pinecone/core-2020-05-10-deduplication huggingface dataset:
Microsatellite and major histocompatibility complex variation in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus)

Genetic diversity is fundamental to maintaining the long‐term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment of adaptive genetic variation in fragmented populations. We compared patterns of microsatellite and MHC variation across three Eastern Massasauga (Sistrurus catenatus) populations representing a gradient of demographic histories to assess the relative roles of natural selection and genetic drift. Using 454 deep amplicon sequencing, we identified 24 putatively functional MHC IIB exon 2 alleles belonging to a minimum of six loci. Analysis of synonymous and nonsynonymous substitution rates provided evidence of historical positive selection at the nucleotide level, and Tajima's D provided support for balancing selection in each population. As predicted, estimates of microsatellite allelic richness, observed, heterozygosity, and expected heterozygosity varied among populations in a pattern qualitatively consistent with demographic history and abundance. While MHC allelic richness at the population and individual levels revealed similar trends, MHC nucleotide diversity was unexpectedly high in the smallest population. Overall, these results suggest that genetic variation in the Eastern Massasauga populations in Illinois has been shaped by multiple evolutionary mechanisms. Thus, conservation efforts should consider both neutral and functional genetic variation when managing captive and wild Eastern Massasauga populations.NIU Library Open Access Grant
Department of Biological Sciences at Northern Illinois University
We thank M. Redmer for providing tissue samples from Cook County, A. Stedman and R. Hoffman for their valuable assistance in the lab, and three anonymous reviewers' comments on an earlier version of this manuscript. This work was funded by grants to R.B.K. from the Department of Biological Sciences at Northern Illinois University. Protocols were approved by the University of Illinois Urbana‐Champaign IACUC (protocol 99283, 02010, 04311, 08019, 10238, 13007, 14000) and Northern Illinois University IACUC (protocol LA10‐0011)
Harvested populations are more variable only in more variable environments

© 2016 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. The interaction between environmental variation and population dynamics is of major importance, particularly for managed and economically important species, and especially given contemporary changes in climate variability. Recent analyses of exploited animal populations contested whether exploitation or environmental variation has the greatest influence on the stability of population dynamics, with consequences for variation in yield and extinction risk. Theoretical studies however have shown that harvesting can increase or decrease population variability depending on environmental variation, and requested controlled empirical studies to test predictions. Here, we use an invertebrate model species in experimental microcosms to explore the interaction between selective harvesting and environmental variation in food availability in affecting the variability of stage-structured animal populations over 20 generations. In a constant food environment, harvesting adults had negligible impact on population variability or population size, but in the variable food environments, harvesting adults increased population variability and reduced its size. The impact of harvesting on population variability differed between proportional and threshold harvesting, between randomly and periodically varying environments, and at different points of the time series. Our study suggests that predicting the responses to selective harvesting is sensitive to the demographic structures and processes that emerge in environments with different patterns of environmental variation
A review of the extensive variation in the design of pitfall traps, and a proposal for a standard pitfall trap design for monitoring ground-active arthropod biodiversity

Natural Environment Research Council (Grant/Award Number: NERC DTG NE/H524930/1 NE/I528634/1).To understand change in global biodiversity patterns requires large-scale, long-term monitoring. The ability to draw meaningful comparison across studies is severely hampered by extensive variation in the design of the sampling equipment and how it is used. Here, we present a meta-analysis and description highlighting this variation in a common, widely used entomological survey technique. We report a decline in the completeness of methodological reporting over a 20-year period, while there has been no clear reduction in the methodological variation between researchers using pitfall traps for arthropod sampling. There is a growing need for improved comparability between studies to facilitate the generation of large-scale, long-term biodiversity datasets. However, our results show that, counterproductive to this goal, over the last 20 years there has little progress in reducing the methodological variation. We propose a standardized pitfall trap design for the study of ground-active arthropods. In addition, we provide a table to promote a more standardized reporting of the key methodological variables. Widespread adoption of more standardized methods and reporting would facilitate more nuanced analysis of biodiversity change.Publisher PDFPeer reviewe
Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species Archocentrus centrarchus

Established empirical cases of sympatric speciation are scarce, although there is an increasing consensus that sympatric speciation might be more common than previously thought. Midas cichlid fish are one of the few substantiated cases of sympatric speciation, and they formed repeated radiations in crater lakes. In contrast, in the same environment, such radiation patterns have not been observed in other species of cichlids and other families of fish. We analyze morphological and genetic variation in a cichlid species (Archocentrus centrarchus) that co-inhabits several crater lakes with the Midas species complex. In particular, we analyze variation in body and pharyngeal jaw shape (two ecologically important traits in sympatrically divergent Midas cichlids) and relate that to genetic variation in mitochondrial control region and microsatellites. Using these four datasets, we analyze variation between and within two Nicaraguan lakes: a crater lake where multiple Midas cichlids have been described and a lake where the source population lives. We do not observe any within-lake clustering consistent across morphological traits and genetic markers, suggesting the absence of sympatric divergence in A. centrarchus. Genetic differentiation between lakes was low and morphological divergence absent. Such morphological similarity between lakes is found not only in average morphology, but also when analyzing covariation between traits and degree of morphospace occupation. A combined analysis of the mitochondrial control region in A. centrarchus and Midas cichlids suggests that a difference between lineages in the timing of crater lake colonization cannot be invoked as an explanation for the difference in their levels of diversification. In light of our results, A. centrarchus represents the ideal candidate to study the genomic differences between these two lineages that might explain why some lineages are more likely to speciate and diverge in sympatry than others
Mate choice for neutral and MHC genetic characteristics in Alpine marmots : different targets in different contexts?

We warmly thank all students and Earthwatch volunteers involved in catching the marmots and the authorities of the Vanoise National Park for granting us permission to work in the Grande Sassière Nature Reserve. We thank M. Harrington for English editing and Dr. E. Rajon for