solid cancers are characterized by chromosomal instability (CIN)-an elevated rate of large-scale chromosomal aberrations and ploidy changes. Chromosomal instability may arise through mutations in a range of genomic integrity loci and is commonly associated with fast disease progression, poor prognosis, and multidrug resistance. However, the evolutionary forces promoting CIN-inducing alleles (hereafter, CIN mutators) during carcinogenesis remain poorly understood. Here, we develop a stochastic, individual-based model of indirect selection experienced by CIN mutators via genomic associations with fitness-affecting mutations. Because mutations associated with CIN affect large swaths of the genome and have the potential to simultaneously comprise many individual loci, we show that indirect selection on CIN mutators is critically influenced by genome organization. In particular, we find strong support for a key role played by the spatial clustering of loci with either beneficial or deleterious mutational effects. Genomic clustering of selected loci allows CIN mutators to generate favorable chromosomal changes that facilitate their rapid expansion within a neoplasm and, in turn, accelerate carcinogenesis. We then examine the distribution of oncogenic and tumor-suppressing loci in the human genome and find both to be potentially more clustered along the chromosome than expected, leading us to speculate that human genome may be susceptible to CIN hitchhiking. More quantitative data on fitness effects of individual mutations will be necessary, though, to assess the true levels of clustering in the human genome and the effectiveness of indirect selection for CIN. Finally, we use our model to examine how therapeutic strategies that increase the deleterious burden of genetically unstable cells by raising either the rate of CIN or the cost of deleterious mutations affect CIN evolution. We find that both can inhibit CIN hitchhiking and delay carcinogenesis in some circumstances, yet, in line with earlier work, we find the latter to be considerably more effective.

RevDate: 2019-02-01

Chen M, Su G, Fu J, et al (2019)

Introgression of Chinese haplotypes contributed to the improvement of Danish Duroc pigs.

Evolutionary applications, 12(2):292-300 pii:EVA12716.

The distribution of Asian ancestry in the genome of Danish Duroc pigs was investigated using whole-genome sequencing data from European wild boars, Danish Duroc, Chinese Meishan and Bamaxiang pigs. Asian haplotypes deriving from Meishan and Bamaxiang occur widely across the genome. Signatures of selection on Asian haplotypes are common in the genome, but few of these haplotypes have been fixed. By defining 50-kb windows with more than 50% Chinese ancestry, which did not exhibit extreme genetic differentiation between Meishan and Bamaxiang as candidate regions, the enrichment of quantitative trait loci in candidate regions supports that Asian haplotypes under selection play an important role in contributing genetic variation underlying production, reproduction, meat and carcass, and exterior traits. Gene annotation of regions with the highest proportion of Chinese ancestry revealed genes of biological interest, such as NR6A1. Further haplotype clustering analysis suggested that a haplotype of Chinese origin around the NR6A1 gene was introduced to Europe and then underwent a selective sweep in European pigs. Besides, functional genes in candidate regions, such as AHR and PGRMC2, associated with fertility, and SAL1, associated with meat quality, were identified. Our results demonstrate the contribution of Asian haplotypes to the genomes of European pigs. Findings herein facilitate further genomic studies such as genomewide association study and genomic prediction by providing ancestry information of variants.

RevDate: 2019-02-01

Grueber CE, Fox S, McLennan EA, et al (2019)

Complex problems need detailed solutions: Harnessing multiple data types to inform genetic management in the wild.

Evolutionary applications, 12(2):280-291 pii:EVA12715.

For bottlenecked populations of threatened species, supplementation often leads to improved population metrics (genetic rescue), provided that guidelines can be followed to avoid negative outcomes. In cases where no "ideal" source populations exist, or there are other complicating factors such as prevailing disease, the benefit of supplementation becomes uncertain. Bringing multiple data and analysis types together to plan genetic management activities can help. Here, we consider three populations of Tasmanian devil, Sarcophilus harrisii, as candidates for genetic rescue. Since 1996, devil populations have been severely impacted by devil facial tumour disease (DFTD), causing significant population decline and fragmentation. Like many threatened species, the key threatening process for devils cannot currently be fully mitigated, so species management requires a multifaceted approach. We examined diversity of 31 putatively neutral and 11 MHC-linked microsatellite loci of three remnant wild devil populations (one sampled at two time-points), alongside computational diversity projections, parameterized by field data from DFTD-present and DFTD-absent sites. Results showed that populations had low diversity, connectivity was poor, and diversity has likely decreased over the last decade. Stochastic simulations projected further diversity losses. For a given population size, the effects of DFTD on population demography (including earlier age at death and increased female productivity) did not impact diversity retention, which was largely driven by final population size. Population sizes ≥500 (depending on the number of founders) were necessary for maintaining diversity in otherwise unmanaged populations, even if DFTD is present. Models indicated that smaller populations could maintain diversity with ongoing immigration. Taken together, our results illustrate how multiple analysis types can be combined to address complex population genetic challenges.

RevDate: 2019-02-01

Nietlisbach P, Muff S, Reid JM, et al (2019)

Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load.

Evolutionary applications, 12(2):266-279 pii:EVA12713.

Inbreeding depression, the deterioration in mean trait value in progeny of related parents, is a fundamental quantity in genetics, evolutionary biology, animal and plant breeding, and conservation biology. The magnitude of inbreeding depression can be quantified by the inbreeding load, typically measured in numbers of lethal equivalents, a population genetic quantity that allows for comparisons between environments, populations or species. However, there is as yet no quantitative assessment of which combinations of statistical models and metrics of inbreeding can yield such estimates. Here, we review statistical models that have been used to estimate inbreeding load and use population genetic simulations to investigate how unbiased estimates can be obtained using genomic and pedigree-based metrics of inbreeding. We use simulated binary viability data (i.e., dead versus alive) as our example, but the concepts apply to any trait that exhibits inbreeding depression. We show that the increasingly popular generalized linear models with logit link do not provide comparable and unbiased population genetic measures of inbreeding load, independent of the metric of inbreeding used. Runs of homozygosity result in unbiased estimates of inbreeding load, whereas inbreeding measured from pedigrees results in slight overestimates. Due to widespread use of models that do not yield unbiased measures of the inbreeding load, some estimates in the literature cannot be compared meaningfully. We surveyed the literature for reliable estimates of the mean inbreeding load from wild vertebrate populations and found an average of 3.5 haploid lethal equivalents for survival to sexual maturity. To obtain comparable estimates, we encourage researchers to use generalized linear models with logarithmic links or maximum-likelihood estimation of the exponential equation, and inbreeding coefficients calculated from runs of homozygosity, provided an assembled reference genome of sufficient quality and enough genetic marker data are available.

RevDate: 2019-02-01

Crandall ED, Toonen RJ, ToBo Laboratory, et al (2019)

A coalescent sampler successfully detects biologically meaningful population structure overlooked by F-statistics.

Evolutionary applications, 12(2):255-265 pii:EVA12712.

Assessing the geographic structure of populations has relied heavily on Sewell Wright's F-statistics and their numerous analogues for many decades. However, it is well appreciated that, due to their nonlinear relationship with gene flow, F-statistics frequently fail to reject the null model of panmixia in species with relatively high levels of gene flow and large population sizes. Coalescent genealogy samplers instead allow a model-selection approach to the characterization of population structure, thereby providing the opportunity for stronger inference. Here, we validate the use of coalescent samplers in a high gene flow context using simulations of a stepping-stone model. In an example case study, we then re-analyze genetic datasets from 41 marine species sampled from throughout the Hawaiian archipelago using coalescent model selection. Due to the archipelago's linear nature, it is expected that most species will conform to some sort of stepping-stone model (leading to an expected pattern of isolation by distance), but F-statistics have only supported this inference in ~10% of these datasets. Our simulation analysis shows that a coalescent sampler can make a correct inference of stepping-stone gene flow in nearly 100% of cases where gene flow is ≤100 migrants per generation (equivalent to FST = 0.002), while F-statistics had mixed results. Our re-analysis of empirical datasets found that nearly 70% of datasets with an unambiguous result fit a stepping-stone model with varying population sizes and rates of gene flow, although 37% of datasets yielded ambiguous results. Together, our results demonstrate that coalescent samplers hold great promise for detecting weak but meaningful population structure, and defining appropriate management units.

RevDate: 2019-02-01

Beacham TD, Wallace C, Jonsen K, et al (2019)

Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada.

Evolutionary applications, 12(2):230-254 pii:EVA12711.

Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage-based tagging (PBT) may overcome problems associated with coded-wire tag-based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded-wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774-individual, 267-population baseline available for assignment. Coho salmon from un-CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT-GSI system of identification to individuals in 2017 fisheries and escapements provided high-resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian-origin coho salmon relative to CWTs, and an opportunity for a genetic-based system to replace the current CWT system for coho salmon assessment.

RevDate: 2019-02-01

DeFilippo LB, Schindler DE, Ohlberger J, et al (2019)

Recruitment variation disrupts the stability of alternative life histories in an exploited salmon population.

Evolutionary applications, 12(2):214-229 pii:EVA12709.

Males of many fish species exhibit alternative reproductive tactics, which can influence the maturation schedules, fishery productivity, and resilience to harvest of exploited populations. While alternative mating phenotypes can persist in stable equilibria through frequency-dependent selection, shifts in tactic frequencies have been observed and can have substantial consequences for fisheries. Here, we examine the dynamics of precocious sneaker males called "jacks" in a population of sockeye salmon (Oncorhynchus nerka) from Frazer Lake, Alaska. Jacks, which are of little commercial value due to their small body sizes, have recently been observed at unusually high levels in this stock, degrading the value of regional fisheries. To inform future strategies for managing the prevalence of jacks, we used long-term monitoring data to identify what regulates the frequencies of alternative male phenotypes in the population over time. Expression of the jack life history could not be explained by environmental factors expected to influence juvenile body condition and maturation probability. Instead, we found a strong positive association between the proportion of individuals maturing as jacks within a cohort and the prevalence of jacks among the males that sired that cohort. Moreover, due to differences in age-at-maturity between male phenotypes, and large interannual variability in recruitment strength, jacks from strong year-classes often spawn among older males from the weaker recruitments of earlier cohorts. Through such "cohort mismatches," which are amplified by size-selective harvest on older males, jacks frequently achieve substantial representation in the breeding population, and likely high total fertilizations. The repeated occurrence of these cohort mismatches appears to disrupt the stabilizing influence of frequency-dependent selection, allowing the prevalence of jacks to exceed what might be expected under equilibrium conditions. These results emphasize that the dynamics of alternative life histories can profoundly influence fishery performance and should be explicitly considered in the management of exploited populations.

RevDate: 2019-02-01

Jahner JP, Matocq MD, Malaney JL, et al (2019)

The genetic legacy of 50 years of desert bighorn sheep translocations.

Evolutionary applications, 12(2):198-213 pii:EVA12708.

Conservation biologists have increasingly used translocations to mitigate population declines and restore locally extirpated populations. Genetic data can guide the selection of source populations for translocations and help evaluate restoration success. Bighorn sheep (Ovis canadensis) are a managed big game species that suffered widespread population extirpations across western North America throughout the early 1900s. Subsequent translocation programs have successfully re-established many formally extirpated bighorn herds, but most of these programs pre-date genetically informed management practices. The state of Nevada presents a particularly well-documented case of decline followed by restoration of extirpated herds. Desert bighorn sheep (O. c. nelsoni) populations declined to less than 3,000 individuals restricted to remnant herds in the Mojave Desert and a few locations in the Great Basin Desert. Beginning in 1968, the Nevada Department of Wildlife translocated ~2,000 individuals from remnant populations to restore previously extirpated areas, possibly establishing herds with mixed ancestries. Here, we examined genetic diversity and structure among remnant herds and the genetic consequences of translocation from these herds using a genotyping-by-sequencing approach to genotype 17,095 loci in 303 desert bighorn sheep. We found a signal of population genetic structure among remnant Mojave Desert populations, even across geographically proximate mountain ranges. Further, we found evidence of a genetically distinct, potential relict herd from a previously hypothesized Great Basin lineage of desert bighorn sheep. The genetic structure of source herds was clearly reflected in translocated populations. In most cases, herds retained genetic evidence of multiple translocation events and subsequent admixture when founded from multiple remnant source herds. Our results add to a growing literature on how population genomic data can be used to guide and monitor restoration programs.

RevDate: 2019-02-01

Gous A, Swanevelder DZH, Eardley CD, et al (2019)

Plant-pollinator interactions over time: Pollen metabarcoding from bees in a historic collection.

Evolutionary applications, 12(2):187-197 pii:EVA12707.

Pollination is a key component in agricultural food production and ecosystem maintenance, with plant-pollinator interactions an important research theme in ecological and evolutionary studies. Natural history collections provide unique access to samples collected at different spatial and temporal scales. Identification of the plant origins of pollen trapped on the bodies of pollinators in these collections provides insight into historic plant communities and pollinators' preferred floral taxa. In this study, pollen was sampled from Megachile venusta Smith bees from the National Collection of Insects, South Africa, spanning 93 years. Three barcode regions, the internal transcribed spacer 1 and 2 (ITS1 and ITS2) and ribulose-1,5-biphosphate carboxylase (rbcL), were sequenced from mixed pollen samples using a next-generation sequencing approach (MiSeq, Illumina). Sequenced reads were compared to sequence reference databases that were generated by extracting sequence and taxonomic data from GenBank. ITS1 and ITS2 were amplified successfully across all (or most) samples, while rbcL performed inconsistently. Age of sample had no impact on sequencing success. Plant classification was more informative using ITS2 than ITS1 barcode data. This study also highlights the need for comprehensive reference databases as limited local plant sequence representation in reference databases resulted in higher-level taxon classifications being more confidently interpreted. The results showed that small, insect-carried pollen samples from historic bee specimens collected from as early as 1914 can be used to obtain pollen metabarcodes. DNA metabarcoding of mixed origin pollen samples provided a faster, more accurate method of determining pollen provenance, without the need for expert palynologists. The use of historic collections to sample pollen directly from pollinators provided additional value to these collections. Sampling pollen from historic collections can potentially provide the spatial and temporal scales for investigations into changes in plant community structure or pollinator floral choice in the face of global climate change.

RevDate: 2019-02-01

Robertson BA, G Horváth (2019)

Color polarization vision mediates the strength of an evolutionary trap.

Evolutionary applications, 12(2):175-186 pii:EVA12690.

Evolutionary traps are scenarios in which animals are fooled by rapidly changing conditions into preferring poor-quality resources over those that better improve survival and reproductive success. The maladaptive attraction of aquatic insects to artificial sources of horizontally polarized light (e.g., glass buildings, asphalt roads) has become a first model system by which scientists can investigate the behavioral mechanisms that cause traps to occur. We employ this field-based system to experimentally investigate (a) in which portion(s) of the spectrum are polarizationally water-imitating reflectors attractive to nocturnal terrestrial and aquatics insects, and (b) which modern lamp types result in greater attraction in this typical kind of nocturnal polarized light pollution. We found that most aquatic taxa exhibited preferences for lamps based upon their color spectra, most having lowest preference for lamps emitting blue and red light. Yet, despite previously established preference for higher degrees of polarization of reflected light, most aquatic insect families were attracted to traps based upon their unpolarized spectrum. Chironomid midges, alone, showed a preference for the color of lamplight in both the horizontally polarized and unpolarized spectra indicating only this family has evolved to use light in this color range as a source of information to guide its nocturnal habitat selection. These results demonstrate that the color of artificial lighting can exacerbate or reduce its attractiveness to aquatic insects, but that the strength of attractiveness of nocturnal evolutionary traps, and so their demographic consequences, is primarily driven by unpolarized light pollution. This focuses management attention on limiting broad-spectrum light pollution, as well as its intentional deployment to attract insects back to natural habitats.

RevDate: 2019-02-01

Warwell MV, RG Shaw (2019)

Phenotypic selection on ponderosa pine seed and seedling traits in the field under three experimentally manipulated drought treatments.

Evolutionary applications, 12(2):159-174 pii:EVA12685.

Drought-related selection during seedling emergence and early development may play a strong role in adaptation. Yet this process is poorly understood and particularly so in relation to ongoing climate change. To evaluate drought-induced differences in selection during early life stages, a total of 50 maternal families sampled from three climatically disparate ponderosa pine (Pinus ponderosa Doug.) populations were grown from seed in two common garden field experiments at a location that was warmer and drier than seed origins. Three drought treatments were imposed experimentally. Phenotypic selection was assessed by relating plant fitness measured as survival or unconditional expected height at age 3 to seed density (mass per unit volume), date of emergence, and timing of shoot elongation. In the year of emergence from seed, differential mortality was particularly strong and clearly indicated selection. In contrast, selection in subsequent years was far less pronounced. Phenotypes with high seed density, an intermediate but relatively early emergence date, and high 2nd-year early-season shoot elongation exhibited the greatest estimated fitness under drought. The form of selection varied among seed sources in relation to drought treatment. Selection was generally more acute in the cases of greatest difference between drought treatment and climatic patterns of precipitation at the site of seed origin. These results suggest that populations of ponderosa pine are differentially adapted to drought patterns associated with the climate of their origin. To the extent that the phenotypic traits examined are heritable or correlated with heritable traits, our results provide insight into how tree populations may evolve in response to drought.

RevDate: 2019-02-01

Togawa M, Endo Y, Suzuki N, et al (2018)

Identification of Sox10-positive cells at the dorsal fin base of juvenile flounder that are correlated with blind-side skin ectopic pigmentation.

Journal of experimental zoology. Part B, Molecular and developmental evolution, 330(8):427-437.

Flounder develop left-right asymmetric body color, with a dark ocular side and white blind side. However, ectopic pigmentation often occurs on the blind side when juveniles are reared in tanks. To examine the developmental mechanism underlying ectopic pigmentation, we first examined the pigmentation process on the blind side and the localization of chromatoblasts during spontaneous and regeneration-stimulated ectopic pigmentation. Wild-caught juveniles that had completed metamorphosis in a natural environment were reared in tanks, where they exhibited ectopic pigmentation on the blind side that was initiated at the base of the dorsal and anal fins, with chromatoblasts appearing at the edges of scales and melanophores spreading on the scale papilla beneath the epidermis. During tissue regeneration at the base of the dorsal fin in juvenile before ectopic pigmentation, melanophores and chromatoblasts newly appeared on regenerated blind-side skin, resulting in rapid pigmentation at the wounded site. During regeneration-stimulated pigmentation, gch2-positive chromatoblasts were detected only under the regenerated epidermis. Next, we found that Sox10-positive cells were localized in connective tissue at the base of the dorsal fin and that when connective tissue was labeled with DiO, DiO-labeled melanophores appeared in regenerated skin of the blind side after wounding. Therefore, we conclude that in flounder juveniles, Sox10-positive progenitors of pigment cell lineage reside at the base of the dorsal fin and start migrating to the blind-side skin in response to specific stimuli, resulting in ectopic pigmentation. Ectopic pigmentation in flounder could be a good model for examining the flexibility of pigment cell differentiation.

RevDate: 2019-01-25

Yücel O, Borgert SR, Poehlein A, et al (2018)

The 7α-hydroxysteroid dehydratase Hsh2 is essential for anaerobic degradation of the steroid skeleton of 7α-hydroxyl bile salts in the novel denitrifying bacterium Azoarcus sp. strain Aa7.

Environmental microbiology [Epub ahead of print].

Bile salts are steroid compounds from the digestive tract of vertebrates and enter the environment via defecation. Many aerobic bile-salt degrading bacteria are known but no bacteria that completely degrade bile salts under anoxic conditions have been isolated so far. In this study, the facultatively anaerobic Betaproteobacterium Azoarcus sp. strain Aa7 was isolated that grew with bile salts as sole carbon source under anoxic conditions with nitrate as electron acceptor. Phenotypic and genomic characterization revealed that strain Aa7 used the 2,3-seco pathway for the degradation of bile salts as found in other denitrifying steroid-degrading bacteria such as Sterolibacterium denitrificans. Under oxic conditions strain Aa7 used the 9,10-seco pathway as found in, for example, Pseudomonas stutzeri Chol1. Metabolite analysis during anaerobic growth indicated a reductive dehydroxylation of 7α-hydroxyl bile salts. Deletion of the gene hsh2 Aa7 encoding a 7-hydroxysteroid dehydratase led to strongly impaired growth with cholate and chenodeoxycholate but not with deoxycholate lacking a hydroxyl group at C7. The hsh2 Aa7 deletion mutant degraded cholate and chenodeoxycholate to the corresponding C19 -androstadienediones only while no phenotype change was observed during aerobic degradation of cholate. These results showed that removal of the 7α-hydroxyl group was essential for cleavage of the steroid skeleton under anoxic conditions.

RevDate: 2019-01-29

Ferrier-Pagès C, MC Leal (2019)

Stable isotopes as tracers of trophic interactions in marine mutualistic symbioses.

Ecology and evolution, 9(1):723-740 pii:ECE34712.

Mutualistic nutritional symbioses are widespread in marine ecosystems. They involve the association of a host organism (algae, protists, or marine invertebrates) with symbiotic microorganisms, such as bacteria, cyanobacteria, or dinoflagellates. Nutritional interactions between the partners are difficult to identify in symbioses because they only occur in intact associations. Stable isotope analysis (SIA) has proven to be a useful tool to highlight original nutrient sources and to trace nutrients acquired by and exchanged between the different partners of the association. However, although SIA has been extensively applied to study different marine symbiotic associations, there is no review taking into account of the different types of symbiotic associations, how they have been studied via SIA, methodological issues common among symbiotic associations, and solutions that can be transferred from one type of association with another. The present review aims to fill such gaps in the scientific literature by summarizing the current knowledge of how isotopes have been applied to key marine symbioses to unravel nutrient exchanges between partners, and by describing the difficulties in interpreting the isotopic signal. This review also focuses on the use of compound-specific stable isotope analysis and on statistical advances to analyze stable isotope data. It also highlights the knowledge gaps that would benefit from future research.

RevDate: 2019-01-29

Arias-Martorell J (2019)

The morphology and evolutionary history of the glenohumeral joint of hominoids: A review.

Ecology and evolution, 9(1):703-722 pii:ECE34392.

The glenohumeral joint, the most mobile joint in the body of hominoids, is involved in the locomotion of all extant primates apart from humans. Over the last few decades, our knowledge of how variation in its morphological characteristics relates to different locomotor behaviors within extant primates has greatly improved, including features of the proximal humerus and the glenoid cavity of the scapula, as well as the muscles that function to move the joint (the rotator cuff muscles). The glenohumeral joint is a region with a strong morphofunctional signal, and hence, its study can shed light on the locomotor behaviors of crucial ancestral nodes in the evolutionary history of hominoids (e.g., the last common ancestor between humans and chimpanzees). Hominoids, in particular, are distinct in showing round and relatively big proximal humeri with lowered tubercles and flattened and oval glenoid cavities, morphology suited to engage in a wide range of motions, which enables the use of locomotor behaviors such as suspension. The comparison with extant taxa has enabled more informed functional interpretations of morphology in extinct primates, including hominoids, from the Early Miocene through to the emergence of hominins. Here, I review our current understanding of glenohumeral joint functional morphology and its evolution throughout the Miocene and Pleistocene, as well as highlighting the areas where a deeper study of this joint is still needed.

RevDate: 2019-01-29

Fresneau N, W Müller (2019)

Flexible communication within bird families-The consequences of behavioral plasticity for parent-offspring coadaptation.

Ecology and evolution, 9(1):693-702 pii:ECE34796.

Offspring are selected to demand more resources than what is optimal for their parents to provide, which results in a complex and dynamic interplay during parental care. Parent-offspring communication often involves conspicuous begging by the offspring which triggers a parental response, typically the transfer of food. So begging and parental provisioning reciprocally influence each other and are therefore expected to coevolve. There is indeed empirical evidence for covariation of offspring begging and parental provisioning at the phenotypic level. However, whether this reflects genetic correlations of mean levels of behaviors or a covariation of the slopes of offspring demand and parental supply functions (= behavioral plasticity) is not known. The latter has gone rather unnoticed-despite the obvious dynamics of parent-offspring communication. In this study, we measured parental provisioning and begging behavior at two different hunger levels using canaries (Serinus canaria) as a model species. This enabled us to simultaneously study the plastic responses of the parents and the offspring to changes in offspring need. We first tested whether parent and offspring behaviors covary phenotypically. Then, using a covariance partitioning approach, we estimated whether the covariance predominantly occurred at a between-nest level (i.e., indicating a fixed strategy) or at a within-nest level (i.e., reflecting a flexible strategy). We found positive phenotypic covariation of offspring begging and parental provisioning, confirming previous evidence. Yet, this phenotypic covariation was mainly driven by a covariance at the within-nest level. That is parental and offspring behaviors covary because of a plastic behavioral coadjustment, indicating that behavioral plasticity could be a main driver of parent-offspring coadaptation.

RevDate: 2019-01-29

Hill JM, RB Renfrew (2019)

Migratory patterns and connectivity of two North American grassland bird species.

Ecology and evolution, 9(1):680-692 pii:ECE34795.

Effective management and conservation of migratory bird populations require knowledge and incorporation of their movement patterns and space use throughout the annual cycle. To investigate the little-known migratory patterns of two grassland bird species, we deployed 180 light-level geolocators on Grasshopper Sparrows (Ammodramus savannarum) and 29 Argos-GPS tags on Eastern Meadowlarks (Sturnella magna) at Konza Prairie, Kansas, USA, and six US Department of Defense (DoD) installations distributed across the species' breeding ranges. We analyzed location data from 34 light-level geolocators and five Argos-GPS tags attached for 1 year to Grasshopper Sparrows and Eastern Meadowlarks, respectively. Grasshopper Sparrows were present on the breeding grounds from mid-April through early October, substantially longer than previously estimated, and migrated on average ~2,500 km over ~30 days. Grasshopper Sparrows exhibited strong migratory connectivity only at a continental scale. The North American Great Lakes region likely serves as a migratory divide for Midwest and East Coast Grasshopper Sparrows; Midwest populations (Kansas, Wisconsin, and North Dakota; n = 13) largely wintered in Texas or Mexico, whereas East Coast populations (Maryland and Massachusetts, n = 20) wintered in the northern Caribbean or Florida. Our data from Eastern Meadowlarks provided evidence for a diversity of stationary and short- and long-distance migration strategies. By providing the most extensive examination of the nonbreeding movement ecology for these two North American grassland bird species to date, we refine information gaps and provide key insight for their management and conservation.

RevDate: 2019-01-29

Barthel LMF, Hofer H, A Berger (2019)

An easy, flexible solution to attach devices to hedgehogs (Erinaceus europaeus) enables long-term high-resolution studies.

Ecology and evolution, 9(1):672-679 pii:ECE34794.

Bio-logging is an essential tool for the investigation of behavior, ecology, and physiology of wildlife. This burgeoning field enables the improvement of population monitoring and conservation efforts, particularly for small, elusive animals where data collection is difficult. Device attachment usually requires species-specific solutions to ensure that data loggers exert minimal influence on the animal's behavior and physiology, and ensure high reliability of data capture. External features or peculiar body shapes often make securing devices difficult for long-term monitoring, as in the case with small spiny mammals. Here, we present a method that enables high-resolution, long-term investigations of European hedgehogs (Erinaceus europaeus) via GPS and acceleration loggers. We collected data from 17 wild hedgehogs with devices attached between 9 and 42 days. Our results showed that hedgehogs behaved naturally; as individuals curled, moved through dense vegetation, slipped under fences and built regular day nests without any indication of impediment. Our novel method makes it possible to not only attach high-precision devices for substantially longer than previous efforts, but enables detachment and reattachment of devices to the same individual. This makes it possible to quickly respond to unforeseen events and exchange devices, and overcomes the issue of short battery life common to many lightweight loggers.

RevDate: 2019-01-29

Reisch C, C Schmid (2019)

Species and genetic diversity are not congruent in fragmented dry grasslands.

Ecology and evolution, 9(1):664-671 pii:ECE34791.

Biological diversity comprises both species diversity (SD) and genetic diversity (GD), and it has been postulated that both levels of diversity depend on similar mechanisms. Species-genetic diversity correlations (SGDC) are therefore supposed to be generally positive. However, in contrast to theory, empirical data are contradictory. Furthermore, there is a pronounced lack of multispecies studies including also the ecological factors potentially driving species and genetic diversity. We analyzed the relationship between the species diversity of dry grasslands and the genetic diversity of several dry grassland plant species, therefore, in the context of habitat fragmentation and habitat conditions. Our study revealed a lack of correlation between species and genetic diversity. We demonstrated previously that SD mainly depends on habitat conditions (vegetation height and cover of litter), whereas GD is significantly affected by habitat fragmentation (distance to the nearest dry grassland in 1830 and connectivity in 2013). This seems to be the main reason why SD and GD are not congruent in fragmented grasslands. Our results support, hence, the observation that positive SGDCs can mainly be found in natural, island-like study systems in equilibrium and at similar levels of heterogeneity. In fragmented dry grassland ecosystems, which differ in heterogeneity, this state of equilibrium may not have been reached mitigating the positive relationship between SD and GD. From our study, it can be concluded that in fragmented dry grasslands, the protection of SD does not necessarily ensure the conservation of GD.

RevDate: 2019-01-29

Pennino MG, Paradinas I, Illian JB, et al (2019)

Accounting for preferential sampling in species distribution models.

Ecology and evolution, 9(1):653-663 pii:ECE34789.

Species distribution models (SDMs) are now being widely used in ecology for management and conservation purposes across terrestrial, freshwater, and marine realms. The increasing interest in SDMs has drawn the attention of ecologists to spatial models and, in particular, to geostatistical models, which are used to associate observations of species occurrence or abundance with environmental covariates in a finite number of locations in order to predict where (and how much of) a species is likely to be present in unsampled locations. Standard geostatistical methodology assumes that the choice of sampling locations is independent of the values of the variable of interest. However, in natural environments, due to practical limitations related to time and financial constraints, this theoretical assumption is often violated. In fact, data commonly derive from opportunistic sampling (e.g., whale or bird watching), in which observers tend to look for a specific species in areas where they expect to find it. These are examples of what is referred to as preferential sampling, which can lead to biased predictions of the distribution of the species. The aim of this study is to discuss a SDM that addresses this problem and that it is more computationally efficient than existing MCMC methods. From a statistical point of view, we interpret the data as a marked point pattern, where the sampling locations form a point pattern and the measurements taken in those locations (i.e., species abundance or occurrence) are the associated marks. Inference and prediction of species distribution is performed using a Bayesian approach, and integrated nested Laplace approximation (INLA) methodology and software are used for model fitting to minimize the computational burden. We show that abundance is highly overestimated at low abundance locations when preferential sampling effects not accounted for, in both a simulated example and a practical application using fishery data. This highlights that ecologists should be aware of the potential bias resulting from preferential sampling and account for it in a model when a survey is based on non-randomized and/or non-systematic sampling.

RevDate: 2019-01-29

Beaugeard E, Brischoux F, Henry PY, et al (2019)

Does urbanization cause stress in wild birds during development? Insights from feather corticosterone levels in juvenile house sparrows (Passer domesticus).

Ecology and evolution, 9(1):640-652 pii:ECE34788.

Urban landscapes are associated with abiotic and biotic environmental changes that may result in potential stressors for wild vertebrates. Urban exploiters have physiological, morphological, and behavioral adaptations to live in cities. However, there is increasing evidence that urban exploiters themselves can suffer from urban conditions, especially during specific life-history stages. We looked for a link between the degree of urbanization and the level of developmental stress in an urban exploiter (the house sparrow, Passer domesticus), which has recently been declining in multiple European cities (e.g., London, UK). Specifically, we conducted a large-scale study and sampled juvenile sparrows in 11 urban and rural sites to evaluate their feather corticosterone (CORT) levels. We found that juvenile feather CORT levels were positively correlated with the degree of urbanization, supporting the idea that developing house sparrows may suffer from urban environmental conditions. However, we did not find any correlation between juvenile feather CORT levels and body size, mass, or body condition. This suggests either that the growth and condition of urban sparrows are not impacted by elevated developmental CORT levels, or that urban sparrows may compensate for developmental constraints once they have left the nest. Although feather CORT levels were not correlated with baseline CORT levels, we found that feather CORT levels were slightly and positively correlated with the CORT stress response in juveniles. This suggests that urban developmental conditions may potentially have long-lasting effects on stress physiology and stress sensitivity in this urban exploiter.

RevDate: 2019-01-29

Rytkönen S, Vesterinen EJ, Westerduin C, et al (2019)

From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web.

Ecology and evolution, 9(1):631-639 pii:ECE34787.

Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our understanding of biodiversity and ecosystem functioning. The research of prey preferences of different predators requires knowledge not only of the prey consumed, but also of what is available. In this study, we applied DNA metabarcoding to analyze the diet of 4 bird species (willow tits Poecile montanus, Siberian tits Poecile cinctus, great tits Parus major and blue tits Cyanistes caeruleus) by using the feces of nestlings. The availability of their assumed prey (Lepidoptera) was determined from feces of larvae (frass) collected from the main foraging habitat, birch (Betula spp.) canopy. We identified 53 prey species from the nestling feces, of which 11 (21%) were also detected from the frass samples (eight lepidopterans). Approximately 80% of identified prey species in the nestling feces represented lepidopterans, which is in line with the earlier studies on the parids' diet. A subsequent laboratory experiment showed a threshold for fecal sample size and the barcoding success, suggesting that the smallest frass samples do not contain enough larval DNA to be detected by high-throughput sequencing. To summarize, we apply metabarcoding for the first time in a combined approach to identify available prey (through frass) and consumed prey (via nestling feces), expanding the scope and precision for future dietary studies on insectivorous birds.

RevDate: 2019-01-29

Studd EK, Landry-Cuerrier M, Menzies AK, et al (2019)

Behavioral classification of low-frequency acceleration and temperature data from a free-ranging small mammal.

Ecology and evolution, 9(1):619-630 pii:ECE34786.

The miniaturization and affordability of new technology is driving a biologging revolution in wildlife ecology with use of animal-borne data logging devices. Among many new biologging technologies, accelerometers are emerging as key tools for continuously recording animal behavior. Yet a critical, but under-acknowledged consideration in biologging is the trade-off between sampling rate and sampling duration, created by battery- (or memory-) related sampling constraints. This is especially acute among small animals, causing most researchers to sample at high rates for very limited durations. Here, we show that high accuracy in behavioral classification is achievable when pairing low-frequency acceleration recordings with temperature. We conducted 84 hr of direct behavioral observations on 67 free-ranging red squirrels (200-300 g) that were fitted with accelerometers (2 g) recording tri-axial acceleration and temperature at 1 Hz. We then used a random forest algorithm and a manually created decision tree, with variable sampling window lengths, to associate observed behavior with logger recorded acceleration and temperature. Finally, we assessed the accuracy of these different classifications using an additional 60 hr of behavioral observations, not used in the initial classification. The accuracy of the manually created decision tree classification using observational data varied from 70.6% to 91.6% depending on the complexity of the tree, with increasing accuracy as complexity decreased. Short duration behavior like running had lower accuracy than long-duration behavior like feeding. The random forest algorithm offered similarly high overall accuracy, but the manual decision tree afforded the flexibility to create a hierarchical tree, and to adjust sampling window length for behavioral states with varying durations. Low frequency biologging of acceleration and temperature allows accurate behavioral classification of small animals over multi-month sampling durations. Nevertheless, low sampling rates impose several important limitations, especially related to assessing the classification accuracy of short duration behavior.

RevDate: 2019-01-29

Knapp JL, Becher MA, Rankin CC, et al (2019)

Bombus terrestris in a mass-flowering pollinator-dependent crop: A mutualistic relationship?.

Ecology and evolution, 9(1):609-618 pii:ECE34784.

Bumblebees (Bombus spp.) rely on an abundant and diverse selection of floral resources to meet their nutritional requirements. In farmed landscapes, mass-flowering crops can provide an important forage resource for bumblebees, with increased visitation from bumblebees into mass-flowering crops having an additional benefit to growers who require pollination services. This study explores the mutualistic relationship between Bombus terrestris L. (buff-tailed bumblebee), a common species in European farmland, and the mass-flowering crop courgette (Cucurbita pepo L.) to see how effective B. terrestris is at pollinating courgette and in return how courgette may affect B. terrestris colony dynamics. By combining empirical data on nectar and pollen availability with model simulations using the novel bumblebee model Bumble-BEEHAVE, we were able to quantify and simulate for the first time, the importance of courgette as a mass-flowering forage resource for bumblebees. Courgette provides vast quantities of nectar to ensure a high visitation rate, which combined with abundant pollen grains, enables B. terrestris to have a high pollination potential. While B. terrestris showed a strong fidelity to courgette flowers for nectar, courgette pollen was not found in any pollen loads from returning foragers. Nonetheless, model simulations showed that early season courgette (nectar) increased the number of hibernating queens, colonies, and adult workers in the modeled landscapes. Synthesis and applications. Courgette has the potential to improve bumblebee population dynamics; however, the lack of evidence of the bees collecting courgette pollen in this study suggests that bees can only benefit from this transient nectar source if alternative floral resources, particularly pollen, are also available to fulfill bees' nutritional requirements in space and time. Therefore, providing additional forage resources could simultaneously improve pollination services and bumblebee populations.

RevDate: 2019-01-29

Trubitt RT, Hovick TJ, Gillam EH, et al (2019)

Habitat associations of bats in a working rangeland landscape.

Ecology and evolution, 9(1):598-608 pii:ECE34782.

Land-use change has resulted in rangeland loss and degradation globally. These changes include conversion of native grasslands for row-crop agriculture as well as degradation of remaining rangeland due to fragmentation and changing disturbance regimes. Understanding how these and other factors influence wildlife use of rangelands is important for conservation and management of wildlife populations. We investigated bat habitat associations in a working rangeland in southeastern North Dakota. We used Petterson d500x acoustic detectors to systematically sample bat activity across the study area on a 1-km point grid. We identified calls using Sonobat autoclassification software. We detected five species using this working rangeland, which included Lasionycteris noctivagans (2,722 detections), Lasiurus cinereus (2,055 detections), Eptesicus fuscus (749 detections), Lasiurusborealis (62 detections), and Myotis lucifugus (1 detection). We developed generalized linear mixed-effects models for the four most frequently detected species based on their ecology. The activity of three bat species increased with higher tree cover. While the scale of selection varied between the four species, all three investigated scales were explanatory for at least one bat species. The broad importance of trees to bats in rangelands may put their conservation needs at odds with those of obligate grassland species. Focusing rangeland bat conservation on areas that were treed prior to European settlement, such as riparian forests, can provide important areas for bat conservation while minimizing negative impacts on grassland species.

RevDate: 2019-01-29

Badillo-Montaño R, Aguirre A, MA Munguía-Rosas (2019)

Pollinator-mediated interactions between cultivated papaya and co-flowering plant species.

Ecology and evolution, 9(1):587-597 pii:ECE34781.

Many modern crop varieties rely on animal pollination to set fruit and seeds. Intensive crop plantations usually do not provide suitable habitats for pollinators so crop yield may depend on the surrounding vegetation to maintain pollination services. However, little is known about the effect of pollinator-mediated interactions among co-flowering plants on crop yield or the underlying mechanisms. Plant reproductive success is complex, involving several pre- and post-pollination events; however, the current literature has mainly focused on pre-pollination events in natural plant communities. We assessed pollinator sharing and the contribution to pollinator diet in a community of wild and cultivated plants that co-flower with a focal papaya plantation. In addition, we assessed heterospecific pollen transfer to the stigmatic loads of papaya and its effect on fruit and seed production. We found that papaya shared at least one pollinator species with the majority of the co-flowering plants. Despite this, heterospecific pollen transfer in cultivated papaya was low in open-pollinated flowers. Hand-pollination experiments suggest that heterospecific pollen transfer has no negative effect on fruit production or weight, but does reduce seed production. These results suggest that co-flowering plants offer valuable floral resources to pollinators that are shared with cultivated papaya with little or no cost in terms of heterospecific pollen transfer. Although HP reduced seed production, a reduced number of seeds per se are not negative, given that from an agronomic perspective the number of seeds does not affect the monetary value of the papaya fruit.

RevDate: 2019-01-29

Pureswaran DS, Neau M, Marchand M, et al (2019)

Phenological synchrony between eastern spruce budworm and its host trees increases with warmer temperatures in the boreal forest.

Ecology and evolution, 9(1):576-586 pii:ECE34779.

Climate change is predicted to alter relationships between trophic levels by changing the phenology of interacting species. We tested whether synchrony between two critical phenological events, budburst of host species and larval emergence from diapause of eastern spruce budworm, increased at warmer temperatures in the boreal forest in northeastern Canada. Budburst was up to 4.6 ± 0.7 days earlier in balsam fir and up to 2.8 ± 0.8 days earlier in black spruce per degree increase in temperature, in naturally occurring microclimates. Larval emergence from diapause did not exhibit a similar response. Instead, larvae emerged once average ambient temperatures reached 10°C, regardless of differences in microclimate. Phenological synchrony increased with warmer microclimates, tightening the relationship between spruce budworm and its host species. Synchrony increased by up to 4.5 ± 0.7 days for balsam fir and up to 2.8 ± 0.8 days for black spruce per degree increase in temperature. Under a warmer climate, defoliation could potentially begin earlier in the season, in which case, damage on the primary host, balsam fir may increase. Black spruce, which escapes severe herbivory because of a 2-week delay in budburst, would become more suitable as a resource for the spruce budworm. The northern boreal forest could become more vulnerable to outbreaks in the future.

RevDate: 2019-01-29

Han Z, Li W, Zhu W, et al (2019)

Near-complete genome assembly and annotation of the yellow drum (Nibea albiflora) provide insights into population and evolutionary characteristics of this species.

Ecology and evolution, 9(1):568-575 pii:ECE34778.

Yellow drum (Nibea albiflora) is an important fish species in capture fishery and aquaculture in East Asia. We herein report the first and near-complete genome assembly of an ultra-homologous gynogenic female yellow drum using Illumina short sequencing reads. In summary, a total of 154.2 Gb of raw reads were generated via whole-genome sequencing and were assembled to 565.3 Mb genome with a contig N50 size of 50.3 kb and scaffold N50 size of 2.2 Mb (BUSCO completeness of 97.7%), accounting for 97.3%-98.6% of the estimated genome size of this fish. We further identified 22,448 genes using combined methods of ab initio prediction, RNAseq annotation, and protein homology searching, of which 21,614 (96.3%) were functionally annotated in NCBI nr, trEMBL, SwissProt, and KOG databases. We also investigated the nucleotide diversity (around 1/390) of aquacultured individuals and found the genetic diversity of the aquacultured population decreased due to inbreeding. Evolutionary analyses illustrated significantly expanded and extracted gene families, such as myosin and sodium: neurotransmitter symporter (SNF), could help explain swimming motility of yellow drum. The presented genome will be an important resource for future studies on population genetics, conservation, understanding of evolutionary history and genetic breeding of the yellow drum and other Nibea species.

RevDate: 2019-01-29

Bracken FSA, Rooney SM, Kelly-Quinn M, et al (2019)

Identifying spawning sites and other critical habitat in lotic systems using eDNA "snapshots": A case study using the sea lamprey Petromyzon marinus L.

Ecology and evolution, 9(1):553-567 pii:ECE34777.

Many aquatic species of conservation concern exist at low densities and are inherently difficult to detect or monitor using conventional methods. However, the introduction of environmental (e)DNA has recently transformed our ability to detect these species and enables effective deployment of limited conservation resources. Identifying areas for breeding, as well as the ecological distribution of species, is vital to the survival or recovery of a conservation species (i.e., areas of critical habitat). In many species, spawning events are associated with a higher relative abundance of DNA released within an aquatic system (i.e., gametes, skin cells etc.), making this the ideal time to monitor these species using eDNA techniques. This study aims to examine whether a "snapshot" eDNA sampling approach (i.e., samples taken at fixed points in chronological time) could reveal areas of critical habitat including spawning sites for our target species Petromyzon marinus. We utilized a species-specific qPCR assay to monitor spatial and temporal patterns in eDNA concentration within two river catchments in Ireland over three consecutive years. We found that eDNA concentration increased at the onset of observed spawning activity and patterns of concentration increased from downstream to upstream over time, suggesting dispersal into the higher reaches as the spawning season progressed. We found P. marinus to be present upstream of several potential barriers to migration, sometimes in significant numbers. Our results also show that the addition of a lamprey-specific fish pass at an "impassable" weir, although assisting in ascent, did not have any significant impact on eDNA concentration upstream after the pass had been installed. eDNA concentration was also found to be significantly correlated with both the number of fish and the number of nests encountered. The application of snapshot sampling techniques for species monitoring therefore has substantial potential for the management of low-density species in fast-moving aquatic systems.

RevDate: 2019-01-29

Rubene D, Leidefors M, Ninkovic V, et al (2019)

Disentangling olfactory and visual information used by field foraging birds.

Ecology and evolution, 9(1):545-552 pii:ECE34773.

Foraging strategies of birds can influence trophic plant-insect networks with impacts on primary plant production. Recent experiments show that some forest insectivorous birds can use herbivore-induced plant volatiles (HIPVs) to locate herbivore-infested trees, but it is unclear how birds combine or prioritize visual and olfactory information when making foraging decisions. Here, we investigated attraction of ground-foraging birds to HIPVs and visible prey in short vegetation on farmland in a series of foraging choice experiments. Birds showed an initial preference for HIPVs when visual information was the same for all choice options (i.e., one experimental setup had all options with visible prey, another setup with hidden prey). However, if the alternatives within an experimental setup included visible prey (without HIPV) in competition with HIPV-only, then birds preferred the visual option over HIPVs. Our results show that olfactory cues can play an important role in birds' foraging choices when visual information contains little variation; however, visual cues are preferred when variation is present. This suggests certain aspects of bird foraging decisions in agricultural habitats are mediated by olfactory interaction mechanisms between birds and plants. We also found that birds from variety of dietary food guilds were attracted to HIPVs; hence, the ability of birds to use plant cues is probably more general than previously thought, and may influence the biological pest control potential of birds on farmland.

RevDate: 2019-01-29

Arso Civil M, Cheney B, Quick NJ, et al (2019)

Variations in age- and sex-specific survival rates help explain population trend in a discrete marine mammal population.

Ecology and evolution, 9(1):533-544 pii:ECE34772.

Understanding the drivers underlying fluctuations in the size of animal populations is central to ecology, conservation biology, and wildlife management. Reliable estimates of survival probabilities are key to population viability assessments, and patterns of variation in survival can help inferring the causal factors behind detected changes in population size. We investigated whether variation in age- and sex-specific survival probabilities could help explain the increasing trend in population size detected in a small, discrete population of bottlenose dolphins Tursiops truncatus off the east coast of Scotland. To estimate annual survival probabilities, we applied capture-recapture models to photoidentification data collected from 1989 to 2015. We used robust design models accounting for temporary emigration to estimate juvenile and adult survival, multistate models to estimate sex-specific survival, and age models to estimate calf survival. We found strong support for an increase in juvenile/adult annual survival from 93.1% to 96.0% over the study period, most likely caused by a change in juvenile survival. Examination of sex-specific variation showed weaker support for this trend being a result of increasing female survival, which was overall higher than for males and animals of unknown sex. Calf survival was lower in the first than second year; a bias in estimating third-year survival will likely exist in similar studies. There was some support first-born calf survival being lower than for calves born subsequently. Coastal marine mammal populations are subject to the impacts of environmental change, increasing anthropogenic disturbance and the effects of management measures. Survival estimates are essential to improve our understanding of population dynamics and help predict how future pressures may impact populations, but obtaining robust information on the life history of long-lived species is challenging. Our study illustrates how knowledge of survival can be increased by applying a robust analytical framework to photoidentification data.

RevDate: 2019-01-29

Denis V, Chen JW, Chen Q, et al (2019)

Biogeography of functional trait diversity in the Taiwanese reef fish fauna.

Ecology and evolution, 9(1):522-532 pii:ECE34771.

The richness of Taiwanese reef fish species is inversely correlated to latitude as a direct consequence of the abiotic environment and its effects on benthic habitats. However, to date, no studies have investigated the variations in the diversity of traits (FD) linked with the role of these fishes in the ecosystem. FD is usually considered more sensitive than species richness in detecting early changes in response to disturbances, and therefore could serve as an indicator of ecological resilience to environmental changes. Here, we aim to characterize FD in the Taiwanese reef fish fauna and to document its regional variations. Six traits were used to categorize the 1,484 reef fish species occurring in four environmentally contrasted regions around Taiwan. The number of unique trait combinations (FEs), their richness (FRic), their redundancy (FR), their over-redundancy (FOR), and their vulnerability (FV) were compared among these regions. Overall, 416 FEs were identified. Their number decreased from south to north in step with regional species richness but FRic remained similar among regions. FR and FOR were higher to the south. At the local scale, variations in FEs and FRic are in concordance with the worldwide pattern of FD. High-latitude, impoverished fish assemblages, offer a range of trait combinations similar to diversified tropical assemblages. Increasing diversity in the latter mainly contributes to raising FR and supports already over-redundant entities. High vulnerability makes many combinations highly sensitive to species loss, and was higher at intermediate latitudes when using a fine resolution in trait categories. It suggests that the loss of FEs may first be characterized by an increase in their vulnerability, a pattern that could have been overlooked in previous global scale analyses. Overall, this study provides new insights into reef fish trait biogeography with potential ramifications for ecosystem functioning.

RevDate: 2019-01-29

Apfelbeck B, Haussmann MF, Boner W, et al (2019)

Divergent patterns of telomere shortening in tropical compared to temperate stonechats.

Ecology and evolution, 9(1):511-521 pii:ECE34769.

Telomeres have emerged as important biomarkers of health and senescence as they predict chances of survival in various species. Tropical birds live in more benign environments with lower extrinsic mortality and higher juvenile and adult survival than temperate birds. Therefore, telomere biology may play a more important role in tropical compared to temperate birds. We measured mean telomere length of male stonechats (Saxicola spp.) at four age classes from tropical African and temperate European breeding regions. Tropical and temperate stonechats had similarly long telomeres as nestlings. However, while in tropical stonechats pre-breeding first-years had longer telomeres than nestlings, in temperate stonechats pre-breeding first-years had shorter telomeres than nestlings. During their first breeding season, telomere length was again similar between tropical and temperate stonechats. These patterns may indicate differential survival of high-quality juveniles in tropical environments. Alternatively, more favorable environmental conditions, that is, extended parental care, may enable tropical juveniles to minimize telomere shortening. As suggested by previous studies, our results imply that variation in life history and life span may be reflected in different patterns of telomere shortening rather than telomere length. Our data provide first evidence that distinct selective pressures in tropical and temperate environments may be reflected in diverging patterns of telomere loss in birds.

RevDate: 2019-01-29

Kerr Q, Fuentes-Pardo AP, Kho J, et al (2019)

Temporal stability and assignment power of adaptively divergent genomic regions between herring (Clupea harengus) seasonal spawning aggregations.

Ecology and evolution, 9(1):500-510 pii:ECE34768.

Atlantic herring (Clupea harengus), a vital ecosystem component and target of the largest Northwest Atlantic pelagic fishery, undergo seasonal spawning migrations that result in elusive sympatric population structure. Herring spawn mostly in fall or spring, and genomic differentiation was recently detected between these groups. Here we used a subset of this differentiation, 66 single nucleotide polymorphisms (SNPs) to analyze the temporal dynamics of this local adaptation and the applicability of SNP subsets in stock assessment. We showed remarkable temporal stability of genomic differentiation corresponding to spawning season, between samples taken a decade apart (2005 N = 90 vs. 2014 N = 71) in the Gulf of St. Lawrence, and new evidence of limited interbreeding between spawning components. We also examined an understudied and overexploited herring population in Bras d'Or lake (N = 97); using highly reduced SNP panels (NSNPs > 6), we verified little-known sympatric spawning populations within this unique inland sea. These results describe consistent local adaptation, arising from asynchronous reproduction in a migratory and dynamic marine species. Our research demonstrates the efficiency and precision of SNP-based assessments of sympatric subpopulations; and indeed, this temporally stable local adaptation underlines the importance of such fine-scale management practices.

RevDate: 2019-01-29

Tso KL, GJ Allan (2019)

Environmental variation shapes genetic variation in Bouteloua gracilis: Implications for restoration management of natural populations and cultivated varieties in the southwestern United States.

Ecology and evolution, 9(1):482-499 pii:ECE34767.

With the increasing frequency of large-scale restoration efforts, the need to understand the adaptive genetic structure of natural plant populations and their relation to heavily utilized cultivars is critical. Bouteloua gracilis (blue grama) is a wind-dispersed, perennial grass consisting of several cytotypes (2n = 2×-6×) with a widespread distribution in western North America. The species is locally dominant and used regularly in restoration treatments. Using amplified fragment length polymorphism (AFLP) and cpDNA analyses, we assessed the genetic variability and adaptive genetic structure of blue grama within and among 44 sampling sites that are representative of the species' environmental and habitat diversity in the southwestern United States. Five cultivars were also included to investigate genetic diversity and differentiation in natural versus cultivated populations. Three main findings resulted from this study: (a) Ninety-four polymorphic AFLP markers distinguished two population clusters defined largely by samples on and off the Colorado Plateau; (b) substructure of samples on the Colorado Plateau was indicated by genetic divergence between boundary and interior regions, and was supported by cytotype distribution and cpDNA analysis; and (c) six AFLP markers were identified as "outliers," consistent with being under selection. These loci were significantly correlated to mean annual temperature, mean annual precipitation, precipitation of driest quarter, and precipitation of wettest quarter in natural populations, but not in cultivated samples. Marker × environment relationships were found to be largely influenced by cytotype and cultivar development. Our results demonstrate that blue grama is genetically variable, and exhibits genetic structure, which is shaped, in part, by environmental variability across the Colorado Plateau. Information from our study can be used to guide the selection of seed source populations for commercial development and long-term conservation management of B. gracilis, which could include genetic assessments of diversity and the adaptive potential of both natural and cultivated populations for wildland restoration.

RevDate: 2019-01-29

Rubin MJ, Schmid KM, J Friedman (2019)

Assortative mating by flowering time and its effect on correlated traits in variable environments.

Ecology and evolution, 9(1):471-481 pii:ECE34765.

Reproductive timing is a key life-history trait that impacts the pool of available mates, the environment experienced during flowering, and the expression of other traits through genetic covariation. Selection on phenology, and its consequences on other life-history traits, has considerable implications in the context of ongoing climate change and shifting growing seasons. To test this, we grew field-collected seed from the wildflower Mimulus guttatus in a greenhouse to assess the standing genetic variation for flowering time and covariation with other traits. We then created full-sib families through phenological assortative mating and grew offspring in three photoperiod treatments representing seasonal variation in daylength. We find substantial quantitative genetic variation for the onset of flowering time, which covaried with vegetative traits. The assortatively-mated offspring varied in their critical photoperiod by over two hours, so that families differed in their probability of flowering across treatments Allocation to flowering and vegetative growth changed across the daylength treatments, with consistent direction and magnitude of covariation among flowering time and other traits. Our results suggest that future studies of flowering time evolution should consider the joint evolution of correlated traits and shifting seasonal selection to understand how environmental variation influences life histories.

RevDate: 2019-01-29

Hauser SS, Walker L, PL Leberg (2019)

Asymmetrical gene flow of the recently delisted passerine black-capped vireo (Vireo atricapilla) indicates source-sink dynamics in central Texas.

Ecology and evolution, 9(1):463-470 pii:ECE34764.

Habitat fragmentation can produce metapopulations or source-sink systems in which dispersal in crucial for population maintenance. Our objective was to investigate connectivity among black-capped vireo (Vireo atricapilla) populations in tandem with a demographic study (Biological Conservation, 2016, 203, 108-118) to elucidate if central Texas populations act as a source-sink system. We genotyped 343 individuals at 12 microsatellite loci to elucidate the movement ecology of the black-capped vireo in central Texas surrounding Fort Hood; the largest and most stable breeding population of black-capped vireos inhabit Fort Hood. To gain insight into gene flow among populations, we analyzed genetic differentiation, migration rates, number of migrants, and parentage. We found statistically significant, but low levels of genetic differentiation among several populations, suggesting some limited restriction to gene flow. Across approaches to estimate migration, we found consistent evidence for asymmetrical movement from Fort Hood to the other central Texas sites consistent with source-sink dynamics. Our results are complementary to black-capped vireo demographic studies done in tandem showing that portions of Fort Hood are acting as a source population to smaller central Texas populations.

RevDate: 2019-01-29

Dorková M, Naďo L, Jarčuška B, et al (2019)

Size-dependent mating pattern in a nuptial gift-giving insect.

Ecology and evolution, 9(1):454-462 pii:ECE34763.

The reproductive interests of females and males often diverge in terms of the number of mating partners, an individual's phenotype, origin, genes, and parental investment. This conflict may lead to a variety of sex-specific adaptations and also affect mate choice in both sexes. We conducted an experiment with the bush-cricket Pholidoptera griseoaptera (Orthoptera, Tettigoniidae), a species in which females receive direct nutritional benefits during mating. Mated individuals could be assigned due to the genotype of male spermatodoses, which are stored in the female's spermatheca. After 3 weeks of possible copulations in established mating groups which were random replications with four females and males we did not find consistent assortative mating preference regarding to body size of mates. However, our results showed that the frequency of within-pair copulations (192 analyzed mating events in 128 possible pairwise combinations) was positively associated with the body size of both mated individuals with significant interaction between sexes (having one mate very large, association between body size and the number of copulations has weaken). Larger individuals also showed a higher degree of polygamy. This suggests that body size of this nuptial gift-giving insect species is an important sexual trait according to which both sexes choose their optimal mating partner.

RevDate: 2019-01-29

Flores-Manzanero A, Luna-Bárcenas MA, Dyer RJ, et al (2019)

Functional connectivity and home range inferred at a microgeographic landscape genetics scale in a desert-dwelling rodent.

Ecology and evolution, 9(1):437-453 pii:ECE34762.

Gene flow in animals is limited or facilitated by different features within the landscape matrix they inhabit. The landscape representation in landscape genetics (LG) is traditionally modeled as resistance surfaces (RS), where novel optimization approaches are needed for assigning resistance values that adequately avoid subjectivity. Also, desert ecosystems and mammals are scarcely represented in LG studies. We addressed these issues by evaluating, at a microgeographic scale, the effect of landscape features on functional connectivity of the desert-dwelling Dipodomys merriami. We characterized genetic diversity and structure with microsatellites loci, estimated home ranges and movement of individuals using telemetry-one of the first with rodents, generated a set of individual and composite environmental surfaces based on hypotheses of variables influencing movement, and assessed how these variables relate to individual-based gene flow. Genetic diversity and structure results evidenced a family-induced pattern driven by first-order-related individuals, notably determining landscape genetic inferences. The vegetation cover and soil resistance optimized surface (NDVI) were the best-supported model and a significant predictor of individual genetic distance, followed by humidity and NDVI+humidity. Based on an accurate definition of thematic resolution, we also showed that vegetation is better represented as continuously (vs. categorically) distributed. Hence, with a nonsubjective optimization framework for RS and telemetry, we were able to describe that vegetation cover, soil texture, and climatic variables influence D. merriami's functional connectivity at a microgeographic scale, patterns we could further explain based on the home range, habitat use, and activity observed between sexes. We describe the relationship between environmental features and some aspects of D. merriami's behavior and physiology.

RevDate: 2019-01-29

Li R (2019)

Protecting rare and endangered species under climate change on the Qinghai Plateau, China.

Ecology and evolution, 9(1):427-436 pii:ECE34761.

Climate change-induced species range shift may pose severe challenges to species conservation. The Qinghai-Tibet Plateau is the highest and biggest plateau, and also one of the most sensitive areas to global warming in the world, which provides important shelters for a unique assemblage of species. Here, ecological niche-based model was employed to project the potential distributions of 59 key rare and endangered species under three climate change scenarios (RCP2.6, RCP4.5 and RCP8.5) in Qinghai Province. I assessed the potential impacts of climate change on these key species (habitats, species richness and turnover) and effectiveness of nature reserves (NRs) in protecting these species. The results revealed that that climate change would shrink the geographic ranges of about a third studied species and expand the habitats for two thirds of these species, which would thus alter the conservation value of some local areas and conservation effectiveness of some NRs in Qinghai Province. Some regions require special attention as they are expected to experience significant changes in species turnover, species richness or newly colonized species in the future, including Haidong, Haibei and Haixi junctions, the southwestern Yushu, Qinghai Nuomuhong Provincial NR, Qinghai Qaidam and Haloxylon Forest NR. The Haidong and the eastern part of Haibei, are projected to have high species richness and conservation value in both current and future, but they are currently not protected, and thus require extra protection in the future. The results could provide the first basis on the high latitude region to formulate biodiversity conservation strategies on climate change adaptation.

RevDate: 2019-01-29

Thorbjørnsen SH, Moland E, Simpfendorfer C, et al (2019)

Potential of a no-take marine reserve to protect home ranges of anadromous brown trout (Salmo trutta).

Ecology and evolution, 9(1):417-426 pii:ECE34760.

The extent to which no-take marine reserves can benefit anadromous species requires examination. Here, we used acoustic telemetry to investigate the spatial behavior of anadromous brown trout (sea trout, Salmo trutta) in relation to a small marine reserve (~1.5 km2) located inside a fjord on the Norwegian Skagerrak coast. On average, sea trout spent 42.3 % (±5.0% SE) of their time in the fjord within the reserve, a proportion similar to the area of the reserve relative to that of the fjord. On average, sea trout tagged inside the reserve received the most protection, although the level of protection decreased marginally with increasing home range size. Furthermore, individuals tagged outside the reserve received more protection with increasing home range size, potentially opposing selection toward smaller home range sizes inflicted on fish residing within reserves, or through selective fishing methods like angling. Monthly sea trout home ranges in the marine environment were on average smaller than the reserve, with a mean of 0.430 (±0.0265 SE) km2. Hence, the reserve is large enough to protect the full home range of some individuals residing in the reserve. Synthesis and applications: In general, the reserve protects sea trout to a varying degree depending on their individual behavior. These findings highlight evolutionary implications of spatial protection and can guide managers in the design of marine reserves and networks that preserve variation in target species' home range size and movement behavior.

RevDate: 2019-01-29

Marie-Orleach L, Bailey NW, MG Ritchie (2019)

Social effects on fruit fly courtship song.

Ecology and evolution, 9(1):410-416 pii:ECE34759.

Courtship behavior in Drosophila has often been described as a classic innate behavioral repertoire, but more recently extensive plasticity has been described. In particular, prior exposure to acoustic signals of con- or heterspecific males can change courtship traits in both sexes that are liable to be important in reproductive isolation. However, it is unknown whether male courtship song itself is socially plastic. We examined courtship song plasticity of two species in the Drosophila melanogaster subgroup. Sexual isolation between the species is influenced by two male song traits, the interpulse interval (IPI) and sinesong frequency (SSF). Neither of these showed plasticity when males had prior experience of con- and heterospecific social partners. However, males of both species produced longer bursts of song during courtship when they were exposed to social partners (either con- or heterospecific) than when they were reared in isolation. D. melanogaster carrying mutations affecting short- or medium-term memory showed a similar response to the social environment, not supporting a role for learning. Our results demonstrate that the amount of song a male produces during courtship is plastic depending on the social environment, which might reflect the advantage of being able to respond to variation in intrasexual competition, but that song structure itself is relatively inflexible, perhaps due to strong selection against hybridization.

RevDate: 2019-01-29

Doellman MM, Egan SP, Ragland GJ, et al (2019)

Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies.

Ecology and evolution, 9(1):393-409 pii:ECE34758.

Taxa harboring high levels of standing variation may be more likely to adapt to rapid environmental shifts and experience ecological speciation. Here, we characterize geographic and host-related differentiation for 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies to infer whether standing genetic variation in adult eclosion time in the ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new mutations, contributed substantially to its recent shift to earlier fruiting apple (Malus domestica). Allele frequency differences associated with early vs. late eclosion time within each host race were significantly related to geographic genetic variation and host race differentiation across four sites, arrayed from north to south along a 430-km transect, where the host races co-occur in sympatry in the Midwest United States. Host fruiting phenology is clinal, with both apple and hawthorn trees fruiting earlier in the North and later in the South. Thus, we expected alleles associated with earlier eclosion to be at higher frequencies in northern populations. This pattern was observed in the hawthorn race across all four populations; however, allele frequency patterns in the apple race were more complex. Despite the generally earlier eclosion timing of apple flies and corresponding apple fruiting phenology, alleles on chromosomes 2 and 3 associated with earlier emergence were paradoxically at lower frequency in the apple than hawthorn host race across all four sympatric sites. However, loci on chromosome 1 did show higher frequencies of early eclosion-associated alleles in the apple than hawthorn host race at the two southern sites, potentially accounting for their earlier eclosion phenotype. Thus, although extensive clinal genetic variation in the ancestral hawthorn race exists and contributed to the host shift to apple, further study is needed to resolve details of how this standing variation was selected to generate earlier eclosing apple fly populations in the North.

RevDate: 2019-01-29

Helmkampf M, Bellinger MR, Frazier M, et al (2019)

Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata.

Ecology and evolution, 9(1):378-392 pii:ECE34756.

Reef-building corals may harbor genetically distinct lineages of endosymbiotic dinoflagellates in the genus Symbiodinium, which have been shown to affect important colony properties, including growth rates and resilience against environmental stress. However, the molecular processes underlying these differences are not well understood. In this study, we used whole transcriptome sequencing (RNA-seq) to assess gene expression differences between 27 samples of the coral Montipora capitata predominantly hosting two different Symbiodinium types in clades C and D. The samples were further characterized by their origin from two field sites on Hawai'i Island with contrasting environmental conditions. We found that transcriptome-wide gene expression profiles clearly separated by field site first, and symbiont clade second. With 273 differentially expressed genes (DEGs, 1.3% of all host transcripts), symbiont clade had a measurable effect on host gene expression, but the effect of field site proved almost an order of magnitude higher (1,957 DEGs, 9.6%). According to SNP analysis, we found moderate evidence for host genetic differentiation between field sites (FST = 0.046) and among corals harboring alternative symbiont clades (FST = 0.036), suggesting that site-related gene expression differences are likely due to a combination of local adaptation and acclimatization to environmental factors. The correlation between host gene expression and symbiont clade may be due to several factors, including host genotype or microhabitat selecting for alternative clades, host physiology responding to different symbionts, or direct modulation of host gene expression by Symbiodinium. However, the magnitude of these effects at the level of transcription was unexpectedly small considering the contribution of symbiont type to holobiont phenotype.

RevDate: 2019-01-29

Mustafina FU, Yi DK, Choi K, et al (2019)

A comparative analysis of complete plastid genomes from Prangos fedtschenkoi and Prangos lipskyi (Apiaceae).

Ecology and evolution, 9(1):364-377 pii:ECE34753.

Prangos fedtschenkoi (Regel & Schmalh.) Korovin and P. lipskyi Korovin (Apiaceae) are rare plant species endemic to mountainous regions of Middle Asia. Both are edificators of biotic communities and valuable resource plants. The results of recent phylogenetic analyses place them in Prangos subgen. Koelzella (M. Hiroe) Lyskov & Pimenov and suggest they may possibly represent sister species. To aid in development of molecular markers useful for intraspecific phylogeographic and population-level genetic studies of these ecologically and economically important plants, we determined their complete plastid genome sequences and compared the results obtained to several previously published plastomes of Apiaceae. The plastomes of P. fedtschenkoi and P. lipskyi are typical of Apiaceae and most other higher plant plastid DNAs in their sizes (153,626 and 154,143 bp, respectively), structural organization, gene arrangement, and gene content (with 113 unique genes). A total of 49 and 48 short sequence repeat (SSR) loci of 10 bp or longer were detected in P. fedtschenkoi and P. lipskyi plastomes, respectively, representing 42-43 mononucleotides and 6 AT dinucleotides. Seven tandem repeats of 30 bp or longer with a sequence identity ≥90% were identified in each plastome. Further comparisons revealed 319 polymorphic sites between the plastomes (IR, 21; LSC, 234; SSC, 64), representing 43.8% transitions (Ts), 56.1% transversions (Tv), and a Ts/Tv ratio of 0.78. Within genic regions, two indel events were observed in rpoA (6 and 51 bp) and ycf1 (3 and 12 bp), and one in ndhF (6 bp). The most variable intergenic spacer region was that of accD/psaI, with 21.1% nucleotide divergence. Each Prangos species possessed one of two separate inversions (either 5 bp in ndhB intron or 9 bp in petB intron), and these were predicted to form hairpin structures with flanking repeat sequences of 18 and 19 bp, respectively. Both species have also incorporated novel DNA in the LSC region adjacent to the LSC/IRa junction, and BLAST searches revealed it had a 100 bp match (86% sequence identity) to noncoding mitochondrial DNA. Prangos-specific primers were developed for the variable accD/psaI intergenic spacer and preliminary PCR-surveys suggest that this region will be useful for future phylogeographic and population-level studies.

RevDate: 2019-01-29

Milleret C, Dupont P, Bonenfant C, et al (2019)

A local evaluation of the individual state-space to scale up Bayesian spatial capture-recapture.

Ecology and evolution, 9(1):352-363 pii:ECE34751.

Spatial capture-recapture models (SCR) are used to estimate animal density and to investigate a range of problems in spatial ecology that cannot be addressed with traditional nonspatial methods. Bayesian approaches in particular offer tremendous flexibility for SCR modeling. Increasingly, SCR data are being collected over very large spatial extents making analysis computational intensive, sometimes prohibitively so. To mitigate the computational burden of large-scale SCR models, we developed an improved formulation of the Bayesian SCR model that uses local evaluation of the individual state-space (LESS). Based on prior knowledge about a species' home range size, we created square evaluation windows that restrict the spatial domain in which an individual's detection probability (detector window) and activity center location (AC window) are estimated. We used simulations and empirical data analyses to assess the performance and bias of SCR with LESS. LESS produced unbiased estimates of SCR parameters when the AC window width was ≥5σ (σ: the scale parameter of the half-normal detection function), and when the detector window extended beyond the edge of the AC window by 2σ. Importantly, LESS considerably decreased the computation time needed for fitting SCR models. In our simulations, LESS increased the computation speed of SCR models up to 57-fold. We demonstrate the power of this new approach by mapping the density of an elusive large carnivore-the wolverine (Gulo gulo)-with an unprecedented resolution and across the species' entire range in Norway (> 200,000 km2). Our approach helps overcome a major computational obstacle to population and landscape-level SCR analyses. The LESS implementation in a Bayesian framework makes the customization and fitting of SCR accessible for practitioners working at scales that are relevant for conservation and management.

RevDate: 2019-01-29

De Gasperin O, Duarte A, English S, et al (2019)

The early-life environment and individual plasticity in life-history traits.

Ecology and evolution, 9(1):339-351 pii:ECE34749.

We tested whether the early-life environment can influence the extent of individual plasticity in a life-history trait. We asked: can the early-life environment explain why, in response to the same adult environmental cue, some individuals invest more than others in current reproduction? Moreover, can it additionally explain why investment in current reproduction trades off against survival in some individuals, but is positively correlated with survival in others? We addressed these questions using the burying beetle, which breeds on small carcasses and sometimes carries phoretic mites. These mites breed alongside the beetle, on the same resource, and are a key component of the beetle's early-life environment. We exposed female beetles to mites twice during their lives: during their development as larvae and again as adults during their first reproductive event. We measured investment in current reproduction by quantifying average larval mass and recorded the female's life span after breeding to quantify survival. We found no effect of either developing or breeding alongside mites on female reproductive investment, nor on her life span, nor did developing alongside mites influence her size. In post hoc analyses, where we considered the effect of mite number (rather than their mere presence/absence) during the female's adult breeding event, we found that females invested more in current reproduction when exposed to greater mite densities during reproduction, but only if they had been exposed to mites during development as well. Otherwise, they invested less in larvae at greater mite densities. Furthermore, females that had developed with mites exhibited a trade-off between investment in current reproduction and future survival, whereas these traits were positively correlated in females that had developed without mites. The early-life environment thus generates individual variation in life-history plasticity. We discuss whether this is because mites influence the resources available to developing young or serve as important environmental cues.

RevDate: 2019-01-29

Duffy E, Archer CR, Sharma MD, et al (2019)

Wolbachia infection can bias estimates of intralocus sexual conflict.

Ecology and evolution, 9(1):328-338 pii:ECE34744.

Males and females share most of their genome and develop many of the same traits. However, each sex frequently has different optimal values for these shared traits, creating intralocus sexual conflict. This conflict has been observed in wild and laboratory populations of insects and affects important evolutionary processes such as sexual selection, the maintenance of genetic variation, and possibly even speciation. Given the broad impacts of intralocus conflict, accurately detecting and measuring it is important. A common way to detect intralocus sexual conflict is to calculate the intersexual genetic correlation for fitness, with negative values suggesting conflict. Here, we highlight a potential confounder of this measure-cytoplasmic incompatibility caused by the intracellular parasite Wolbachia. Infection with Wolbachia can generate negative intersexual genetic correlations for fitness in insects, suggestive of intralocus sexual conflict. This is because cytoplasmic incompatibility reduces the fitness of uninfected females mated to infected males, while uninfected males will not suffer reductions in fitness if they mate with infected females and may even be fitter than infected males. This can lead to strong negative intersexual genetic correlations for fitness, mimicking intralocus conflict. We illustrate this issue using simulations and then present Drosophila simulans data that show how reproductive incompatibilities caused by Wolbachia infection can generate signals of intralocus sexual conflict. Given that Wolbachia infection in insect populations is pervasive, but populations usually contain both infected and uninfected individuals providing scope for cytoplasmic incompatibility, this is an important consideration for sexual conflict research but one which, to date, has been largely underappreciated.

RevDate: 2019-01-29

Osada Y, Kuriyama T, Asada M, et al (2019)

Estimating range expansion of wildlife in heterogeneous landscapes: A spatially explicit state-space matrix model coupled with an improved numerical integration technique.

Ecology and evolution, 9(1):318-327 pii:ECE34739.

Dispersal as well as population growth is a key demographic process that determines population dynamics. However, determining the effects of environmental covariates on dispersal from spatial-temporal abundance proxy data is challenging owing to the complexity of model specification for directional dispersal permeability and the extremely high computational loads for numerical integration. In this paper, we present a case study estimating how environmental covariates affect the dispersal of Japanese sika deer by developing a spatially explicit state-space matrix model coupled with an improved numerical integration technique (Markov chain Monte Carlo with particle filters). In particular, we explored the environmental drivers of inhomogeneous range expansion, characteristic of animals with short dispersal. Our model framework successfully reproduced the complex population dynamics of sika deer, including rapid changes in densely populated areas and distribution fronts within a decade. Furthermore, our results revealed that the inhomogeneous range expansion of sika deer seemed to be primarily caused by the dispersal process (i.e., movement barriers in fragmented forests) rather than population growth. Our state-space matrix model enables the inference of population dynamics for a broad range of organisms, even those with low dispersal ability, in heterogeneous landscapes, and could address many pressing issues in conservation biology and ecosystem management.

RevDate: 2019-01-29

Abercrombie ST, Koprowski JL, Nichols MH, et al (2019)

Native lagomorphs suppress grass establishment in a shrub-encroached, semiarid grassland.

Ecology and evolution, 9(1):307-317 pii:ECE34730.

Shrub encroachment into arid grasslands has been associated with reduced grass abundance, increased soil erosion, and local declines in biodiversity. Livestock overgrazing and the associated reduction of fine fuels has been a primary driver of shrub encroachment in the southwestern United States, but shrublands continue to persist despite livestock removal and grassland restoration efforts. We hypothesized that an herbivory feedback from native mammals may contribute to continued suppression of grasses after the removal of livestock. Our herbivore exclusion experiment in southeastern Arizona included five treatment levels and allowed access to native mammals based on their relative body size, separating the effects of rodents, lagomorphs, and mule deer. We included two control treatments and replicated each treatment 10 times (n = 50). We introduced uniform divisions of lawn sod (Cynodon dactylon) into each exclosure for 24-hr periods prior to (n = 2) and following (n = 2) the monsoon rains and used motion-activated cameras to document herbivore visitations. In the pre-monsoon trials, treatments that allowed lagomorph access had less sod biomass relative to other treatments (p < 0.001), averaging 44% (SD 36%) and 29% (SD 45%) remaining biomass after the 24-hr trial periods. Following the onset of monsoons, differences in remaining biomass among treatments disappeared. Desert cottontails (Sylvilagus audubonii) were detected more frequently than any of the other 11 herbivore species present at the site, accounting for 83% of detections during the pre-monsoon trials. Significantly more (p < 0.001) desert cottontails were detected during the pre-monsoon trials (2,077) compared to the post-monsoon trials (174), which coincided with biomass removal from lagomorph accessible treatments. We conclude that desert cottontails are significant consumers of herbaceous vegetation in shrub-encroached arid grasslands and they, along with other native herbivores, may act as a biotic feedback contributing to the competitive advantage and persistence of shrubs.

RevDate: 2019-01-29

Yewers MSC, Stuart-Fox D, CA McLean (2019)

Space use and genetic structure do not maintain color polymorphism in a species with alternative behavioral strategies.

Ecology and evolution, 9(1):295-306 pii:ECE34729.

Space use including territoriality and spatial arrangement within a population can reveal important information on the nature, dynamics, and evolutionary maintenance of alternative strategies in color polymorphic species. Despite the prevalence of color polymorphic species as model systems in evolutionary biology, the interaction between space use and genetic structuring of morphs within populations has rarely been examined. Here, we assess the spatial and genetic structure of male throat color morphs within a population of the tawny dragon lizard, Ctenophorus decresii. Male color morphs do not differ in morphology but differ in aggressive and antipredator behaviors as well as androgen levels. Despite these behavioral and endocrine differences, we find that color morphs do not differ in territory size, with their spatial arrangement being essentially random with respect to each other. There were no differences in genetic diversity or relatedness between morphs; however, there was significant, albeit weak, genetic differentiation between morphs, which was unrelated to geographic distance between individuals. Our results indicate potential weak barriers to gene flow between some morphs, potentially due to nonrandom pre- or postcopulatory mate choice or postzygotic genetic incompatibilities. However, space use, spatial structure, and nonrandom mating do not appear to be primary mechanisms maintaining color polymorphism in this system, highlighting the complexity and variation in alternative strategies associated with color polymorphism.

RevDate: 2019-01-29

Haueisen J, Möller M, Eschenbrenner CJ, et al (2019)

Highly flexible infection programs in a specialized wheat pathogen.

Ecology and evolution, 9(1):275-294 pii:ECE34724.

Many filamentous plant pathogens exhibit high levels of genomic variability, yet the impact of this variation on host-pathogen interactions is largely unknown. We have addressed host specialization in the wheat pathogen Zymoseptoria tritici. Our study builds on comparative analyses of infection and gene expression phenotypes of three isolates and reveals the extent to which genomic variation translates into phenotypic variation. The isolates exhibit genetic and genomic variation but are similarly virulent. By combining confocal microscopy, disease monitoring, staining of ROS, and comparative transcriptome analyses, we conducted a detailed comparison of the infection processes of these isolates in a susceptible wheat cultivar. We characterized four core infection stages: establishment, biotrophic growth, lifestyle transition, and necrotrophic growth and asexual reproduction that are shared by the three isolates. However, we demonstrate differentiated temporal and spatial infection development and significant differences in the expression profiles of the three isolates during the infection stages. More than 20% of the genes were differentially expressed and these genes were located significantly closer to transposable elements, suggesting an impact of epigenetic regulation. Further, differentially expressed genes were enriched in effector candidates suggesting that isolate-specific strategies for manipulating host defenses are present in Z. tritici. We demonstrate that individuals of a host-specialized pathogen have highly differentiated infection programs characterized by flexible infection development and functional redundancy. This illustrates how high genetic diversity in pathogen populations results in highly differentiated infection phenotypes, which fact needs to be acknowledged to understand host-pathogen interactions and pathogen evolution.

RevDate: 2019-01-29

Munden R, Börger L, Wilson RP, et al (2019)

Making sense of ultrahigh-resolution movement data: A new algorithm for inferring sites of interest.

Ecology and evolution, 9(1):265-274 pii:ECE34721.

Decomposing the life track of an animal into behavioral segments is a fundamental challenge for movement ecology. The proliferation of high-resolution data, often collected many times per second, offers much opportunity for understanding animal movement. However, the sheer size of modern data sets means there is an increasing need for rapid, novel computational techniques to make sense of these data. Most existing methods were designed with smaller data sets in mind and can thus be prohibitively slow. Here, we introduce a method for segmenting high-resolution movement trajectories into sites of interest and transitions between these sites. This builds on a previous algorithm of Benhamou and Riotte-Lambert (2012). Adapting it for use with high-resolution data. The data's resolution removed the need to interpolate between successive locations, allowing us to increase the algorithm's speed by approximately two orders of magnitude with essentially no drop in accuracy. Furthermore, we incorporate a color scheme for testing the level of confidence in the algorithm's inference (high = green, medium = amber, low = red). We demonstrate the speed and accuracy of our algorithm with application to both simulated and real data (Alpine cattle at 1 Hz resolution). On simulated data, our algorithm correctly identified the sites of interest for 99% of "high confidence" paths. For the cattle data, the algorithm identified the two known sites of interest: a watering hole and a milking station. It also identified several other sites which can be related to hypothesized environmental drivers (e.g., food). Our algorithm gives an efficient method for turning a long, high-resolution movement path into a schematic representation of broadscale decisions, allowing a direct link to existing point-to-point analysis techniques such as optimal foraging theory. It is encoded into an R package called SitesInterest, so should serve as a valuable tool for making sense of these increasingly large data streams.

RevDate: 2019-01-29

Graham J, M Kimble (2019)

Visualizing uncertainty in habitat suitability models with the hyper-envelope modeling interface, version 2.

Ecology and evolution, 9(1):251-264 pii:ECE34720.

Habitat suitability models (HSMs) are popular and used for a wide variety of applications but most do not include analysis of the uncertainty of the model outputs. Additionally, some overfit the data and few allow the ability to fill data gaps with expert opinion. HEMI 1 addressed issues with overfitting data and allowed models to incorporate both occurrence data and expert opinion. HEMI 2 improves on HEMI 1 with a simplified interface and the ability to inject random noise into occurrence locations and environmental variable values to generate uncertainty maps. HEMI 2 uses Monte Carlo methods to perform uncertainty, validation, and sensitivity testing and generates mean and standard deviation habitat suitability maps.

RevDate: 2019-01-29

Lenormand M, Papuga G, Argagnon O, et al (2019)

Biogeographical network analysis of plant species distribution in the Mediterranean region.

Ecology and evolution, 9(1):237-250 pii:ECE34718.

The delimitation of bioregions helps to understand historical and ecological drivers of species distribution. In this work, we performed a network analysis of the spatial distribution patterns of plants in south of France (Languedoc-Roussillon and Provence-Alpes-Côte d'Azur) to analyze the biogeographical structure of the French Mediterranean flora at different scales. We used a network approach to identify and characterize biogeographical regions, based on a large database containing 2.5 million of geolocalized plant records corresponding to more than 3,500 plant species. This methodology is performed following five steps, from the biogeographical bipartite network construction to the identification of biogeographical regions under the form of spatial network communities, the analysis of their interactions, and the identification of clusters of plant species based on the species contribution to the biogeographical regions. First, we identified two sub-networks that distinguish Mediterranean and temperate biota. Then, we separated eight statistically significant bioregions that present a complex spatial structure. Some of them are spatially well delimited and match with particular geological entities. On the other hand, fuzzy transitions arise between adjacent bioregions that share a common geological setting, but are spread along a climatic gradient. The proposed network approach illustrates the biogeographical structure of the flora in southern France and provides precise insights into the relationships between bioregions. This approach sheds light on ecological drivers shaping the distribution of Mediterranean biota: The interplay between a climatic gradient and geological substrate shapes biodiversity patterns. Finally, this work exemplifies why fragmented distributions are common in the Mediterranean region, isolating groups of species that share a similar eco-evolutionary history.

RevDate: 2019-01-29

Orgeret F, Cox SL, Weimerskirch H, et al (2019)

Body condition influences ontogeny of foraging behavior in juvenile southern elephant seals.

Ecology and evolution, 9(1):223-236 pii:ECE34717.

Ontogeny of diving and foraging behavior in marine top predators is poorly understood despite its importance in population recruitment. This lack of knowledge is partly due to the difficulties of monitoring juveniles in the wild, which is linked to high mortality early in life. Pinnipeds are good models for studying the development of foraging behaviors because juveniles are large enough to robustly carry tracking devices for many months. Moreover, parental assistance is absent after a juvenile departs for its first foraging trip, minimizing confounding effects of parental input on the development of foraging skills. In this study, we tracked 20 newly weaned juvenile southern elephant seals from Kerguelen Islands for up to 338 days during their first trip at sea following weaning. We used a new generation of satellite relay tags, which allow for the transmission of dive, accelerometer, and location data. We also monitored, at the same time, nine adult females from the colony during their post-breeding trips, in order to compare diving and foraging behaviors. Juveniles showed a gradual improvement through time in their foraging skills. Like adults females, they remarkably adjusted their swimming effort according to temporal changes in buoyancy (i.e., a proxy of their body condition). They also did not appear to exceed their aerobic physiological diving limits, although dives were constrained by their smaller size compared to adults. Changes in buoyancy appeared to also influence their decision to either keep foraging or return to land, alongside the duration of their haul outs and choice of foraging habitat (oceanic vs. plateau). Further studies are thus needed to better understand how patterns in juveniles survival, and therefore elephant seal populations, might be affected by their changes in foraging skills and changes in their environmental conditions.

RevDate: 2019-01-29

Robertsen G, Reid D, Einum S, et al (2019)

Can variation in standard metabolic rate explain context-dependent performance of farmed Atlantic salmon offspring?.

Ecology and evolution, 9(1):212-222 pii:ECE34716.

Escaped farmed Atlantic salmon interbreed with wild Atlantic salmon, leaving offspring that often have lower success in nature than pure wild salmon. On top of this, presence of farmed salmon descendants can impair production of wild-type recruits. We hypothesize that both these effects connect with farmed salmon having acquired higher standard metabolic rates (SMR, the energetic cost of self-maintenance) during domestication. Fitness-related advantages of phenotypic traits associated with both high SMR and farmed salmon (e.g., social dominance) depend on environmental conditions, such as food availability. We hypothesize that farmed offspring have an advantage at high food availability due to, for example, dominance behavior but suffer increased risks of starvation when food is scarce because this behavior is energy-demanding. To test these hypotheses, we first compare embryo SMR of pure farmed, farmed-wild hybrids and pure wild offspring. Next, we test early-life performance (in terms of survival and growth) of hybrids relative to that of their wild half-siblings, as well as their competitive abilities, in semi-natural conditions of high and low food availability. Finally, we test how SMR affects early-life performance at high and low food availability. We find inconclusive support for the hypothesis that domestication has induced increased SMR. Further, wild and hybrid juveniles had similar survival and growth in the semi-natural streams. Yet, the presence of hybrids led to decreased survival of their wild half-siblings. Contrary to our hypothesis about context-dependency, these effects were not modified by food availability. However, wild juveniles with high SMR had decreased survival when food was scarce, but there was no such effect at high food availability. This study provides further proof that farmed salmon introgression may compromise the viability of wild salmon populations. We cannot, however, conclude that this is connected to alterations in the metabolic phenotype of farmed salmon.

RevDate: 2019-01-29

Reum JCP, Holsman KK, Aydin KY, et al (2019)

Energetically relevant predator-prey body mass ratios and their relationship with predator body size.

Ecology and evolution, 9(1):201-211 pii:ECE34715.

Food web structure and dynamics depend on relationships between body sizes of predators and their prey. Species-based and community-wide estimates of preferred and realized predator-prey mass ratios (PPMR) are required inputs to size-based size spectrum models of marine communities, food webs, and ecosystems. Here, we clarify differences between PPMR definitions in different size spectrum models, in particular differences between PPMR measurements weighting prey abundance in individual predators by biomass (rbio) and numbers (rnum). We argue that the former weighting generates PPMR as usually conceptualized in equilibrium (static) size spectrum models while the latter usually applies to dynamic models. We use diet information from 170,689 individuals of 34 species of fish in Alaskan marine ecosystems to calculate both PPMR metrics. Using hierarchical models, we examine how explained variance in these metrics changed with predator body size, predator taxonomic resolution, and spatial resolution. In the hierarchical analysis, variance in both metrics emerged primarily at the species level and substantially less variance was associated with other (higher) taxonomic levels or with spatial resolution. This suggests that changes in species composition are the main drivers of community-wide mean PPMR. At all levels of analysis, relationships between weighted mean rbio or weighted mean rnum and predator mass tended to be dome-shaped. Weighted mean rnum values, for species and community-wide, were approximately an order of magnitude higher than weighted mean rbio, reflecting the consistent numeric dominance of small prey in predator diets. As well as increasing understanding of the drivers of variation in PPMR and providing estimates of PPMR in the north Pacific Ocean, our results demonstrate that that rbio or rnum, as well as their corresponding weighted means for any defined group of predators, are not directly substitutable. When developing equilibrium size-based models based on bulk energy flux or comparing PPMR estimates derived from the relationship between body mass and trophic level with those based on diet analysis, weighted mean rbio is a more appropriate measure of PPMR. When calibrating preference PPMR in dynamic size spectrum models then weighted mean rnum will be a more appropriate measure of PPMR.

RevDate: 2019-01-29

Brossette L, Meunier J, Dupont S, et al (2019)

Unbalanced biparental care during colony foundation in two subterranean termites.

Ecology and evolution, 9(1):192-200 pii:ECE34710.

Parental care is a major component of reproduction in social organisms, particularly during the foundation steps. Because investment into parental care is often costly, each parent is predicted to maximize its fitness by providing less care than its partner. However, this sexual conflict is expected to be low in species with lifelong monogamy, because the fitness of each parent is typically tied to the other's input. Somewhat surprisingly, the outcomes of this tug-of-war between maternal and paternal investments have received important attention in vertebrate species, but remain less known in invertebrates. In this study, we investigated how queens and kings share their investment into parental care and other social interactions during colony foundation in two termites with lifelong monogamy: the invasive species Reticulitermes flavipes and the native species R. grassei. Behaviors of royal pairs were recorded during six months using a non-invasive approach. Our results showed that queens and kings exhibit unbalanced investment in terms of grooming, antennation, trophallaxis, and vibration behavior. Moreover, both parents show behavioral differences toward their partner or their descendants. Our results also revealed differences among species, with R. flavipes exhibiting shorter periods of grooming and antennation toward eggs or partners. They also did more stomodeal trophallaxis and less vibration behavior. Overall, this study emphasizes that despite lifelong monogamy, the two parents are not equally involved in the measured forms of parental care and suggests that kings might be specialized in other tasks. It also indicates that males could play a central, yet poorly studied role in the evolution and maintenance of the eusocial organization.

RevDate: 2019-01-29

Bhattacharyya S, F Ishtiaq (2019)

Noninvasive sampling reveals population genetic structure in the Royle's pika, Ochotona roylei, in the western Himalaya.

Ecology and evolution, 9(1):180-191 pii:ECE34707.

Understanding population genetic structure of climate-sensitive herbivore species is important as it provides useful insights on how shifts in environmental conditions can alter their distribution and abundance. Herbivore responses to the environment can have a strong indirect cascading effect on community structure. This is particularly important for Royle's pika (Lagomorpha: Ochotona roylei), a herbivorous talus-dwelling species in alpine ecosystem, which forms a major prey base for many carnivores in the Himalayan arc. In this study, we used seven polymorphic microsatellite loci to detect evidence for recent changes in genetic diversity and population structure in Royle's pika across five locations sampled between 8 and 160 km apart in the western Himalaya. Using four clustering approaches, we found the presence of significant contemporary genetic structure in Royle's pika populations. The detected genetic structure could be primarily attributed to the landscape features in alpine habitat (e.g., wide lowland valleys, rivers) that may act as semipermeable barriers to gene flow and distribution of food plants, which are key determinants in spatial distribution of herbivores. Pika showed low inbreeding coefficients (FIS) and a high level of pairwise relatedness for individuals within 1 km suggesting low dispersal abilities of talus-dwelling pikas. We have found evidence of a recent population bottleneck, possibly due to effects of environmental disturbances (e.g., snow melting patterns or thermal stress). Our results reveal significant evidence of isolation by distance in genetic differentiation (FST range = 0.04-0.19). This is the first population genetics study on Royle's pika, which helps to address evolutionary consequences of climate change which are expected to significantly affect the distribution and population dynamics in this talus-dwelling species.

RevDate: 2019-01-29

Tapolczai K, Vasselon V, Bouchez A, et al (2019)

The impact of OTU sequence similarity threshold on diatom-based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean).

Ecology and evolution, 9(1):166-179 pii:ECE34701.

Extensive studies on the taxonomic resolution required for bioassessment purposes have determined that resolution above species level (genus, family) is sufficient for their use as indicators of relevant environmental pressures. The high-throughput sequencing (HTS) and meta-barcoding methods now used for bioassessment traditionally employ an arbitrary sequence similarity threshold (SST) around 95% or 97% to cluster sequences into operational taxonomic units, which is considered descriptive of species-level resolution. In this study, we analyzed the effect of the SST on the resulting diatom-based ecological quality index, which is based on OTU abundance distribution along a defined environmental gradient, ideally avoiding taxonomic assignments that could result in high rates of unclassified OTUs and biased final values. A total of 90 biofilm samples were collected in 2014 and 2015 from 51 stream sites on Mayotte Island in parallel with measures of relevant physical and chemical parameters. HTS sequencing was performed on the biofilms using the rbcL region as the genetic marker and diatom-specific primers. Hierarchical clustering was used to group sequences into OTUs using 20 experimental SST levels (80%-99%). An OTU-based quality index (IdxOTU) was developed based on a weighted average equation using the abundance profiles of the OTUs. The developed IdxOTU revealed significant correlations between the IdxOTU values and the reference pressure gradient, which reached maximal performance using an SST of 90% (well above species level delimitation). We observed an interesting and important trade-off with the power to discriminate between sampling sites and index stability that will greatly inform future applications of the index. Taken together, the results from this study detail a thoroughly optimized and validated approach to generating robust, reproducible, and complete indexes that will greatly facilitate effective and efficient environmental monitoring.

RevDate: 2019-01-29

Dalerum F, Retief TA, Havemann CP, et al (2019)

The influence of distance to perennial surface water on ant communities in Mopane woodlands, northern Botswana.

Ecology and evolution, 9(1):154-165 pii:ECE34692.

Studies of biodiversity along environmental gradients provide information on how ecological communities change in response to biotic and abiotic factors. For instance, distance to water is associated with several factors that shape the structure and the functioning of ecosystems at a range of spatial scales. We investigated the influence of distance to a perennial water source on ant communities in a semi-arid savanna in northern Botswana. Ant abundance, taxonomic richness, and both alpha and beta diversity were generally higher during the wet than the dry season. However, there were strong seasonal influences on the effects of distance to water, with more pronounced effects during the wet season. While both abundance and beta diversity declined with increasing distances to water during the wet season, there was a contrasting increase in alpha diversity. There was no major effect of distance to water on taxonomic richness during either season. Beta diversity was as high across as along gradients, and we found support for modular rather than nested community structures along gradients. Our study demonstrated that small-scale gradients in distance to water can influence several aspects of ant communities in semi-arid savannas. However, our results also point to strong effects of small-scale environmental variation, for instance associated with vegetation characteristics, soil properties, and plant community structure that are not directly linked to water access.

RevDate: 2019-01-29

Priadka P, Manseau M, Trottier T, et al (2019)

Partitioning drivers of spatial genetic variation for a continuously distributed population of boreal caribou: Implications for management unit delineation.

Ecology and evolution, 9(1):141-153 pii:ECE34682.

Isolation by distance (IBD) is a natural pattern not readily incorporated into theoretical models nor traditional metrics for differentiating populations, although clinal genetic differentiation can be characteristic of many wildlife species. Landscape features can also drive population structure additive to baseline IBD resulting in differentiation through isolation-by-resistance (IBR). We assessed the population genetic structure of boreal caribou across western Canada using nonspatial (STRUCTURE) and spatial (MEMGENE) clustering methods and investigated the relative contribution of IBD and IBR on genetic variation of 1,221 boreal caribou multilocus genotypes across western Canada. We further introduced a novel approach to compare the partitioning of individuals into management units (MU) and assessed levels of genetic connectivity under different MU scenarios. STRUCTURE delineated five genetic clusters while MEMGENE identified finer-scale differentiation across the study area. IBD was significant and did not differ for males and females both across and among detected genetic clusters. MEMGENE landscape analysis further quantified the proportion of genetic variation contributed by IBD and IBR patterns, allowing for the relative importance of spatial drivers, including roads, water bodies, and wildfires, to be assessed and incorporated into the characterization of population structure for the delineation of MUs. Local population units, as currently delineated in the boreal caribou recovery strategy, do not capture the genetic variation and connectivity of the ecotype across the study area. Here, we provide the tools to assess fine-scale spatial patterns of genetic variation, partition drivers of genetic variation, and evaluate the best management options for maintaining genetic connectivity. Our approach is highly relevant to vagile wildlife species that are of management and conservation concern and demonstrate varying degrees of IBD and IBR with clinal spatial genetic structure that challenges the delineation of discrete population boundaries.

RevDate: 2019-01-29

van der Loos LM, Schmid M, Leal PP, et al (2019)

Responses of macroalgae to CO2 enrichment cannot be inferred solely from their inorganic carbon uptake strategy.

Ecology and evolution, 9(1):125-140 pii:ECE34679.

Increased plant biomass is observed in terrestrial systems due to rising levels of atmospheric CO2, but responses of marine macroalgae to CO2 enrichment are unclear. The 200% increase in CO2 by 2100 is predicted to enhance the productivity of fleshy macroalgae that acquire inorganic carbon solely as CO2 (non-carbon dioxide-concentrating mechanism [CCM] species-i.e., species without a carbon dioxide-concentrating mechanism), whereas those that additionally uptake bicarbonate (CCM species) are predicted to respond neutrally or positively depending on their affinity for bicarbonate. Previous studies, however, show that fleshy macroalgae exhibit a broad variety of responses to CO2 enrichment and the underlying mechanisms are largely unknown. This physiological study compared the responses of a CCM species (Lomentaria australis) with a non-CCM species (Craspedocarpus ramentaceus) to CO2 enrichment with regards to growth, net photosynthesis, and biochemistry. Contrary to expectations, there was no enrichment effect for the non-CCM species, whereas the CCM species had a twofold greater growth rate, likely driven by a downregulation of the energetically costly CCM(s). This saved energy was invested into new growth rather than storage lipids and fatty acids. In addition, we conducted a comprehensive literature synthesis to examine the extent to which the growth and photosynthetic responses of fleshy macroalgae to elevated CO2 are related to their carbon acquisition strategies. Findings highlight that the responses of macroalgae to CO2 enrichment cannot be inferred solely from their carbon uptake strategy, and targeted physiological experiments on a wider range of species are needed to better predict responses of macroalgae to future oceanic change.

RevDate: 2019-01-29

Kärcher O, Hering D, Frank K, et al (2019)

Freshwater species distributions along thermal gradients.

Ecology and evolution, 9(1):111-124 pii:ECE34659.

The distribution of a species along a thermal gradient is commonly approximated by a unimodal response curve, with a characteristic single optimum near the temperature where a species is most likely to be found, and a decreasing probability of occurrence away from the optimum. We aimed at identifying thermal response curves (TRCs) of European freshwater species and evaluating the potential impact of climate warming across species, taxonomic groups, and latitude. We first applied generalized additive models using catchment-scale global data on distribution ranges of 577 freshwater species native to Europe and four different temperature variables (the current annual mean air/water temperature and the maximum air/water temperature of the warmest month) to describe species TRCs. We then classified TRCs into one of eight curve types and identified spatial patterns in thermal responses. Finally, we integrated empirical TRCs and the projected geographic distribution of climate warming to evaluate the effect of rising temperatures on species' distributions. For the different temperature variables, 390-463 of 577 species (67.6%-80.2%) were characterized by a unimodal TRC. The number of species with a unimodal TRC decreased from central toward northern and southern Europe. Warming tolerance (WT = maximum temperature of occurrence-preferred temperature) was higher at higher latitudes. Preferred temperature of many species is already exceeded. Rising temperatures will affect most Mediterranean species. We demonstrated that freshwater species' occurrence probabilities are most frequently unimodal. The impact of the global climate warming on species distributions is species and latitude dependent. Among the studied taxonomic groups, rising temperatures will be most detrimental to fish. Our findings support the efforts of catchment-based freshwater management and conservation in the face of global warming.

RevDate: 2019-01-29

Leatherbury KN, J Travis (2019)

The effects of food level and social density on reproduction in the Least Killifish, Heterandria formosa.

Ecology and evolution, 9(1):100-110 pii:ECE34634.

The feedbacks from population density to demographic parameters, which drive population regulation, are the accumulated results of several ecological processes. The compensatory feedback from increased population density to fertility includes at least two distinct factors, the effects of decreases in per capita food level and increases in the social density (the number of interacting individuals). Because these effects have been studied separately, their relative importance is unknown. It is also unclear whether food limitation and social density combine additively to influence fertility. We investigated these questions with two factorial experiments on reproduction in the Least Killifish, Heterandria formosa. In one experiment, we crossed two levels of density with two levels of a total food ration that was distributed to all individuals. In the other experiment, we crossed two levels of density with two levels of per capita food. Whereas the first experiment suggested that the effects of variation in food level and density were synergistic, the second experiment indicated that they were not. The apparent synergism-the statistical interaction of food and density levels-was the result of confounding per capita food with social density in that design. In the second experiment, the effects of social density on reproductive rate were stronger than the effects of food level, whereas the effects of food level were stronger on offspring size at parturition than those of social density. The results suggest that the social stresses that emerge at higher densities play an important role in the compensatory response of fertility to density, a role, that is, at least as important as that of decreased per capita food levels.

RevDate: 2019-01-29

Bird T, Lyon J, Wotherspoon S, et al (2019)

Combining capture-recapture data and known ages allows estimation of age-dependent survival rates.

Ecology and evolution, 9(1):90-99 pii:ECE34633.

In many animal populations, demographic parameters such as survival and recruitment vary markedly with age, as do parameters related to sampling, such as capture probability. Failing to account for such variation can result in biased estimates of population-level rates. However, estimating age-dependent survival rates can be challenging because ages of individuals are rarely known unless tagging is done at birth. For many species, it is possible to infer age based on size. In capture-recapture studies of such species, it is possible to use a growth model to infer the age at first capture of individuals. We show how to build estimates of age-dependent survival into a capture-mark-recapture model based on data obtained in a capture-recapture study. We first show how estimates of age based on length increments closely match those based on definitive aging methods. In simulated analyses, we show that both individual ages and age-dependent survival rates estimated from simulated data closely match true values. With our approach, we are able to estimate the age-specific apparent survival rates of Murray and trout cod in the Murray River, Australia. Our model structure provides a flexible framework within which to investigate various aspects of how survival varies with age and will have extensions within a wide range of ecological studies of animals where age can be estimated based on size.

RevDate: 2019-01-29

Loosen AE, Morehouse AT, MS Boyce (2019)

Land tenure shapes black bear density and abundance on a multi-use landscape.

Ecology and evolution, 9(1):73-89 pii:ECE34617.

Global biodiversity is decreasing rapidly. Parks and protected lands, while designed to conserve wildlife, often cannot provide the habitat protection needed for wide-ranging animals such as the American black bear (Ursus americanus). Conversely, private lands are often working landscapes (e.g., farming) that have high human footprints relative to protected lands. In southwestern Alberta, road densities are highest on private lands and black bears can be hunted year-round. On protected lands, road densities are lowest, and hunting is prohibited. On public lands under the jurisdiction of the provincial government (Crown lands), seasonal hunting is permitted. Population estimates are needed to calculate sustainable harvest levels and to monitor population trends. In our study area, there has never been a robust estimate of black bear density and spatial drivers of black bear density are poorly understood. We used non-invasive genetic sampling and indices of habitat productivity and human disturbance to estimate density and abundance for male and female black bears in 2013 and 2014 using two methods: spatially explicit capture-recapture (SECR) and resource-selection functions (RSF). Land tenure best explained spatial variation in black bear density. Black bear densities for females and males were highest on parkland and lowest on Crown lands. Sex ratios were female-biased on private lands, likely a result of lower harvests and movement of females out of areas with high male density. Synthesis and application: Both SECR and RSF methods clearly indicate spatial structuring of black bear density, with a strong influence based on how lands are managed. Land tenure influences the distribution of available foods and risk from humans. We emphasize the need for improved harvest reporting, particularly for non-licensed hunting on private land, to estimate the extent of black bear harvest mortality.

RevDate: 2019-01-29

Bhardwaj M, Soanes K, Lahoz-Monfort JJ, et al (2019)

Little evidence of a road-effect zone for nocturnal, flying insects.

Ecology and evolution, 9(1):65-72 pii:ECE34609.

Roads and traffic may be contributing to global declines of insect populations. The ecological effects of roads often extend far into the surrounding habitat, over a distance known as the road-effect zone. The quality of habitat in the road-effect zone is generally degraded (e.g., due to edge effects, noise, light, and chemical pollution) and can be reflected in species presence, abundance, or demographic parameters. Road-effect zones have been quantified for some vertebrate species but are yet to be quantified for insects. Investigating the road-effect zone for insects will provide a better understanding of how roads impact ecosystems, which is particularly important given the role insects play as pollinators, predators, and prey for other species. We quantified the road-effect zone for nocturnal flying insects along three major freeways in agricultural landscapes in southeast Australia. We collected insects using light traps at six points along 2-km transects perpendicular to each highway (n = 17). We sorted the samples into order, and dried and weighed each order to obtain a measure of dry biomass. Using regression models within a Bayesian framework of inference, we estimated the change in biomass of each order with distance from the road, while accounting for environmental variables such as temperature, moon phase, and vegetation structure. The biomass of nine of the ten orders sampled did not change with distance from the freeway. Orthoptera (i.e., grasshoppers and crickets) was the only order whose biomass increased with distance from the freeway. From our findings, we suggest that the impacts of roads on insects are unlikely extending into the surrounding landscape over a distance of 2 km. Therefore, if there are impacts of roads on insects, these are more likely to be concentrated at the road itself, or on finer taxonomic scales such as family or genus level.

RevDate: 2019-01-29

Hirota SK, Miki N, Yasumoto AA, et al (2019)

UV bullseye contrast of Hemerocallis flowers attracts hawkmoths but not swallowtail butterflies.

Ecology and evolution, 9(1):52-64 pii:ECE34604.

The color and patterns of animal-pollinated flowers are known to have effects on pollinator attraction. In this study, the relative importance of flower color and color contrast patterns on pollinator attraction was examined in two pollinator groups, swallowtail butterflies and hawkmoths using two Hemerocallis species; butterfly-pollinated H. fulva and hawkmoth-pollinated H. citrina, having reddish and yellowish flowers in human vision, respectively. Flowers of both species have UV bullseye patterns, composed of UV-absorbing centers and UV-reflecting peripheries, known to function as a typical nectar guide, but UV reflectance was significantly more intense in the peripheries of H. citrina flowers than in those of H. fulva flowers. Comparison based on the visual systems of butterflies and hawkmoths showed that the color contrast of the bullseye pattern in H. citrina was more intense than that in H. fulva. To evaluate the relative importance of flower color and the color contrast of bullseye pattern on pollinator attraction, we performed a series of observations using experimental arrays consisting of Hemerocallis species and their hybrids. As a result, swallowtail butterflies and crepuscular/nocturnal hawkmoths showed contrasting preferences for flower color and patterns: butterflies preferred H. fulva-like colored flower whereas the preference of hawkmoths was affected by the color contrast of the bullseye pattern rather than flower color. Both crepuscular and nocturnal hawkmoths consistently preferred flowers with stronger contrast of the UV bullseye pattern, whereas the preference of hawkmoths for flower color was incoherent. Our finding suggests that hawkmoths can use UV-absorbing/reflecting bullseye patterns for foraging under light-limited environments and that the intensified bullseye contrast of H. citrina evolved as an adaptation to hawkmoths. Our results also showed the difference of visual systems between pollinators, which may have promoted floral divergence.

RevDate: 2019-01-29

Gotanda KM, Pack A, LeBlond C, et al (2019)

Do replicates of independent guppy lineages evolve similarly in a predator-free laboratory environment?.

Ecology and evolution, 9(1):36-51 pii:ECE34585.

The Trinidadian guppy is emblematic of parallel and convergent evolution, with repeated demonstrations that predation regime is a driver of adaptive trait evolution. A classic and foundational experiment in this system was conducted by John Endler 40 years ago, where male guppies placed into low-predation environments in the laboratory evolved increased color in a few generations. However, Endler's experiment did not employ the now typical design for a parallel/convergent evolution study, which would employ replicates of different ancestral lineages. We therefore implemented an experiment that seeded replicate mesocosms with small founding populations of guppies originating from high-predation populations of two very different lineages. The different mesocosms were maintained identically, and male guppy color was quantified every four months. After one year, we tested whether male color had increased, whether replicates within a lineage had parallel phenotypic trajectories, and whether the different lineages converged on a common phenotype. Results showed that male guppy color generally increased through time, primarily due to changes in melanic color, whereas the other colors showed inconsistent and highly variable trajectories. Most of the nonparallelism in phenotypic trajectories was among mesocosms containing different lineages. In addition to this mixture of parallelism and nonparallelism, convergence was not evident in that the variance in color among the mesocosms actually increased through time. We suggest that our results reflect the potential importance of high variation in female preference and stochastic processes such as drift and founder effects, both of which could be important in nature.

RevDate: 2019-01-29

Wang Y, DE Rozen (2019)

Fitness costs of phoretic nematodes in the burying beetle, Nicrophorus vespilloides.

Ecology and evolution, 9(1):26-35 pii:ECE34570.

Nicrophorusvespilloides is a social beetle that rears its offspring on decomposing carrion. Wild beetles are frequently associated with two types of macrobial symbionts, mites, and nematodes. Although these organisms are believed to be phoretic commensals that harmlessly use beetles as a means of transfer between carcasses, the role of these symbionts on N. vespilloides fitness is poorly understood. Here, we show that nematodes have significant negative effects on beetle fitness across a range of worm densities and also quantify the density-dependent transmission of worms between mating individuals and from parents to offspring. Using field-caught beetles, we provide the first report of a new nematode symbiont in N. vespilloides, most closely related to Rhabditoides regina, and show that worm densities are highly variable across individuals isolated from nature but do not differ between males and females. Next, by inoculating mating females with increasing densities of nematodes, we show that worm infections significantly reduce brood size, larval survival, and larval mass, and also eliminate the trade-off between brood size and larval mass. Finally, we show that nematodes are efficiently transmitted between mating individuals and from mothers to larvae, directly and indirectly via the carcass, and that worms persist through pupation. These results show that the phoretic nematode R. regina can be highly parasitic to burying beetles but can nevertheless persist because of efficient mechanisms of intersexual and intergenerational transmission. Phoretic species are exceptionally common and may cause significant harm to their hosts, even though they rely on these larger species for transmission to new resources. However, this harm may be inevitable and unavoidable if transmission of phoretic symbionts requires nematode proliferation. It will be important to determine the generality of our results for other phoretic associates of animals. It will equally be important to assess the fitness effects of phoretic species under changing resource conditions and in the field where diverse interspecific interactions may exacerbate or reduce the negative effects of phoresy.

RevDate: 2019-01-29

Davis MJ, Andersen JC, J Elkinton (2019)

Identification of the parasitoid community associated with an outbreaking gall wasp, Zapatella davisae, and their relative abundances in New England and Long Island, New York.

Ecology and evolution, 9(1):19-25 pii:ECE34543.

Gall wasps (Hymenoptera: Cynipidae) are phytophagous insects that often go unnoticed; however, when they are introduced to a new area or released from their natural enemies, they have the capacity to outbreak and cause extensive foliar damage. One such outbreaking pest, Zapatella davisae (Cynipidae: Cynipini), causes significant damage and mortality to black oak, Quercus velutina, in the northeastern United States. In this study, we aimed to identify the parasitoid community associated with Z. davisae, compare differences in percent parasitism of Z. davisae in Cape Cod and Long Island, and determine which parasitoid species contribute most to parasitism in each region. From both locations, we reared parasitoids, identified morphological groups, analyzed percent parasitism rates for each group, and used DNA barcoding to provide species-level identifications. On Long Island, there was nearly 100% parasitism in 2015 followed by a near total collapse of the population in 2016. In contrast, parasitism rates were lower and remained consistent on Cape Cod between 2015 and 2016, which may explain the greater canopy damage observed in that region. Species of Sycophila were the dominant parasitoids, with one species Sycophila nr. novascotiae representing ~65% of reared parasitoids from Long Island, and two species of Sycophila (S. nr. novascotiae and S. foliatae) with near equal representations on Cape Cod. In order to manage an insect pest, it is important to understand factors that influence its mortality and survival. An understanding of how these infestations progress overtime can help predict the impact that newer infestations in Nantucket, MA, and coastal Rhode Island will have on black oak populations and will aid in the management of this rapidly spreading gall wasp pest.

RevDate: 2019-01-29

Singh PB, Saud P, Cram D, et al (2019)

Ecological correlates of Himalayan musk deer Moschus leucogaster.

Ecology and evolution, 9(1):4-18 pii:ECE34435.

Himalayan musk deer (Moschus leucogaster; hereafter musk deer) are endangered as a result of poaching and habitat loss. The species is nocturnal, crepuscular, and elusive, making direct observation of habitat use and behavior difficult. However, musk deer establish and repeatedly use the same latrines for defecation. To quantify musk deer habitat correlates, we used observational spatial data based on presence-absence of musk deer latrines, as well as a range of fine spatial-scale ecological covariates. To determine presence-absence of musk deer, we exhaustively searched randomly selected forest trails using a 20-m belt transect in different study sites within the Neshyang Valley in the Annapurna Conservation Area. In a subsequent way, study sites were classified as habitat or nonhabitat for musk deer. A total of 252 plots, 20 × 20 m, were systematically established every 100 m along 51 transects (each ~0.5 km long) laid out at different elevations to record a range of ecological habitat variables. We used mixed-effect models and principal component analysis to characterize relationships between deer presence-absence data and habitat variables. We confirmed musk deer use latrines in forests located at higher elevations (3,200-4,200 m) throughout multiple seasons and years. Himalayan birch (Betula utilis) dominated forest, mixed Himalayan fir (Abies spectabilis), and birch forest were preferred over pure Himalayan fir and blue pine (Pinus wallichiana) forest. Greater crown cover and shrub diversity were associated with the presence of musk deer whereas tree height, diameter, and diversity were weakly correlated. Topographical attributes including aspect, elevation, distance to water source, and slope were also discriminated by musk deer. Over- and understory forest management can be used to protect forests likely to have musk deer as predicted by the models to ensure long-term conservation of this rare deer.

RevDate: 2019-01-26

Gestal MC, Whitesides LT, ET Harvill (2019)

Integrated Signaling Pathways Mediate Bordetella Immunomodulation, Persistence, and Transmission.

Trends in microbiology, 27(2):118-130.

The mammalian immune system includes a sophisticated array of antimicrobial mechanisms. However, successful pathogens have developed subversive strategies to detect, modulate, and/or evade immune control and clearance. Independent disciplines study host immunology and bacterial pathogenesis, but interkingdom signaling between bacteria and host during natural infection remains poorly understood. An efficient natural host infection system has revealed complex communication between Bordetella spp. and mice, identified novel regulatory mechanisms, and demonstrated that bordetellae can respond to microenvironment and inflammatory status cues. Understanding these bacterial signaling pathways and their complex network that allows precisely timed expression of numerous immunomodulatory factors will serve as a paradigm for other organisms lacking such a powerful experimental infection system. VIDEO ABSTRACT.

RevDate: 2019-02-01

Zhan C, Liu W, Hegazy AM, et al (2018)

Explorations of the optimal method for isolating oocytes from zebrafish (Danio rerio) ovary.

Journal of experimental zoology. Part B, Molecular and developmental evolution, 330(8):417-426.

Obtaining oocytes from the adult female zebrafish (Danio rerio) ovary has enormous importance in the studies of developmental biology, toxicology, and genetics. It is vital to establish a simple and effective approach to ensure the quantity and quality of oocytes, which will enable the success of follow-up experimental investigation finally. Usually, oocytes are separated with mechanical or enzymatic methods, however, little studies have been done with concerns about the comparative effects. The present study separated zebrafish oocytes of Stage III with five frequently used methods, including stripping, pipetting, hyaluronidase (1.6 mg/ml), collagenase (0.4 mg/ml), and trypsin (0.1%). The cell viability, oxidative stress, mitogen-activated protein kinase (MAPK) protein phosphorylation, and apoptosis levels were selected as main biomarkers to evaluate the oocytes health status. The results showed that both trypsin and hyaluronidase isolation significantly upregulated germinal vesicle breakdown (GVBD) rates and downregulated p38 MAPK activity simultaneously. GVBD rates and survival rates were decreased notably in oocytes separated by the collagenase method. Above results indicate that zebrafish oocytes in vitro are sensitive to enzymatic treatments and the enzymatic isolation is not the suitable mean for collecting zebrafish oocytes although it is time-saving. The mechanical strategy of pipetting remarkably increased the reactive oxygen species and malondialdehyde level in isolated oocytes. Interestingly, oocytes separated with stripping show less physiological and biochemical damages. Therefore, stripping isolation is comparatively recommended as the optimum method for separating and collecting numerous intact and healthy zebrafish oocytes in vitro for the subsequent developmental research.

RevDate: 2019-01-18

Rojas-Bracho L, Brusca RC, Álvarez-Borrego S, et al (2019)

Unsubstantiated Claims Can Lead to Tragic Conservation Outcomes.

Bioscience, 69(1):12-14.

RevDate: 2019-01-31

Wu X, Cabanos C, TA Rapoport (2018)

Structure of the post-translational protein translocation machinery of the ER membrane.

Nature pii:10.1038/s41586-018-0856-x [Epub ahead of print].

Many proteins must translocate through the protein-conducting Sec61 channel in the eukaryotic endoplasmic reticulum membrane or the SecY channel in the prokaryotic plasma membrane1,2. Proteins with highly hydrophobic signal sequences are first recognized by the signal recognition particle (SRP)3,4 and then moved co-translationally through the Sec61 or SecY channel by the associated translating ribosome. Substrates with less hydrophobic signal sequences bypass the SRP and are moved through the channel post-translationally5,6. In eukaryotic cells, post-translational translocation is mediated by the association of the Sec61 channel with another membrane protein complex, the Sec62-Sec63 complex7-9, and substrates are moved through the channel by the luminal BiP ATPase9. How the Sec62-Sec63 complex activates the Sec61 channel for post-translational translocation is not known. Here we report the electron cryo-microscopy structure of the Sec complex from Saccharomyces cerevisiae, consisting of the Sec61 channel and the Sec62, Sec63, Sec71 and Sec72 proteins. Sec63 causes wide opening of the lateral gate of the Sec61 channel, priming it for the passage of low-hydrophobicity signal sequences into the lipid phase, without displacing the channel's plug domain. Lateral channel opening is triggered by Sec63 interacting both with cytosolic loops in the C-terminal half of Sec61 and transmembrane segments in the N-terminal half of the Sec61 channel. The cytosolic Brl domain of Sec63 blocks ribosome binding to the channel and recruits Sec71 and Sec72, positioning them for the capture of polypeptides associated with cytosolic Hsp7010. Our structure shows how the Sec61 channel is activated for post-translational protein translocation.

RevDate: 2019-02-01

Holthaus KB, Eckhart L, Dalla Valle L, et al (2018)

Review: Evolution and diversification of corneous beta-proteins, the characteristic epidermal proteins of reptiles and birds.

Journal of experimental zoology. Part B, Molecular and developmental evolution, 330(8):438-453.

In all amniotes specialized intermediate filament keratins (IF-keratins), in addition to keratin-associated and corneous proteins form the outermost cornified layer of the epidermis. Only in reptiles and birds (sauropsids) the epidermis of scales, claws, beaks, and feathers, largely comprises small proteins formerly indicated as "beta-keratins" but here identified as corneous beta-proteins (CBPs) to avoid confusion with true keratins. Genes coding for CBPs have evolved within the epidermal differentiation complex (EDC), a locus with no relationship with those of IF-keratins. CBP genes have the same exon-intron structure as EDC genes encoding other corneous proteins of sauropsids and mammals, but they are unique by encoding a peculiar internal amino acid sequence motif beta-sheet region that allows formation of CBP filaments in the epidermis and epidermal appendages of reptiles and birds. In contrast, skin appendages of mammals, like hairs, claws, horns and nails, contain keratin-associated proteins that, like IF-keratin genes, are encoded by genes in loci different from the EDC. Phylogenetic analysis shows that lepidosaurian (lizards and snakes) and nonlepidosaurian (crocodilians, birds, and turtles) CBPs form two separate clades that likely originated after the divergence of these groups of sauropsids in the Permian Period. Clade-specific CBPs evolved to make most of the corneous material of feathers in birds and of the shell in turtles. Based on the recent identification of the complete sets of CBPs in all major phylogenetic clades of sauropsids, this review provides a comprehensive overview of the molecular evolution of CBPs.

RevDate: 2019-01-13

Kume K, Amagasa T, Hashimoto T, et al (2018)

NommPred: Prediction of Mitochondrial and Mitochondrion-Related Organelle Proteins of Nonmodel Organisms.

Evolutionary bioinformatics online, 14:1176934318819835 pii:10.1177_1176934318819835.

To estimate the functions of mitochondria of diverse eukaryotic nonmodel organisms in which the mitochondrial proteomes are not available, it is necessary to predict the protein sequence features of the mitochondrial proteins computationally. Various prediction methods that are trained using the proteins of model organisms belonging particularly to animals, plants, and fungi exist. However, such methods may not be suitable for predicting the proteins derived from nonmodel organisms because the sequence features of the mitochondrial proteins of diversified nonmodel organisms can differ from those of model organisms that are present only in restricted parts of the tree of eukaryotes. Here, we proposed NommPred, which predicts the mitochondrial proteins of nonmodel organisms that are widely distributed over eukaryotes. We used a gradient boosting machine to develop 2 predictors-one for predicting the proteins of mitochondria and the other for predicting the proteins of mitochondrion-related organelles that are highly reduced mitochondria. The performance of both predictors was found to be better than that of the best method available.

RevDate: 2019-02-02

Wilkinson AW, Diep J, Dai S, et al (2019)

SETD3 is an actin histidine methyltransferase that prevents primary dystocia.

Nature, 565(7739):372-376.

For more than 50 years, the methylation of mammalian actin at histidine 73 has been known to occur1. Despite the pervasiveness of His73 methylation, which we find is conserved in several model animals and plants, its function remains unclear and the enzyme that generates this modification is unknown. Here we identify SET domain protein 3 (SETD3) as the physiological actin His73 methyltransferase. Structural studies reveal that an extensive network of interactions clamps the actin peptide onto the surface of SETD3 to orient His73 correctly within the catalytic pocket and to facilitate methyl transfer. His73 methylation reduces the nucleotide-exchange rate on actin monomers and modestly accelerates the assembly of actin filaments. Mice that lack SETD3 show complete loss of actin His73 methylation in several tissues, and quantitative proteomics analysis shows that actin His73 methylation is the only detectable physiological substrate of SETD3. SETD3-deficient female mice have severely decreased litter sizes owing to primary maternal dystocia that is refractory to ecbolic induction agents. Furthermore, depletion of SETD3 impairs signal-induced contraction in primary human uterine smooth muscle cells. Together, our results identify a mammalian histidine methyltransferase and uncover a pivotal role for SETD3 and actin His73 methylation in the regulation of smooth muscle contractility. Our data also support the broader hypothesis that protein histidine methylation acts as a common regulatory mechanism.

RevDate: 2019-01-09

Abdelaziz M, Bakkali M, Gómez JM, et al (2019)

Anther Rubbing, a New Mechanism That Actively Promotes Selfing in Plants.

The American naturalist, 193(1):140-147.

Self-fertilization has recurrently evolved in plants, involving different strategies and traits and often loss of attractive functions, collectively known as the selfing syndrome. However, few traits that actively promote self-fertilization have been described. Here we describe a novel mechanism promoting self-fertilization in the Brassicaceae species Erysimum incanum. This mechanism, which we called "anther rubbing," consists of autonomous, repeated, and coordinated movements of the stamens over the stigma during flower opening. We have documented anther rubbing by time-lapse videos and experimentally show that it causes self-pollen deposition on stigmas and is sufficient to achieve maximal reproductive output in E. incanum. We predict that these movements should occur in species with limited inbreeding depression, and indeed we find that inbreeding depression in seed production is negligible in this species. While many studies have documented complex floral traits that promote outcrossing, the occurrence of anther rubbing demonstrates that plants can evolve elaborate and underappreciated adaptations to promote self-fertilization.

RevDate: 2019-01-09

Backmann P, Grimm V, Jetschke G, et al (2019)

Delayed Chemical Defense: Timely Expulsion of Herbivores Can Reduce Competition with Neighboring Plants.

The American naturalist, 193(1):125-139.

Time delays in plant responses to insect herbivory are thought to be the principal disadvantage of induced over constitutive defenses, suggesting that there should be strong selection for rapid responses. However, observed time delays between the onset of herbivory and defense induction vary considerably among plants. We postulate that strong competition with conspecifics is an important codeterminant of the cost-benefit balance for induced responses. There may be a benefit to the plant to delay mounting a full defense response until the herbivore larvae are mobile enough to leave and large enough to cause severe damage to neighboring plants. Thus, delayed responses could reduce the competitive pressure on the focal plant. To explore this idea, we developed an individual-based model using data from wild tobacco, Nicotiana attenuata, and its specialized herbivore, Manduca sexta. Chemical defense was assumed to be costly in terms of reduced plant growth. We used a genetic algorithm with the plant's delay time as a heritable trait. A stationary distribution of delay times emerged, which under high herbivore densities peaked at higher values, which were related to the time larvae need to grow large enough to severely damage neighboring plants. Plants may thus tip the competitive balance by expelling insect herbivores to move to adjacent plants when the herbivores are most damaging. Thus, herbivores become part of a plant's strategy for reducing competition and increasing fitness.

RevDate: 2019-01-09

Wardlaw AM, AF Agrawal (2019)

Sexual Conflict and Sexually Transmitted Infections (STIs): Coevolution of Sexually Antagonistic Host Traits with an STI.

The American naturalist, 193(1):E1-E14.

In many taxa, there is a conflict between the sexes over mating rate. The outcome of sexually antagonistic coevolution depends on the costs of mating and natural selection against sexually antagonistic traits. A sexually transmitted infection (STI) changes the relative strength of these costs. We study the three-way evolutionary interaction among male persistence, female resistance, and STI virulence for two types of STIs: a viability-reducing STI and a reproduction-reducing STI. A viability-reducing STI escalates conflict between the sexes. This leads to increased STI virulence (i.e., full coevolution) if the costs of sexually antagonistic traits occur through viability but not through reproduction. In contrast, a reproduction-reducing STI de-escalates the sexual conflict, but STI virulence does not coevolve in response. We also investigated the establishment probability of STIs under different combinations of evolvability. Successful invasion by a viability-reducing STI becomes less likely if hosts (but not parasites) are evolvable, especially if only the female trait can evolve. A reproduction-reducing STI can almost always invade because it does not kill its host. We discuss how the evolution of host and parasite traits in a system with sexual conflict differs from a system with female mate choice.

RevDate: 2019-01-09

Ferrari M, Lindholm AK, B König (2019)

Fitness Consequences of Female Alternative Reproductive Tactics in House Mice (Mus musculus domesticus).

The American naturalist, 193(1):106-124.

Alternative reproductive tactics (ARTs) are defined as discrete differences in morphological, physiological, and/or behavioral traits associated with reproduction that occur within the same sex and population. House mice provide a rare example of ARTs in females, which can rear their young either solitarily or together with one or several other females in a communal nest. We assessed the fitness consequences of communal and solitary breeding in a wild population to understand how the two tactics can be evolutionarily stable. Females switched between the two tactics (with more than 50% of all females having two or more litters using both tactics), pointing toward communal and solitary breeding being two tactics within a single strategy and not two genetically determined strategies. Communal breeding resulted in reduced pup survival and negatively impacted female reproductive success. Older and likely heavier females more often reared their litters solitarily, indicating that females use a condition-dependent strategy. Solitary breeding seems the more successful tactic, and only younger and likely less competitive females might opt for communal nursing, even at the cost of increased pup mortality. This study emphasizes the importance of analyzing phenotypic plasticity and its role in cooperation in the context of female ARTs.

RevDate: 2019-01-09

Gouveia SF, Bovo RP, Rubalcaba JG, et al (2019)

Biophysical Modeling of Water Economy Can Explain Geographic Gradient of Body Size in Anurans.

The American naturalist, 193(1):51-58.

Geographical gradients of body size express climate-driven constraints on animals, but whether they exist and what causes them in ectotherms remains contentious. For amphibians, the water conservation hypothesis posits that larger bodies reduce evaporative water loss (EWL) along dehydrating gradients. To address this hypothesis mechanistically, we build on well-established biophysical equations of water exchange in anurans to propose a state-transition model that predicts an increase of either body size or resistance to EWL as alternative specialization along dehydrating gradients. The model predicts that species whose water economy is more sensitive to variation in body size than to variation in resistance to EWL should increase in size in response to increasing potential evapotranspiration (PET). To evaluate the model predictions, we combine physiological measurements of resistance to EWL with geographic data of body size for four different anuran species. Only one species, Dendropsophus minutus, was predicted to exhibit a positive body size-PET relationship. Results were as predicted for all cases, with one species-Boana faber-showing a negative relationship. Based on an empirically verified mathematical model, we show that clines of body size among anurans depend on the current values of those traits and emerge as an advantage for water conservation. Our model offers a mechanistic and compelling explanation for the cause and variation of gradients of body size in anurans.

RevDate: 2019-01-09

Anonymous (2019)

2018 American Society of Naturalists Awards.

The American naturalist, 193(1):ii-iii.

RevDate: 2019-01-09

Hahn PG, Agrawal AA, Sussman KI, et al (2019)

Population Variation, Environmental Gradients, and the Evolutionary Ecology of Plant Defense against Herbivory.

The American naturalist, 193(1):20-34.

A central tenet of plant defense theory is that adaptation to the abiotic environment sets the template for defense strategies, imposing a trade-off between plant growth and defense. Yet this trade-off, commonly found among species occupying divergent resource environments, may not occur across populations of single species. We hypothesized that more favorable climates and higher levels of herbivory would lead to increases in growth and defense across plant populations. We evaluated whether plant growth and defense traits covaried across 18 populations of showy milkweed (Asclepias speciosa) inhabiting an east-west climate gradient spanning 25° of longitude. A suite of traits impacting defense (e.g., latex, cardenolides), growth (e.g., size), or both (e.g., specific leaf area [SLA], trichomes) were measured in natural populations and in a common garden, allowing us to evaluate plastic and genetically based variation in these traits. In natural populations, herbivore pressure increased toward warmer sites with longer growing seasons. Growth and defense traits showed strong clinal patterns and were positively correlated. In a common garden, clines with climatic origin were recapitulated only for defense traits. Correlations between growth and defense traits were also weaker and more negative in the common garden than in the natural populations. Thus, our data suggest that climatically favorable sites likely facilitate the evolution of greater defense at minimal costs to growth, likely because of increased resource acquisition.

RevDate: 2019-01-09

Patin R, Fortin D, Sueur C, et al (2019)

Space Use and Leadership Modify Dilution Effects on Optimal Vigilance under Food-Safety Trade-Offs.

The American naturalist, 193(1):E15-E28.

Dilution of predation risk within groups allows individuals to be less vigilant and forage more while still facing lower risk than if they were alone. How group size influences vigilance when individuals can also adjust their space use and whether this relationship differs among individuals contributing differently to space use decisions remain unknown. We present a model-based study of how dilution affects the optimal antipredator behavior of group members in groups where all individuals determine their vigilance level while group leaders also determine space use. We showed that optimal vigilance did not always decrease with group size, as it was sometimes favorable for individuals in larger groups to use riskier patches while remaining vigilant. Followers were also generally less vigilant than leaders. Indeed, followers needed to acquire more resources than leaders, as only the latter could decide when to go to richer patches. Followers still benefit from dilution of predation risk compared with solitary individuals. For leaders, keeping their leadership status can be more important than incorporating new group members to increase dilution. We demonstrate that risk dilution impacts both optimal vigilance and space use, with fitness reward being tied to a member's ability to influence group space use.

RevDate: 2019-01-09

Webb MH, Heinsohn R, Sutherland WJ, et al (2019)

An Empirical and Mechanistic Explanation of Abundance-Occupancy Relationships for a Critically Endangered Nomadic Migrant.

The American naturalist, 193(1):59-69.

The positive abundance-occupancy relationship (AOR) is a pervasive pattern in macroecology. Similarly, the association between occupancy (or probability of occurrence) and abundance is also usually assumed to be positive and in most cases constant. Examples of AORs for nomadic species with variable distributions are extremely rare. Here we examined temporal and spatial trends in the AOR over 7 years for a critically endangered nomadic migrant that relies on dynamic pulses in food availability to breed. We predicted a negative temporal relationship, where local mean abundances increase when the number of occupied sites decreases, and a positive relationship between local abundances and the probability of occurrence. We also predicted that these patterns are largely attributable to spatiotemporal variation in food abundance. The temporal AOR was significantly negative, and annual food availability was significantly positively correlated with the number of occupied sites but negatively correlated with abundance. Thus, as food availability decreased, local densities of birds increased, and vice versa. The abundance-probability of occurrence relationship was positive and nonlinear but varied between years due to differing degrees of spatial aggregation caused by changing food availability. Importantly, high abundance (or occupancy) did not necessarily equate to high-quality habitat and may be indicative of resource bottlenecks or exposure to other processes affecting vital rates. Our results provide a rare empirical example that highlights the complexity of AORs for species that target aggregated food resources in dynamic environments.

RevDate: 2019-01-09

Leimar O, Dall SRX, McNamara JM, et al (2019)

Ecological Genetic Conflict: Genetic Architecture Can Shift the Balance between Local Adaptation and Plasticity.

The American naturalist, 193(1):70-80.

Genetic polymorphism can contribute to local adaptation in heterogeneous habitats, for instance, as a single locus with alleles adapted to different habitats. Phenotypic plasticity can also contribute to trait variation across habitats, through developmental responses to habitat-specific cues. We show that the genetic architecture of genetically polymorphic and plasticity loci may influence the balance between local adaptation and phenotypic plasticity. These effects of genetic architecture are instances of ecological genetic conflict. A reduced effective migration rate for genes tightly linked to a genetic polymorphism provides an explanation for the effects, and they can occur both for a single trait and for a syndrome of coadapted traits. Using individual-based simulations and numerical analysis, we investigate how among-habitat genetic polymorphism and phenotypic plasticity depend on genetic architecture. We also study the evolution of genetic architecture itself, in the form of rates of recombination between genetically polymorphic loci and plasticity loci. Our main result is that for plasticity genes that are unlinked to loci with between-habitat genetic polymorphism, the slope of a reaction norm is steeper in comparison with the slope favored by plasticity genes that are tightly linked to genes for local adaptation.

RevDate: 2019-01-09

Yeh DJ (2019)

Assortative Mating by an Obliquely Transmitted Local Cultural Trait Promotes Genetic Divergence: A Model.

The American naturalist, 193(1):81-92.

The effect of learned culture (e.g., birdsong dialects and human languages) on genetic divergence is unclear. Previous theoretical research suggests that because oblique learning allows phenotype transmission from individuals with no offspring to an unrelated individual in the next generation, the effect of sexual selection on the learned trait is masked. However, I propose that migration and spatially constrained learning can form statistical associations between cultural and genetic traits, which may allow selection on the cultural traits to indirectly affect the genetic traits. Here, I build a population genetic model that allows such statistical associations to form and find that sexual selection and divergent selection on the cultural trait can indeed help maintain genetic divergence through such statistical associations, while selection against genetic hybrids does not affect cultural trait divergence. Furthermore, I find that even when the cultural trait changes over time due to drift and mutation, it can still help maintain genetic divergence. These results suggest the role of obliquely transmitted traits in evolution may be underrated, and the lack of one-to-one associations between cultural and genetic traits may not be sufficient to disprove the role of culture in genetic divergence.

RevDate: 2019-01-09

Connallon T, Sharma S, C Olito (2019)

Evolutionary Consequences of Sex-Specific Selection in Variable Environments: Four Simple Models Reveal Diverse Evolutionary Outcomes.

The American naturalist, 193(1):93-105.

The evolutionary trajectories of species with separate sexes depend on the effects of genetic variation on female and male traits as well as the direction and alignment of selection between the sexes. Classical theory has shown that evolution is equally responsive to selection on females and males, with natural selection increasing the product of the average relative fitness of each sex over time. This simple rule underlies several important predictions regarding the maintenance of genetic variation, the genetic basis of adaptation, and the dynamics of "sexually antagonistic" alleles. Nevertheless, theories of sex-specific selection overwhelmingly focus on evolution in constant environments, and it remains unclear whether they apply under changing conditions. We derived four simple models of sex-specific selection in variable environments and explored how conditions of population subdivision, the timing of dispersal, sex differences in dispersal, and the nature of environmental change mediate the evolutionary dynamics of sex-specific adaptation. We find that these dynamics are acutely sensitive to ecological, demographic, and life-history attributes that vary widely among species, with classical predictions breaking down in contexts of environmental heterogeneity. The evolutionary rules governing sex-specific adaptation may therefore differ between species, suggesting new avenues for research on the evolution of sexual dimorphism.

RevDate: 2019-01-09

Stuart YE (2019)

Divergent Uses of "Parallel Evolution" during the History of The American Naturalist.

The American naturalist, 193(1):11-19.

The mechanistic link between natural selection and parallel evolution is well established. Natural selection is the only known deterministic process that can regularly overcome chance and historical contingency to generate the evolution of similar characteristics in independent populations inhabiting similar environments. However, the ready inference of natural selection from parallel evolution has been established only relatively recently. Here, I review the use of "parallel evolution" in the first 125 years of The American Naturalist and show that there were other well-accepted definitions of the term through the history of the field. I discuss the legacy of those alternative ideas and how they helped to shape evolution and ecology as we know them today and finish by discussing a geometric use for "parallel" that may reduce terminological confusion.

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RJR Experience and Expertise

Researcher

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.

Educator

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.

Administrator

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.

Technologist

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.

Publisher

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.

Speaker

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.

Facilitator

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.

Designer

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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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

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

Research Gate page for R J Robbins

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

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

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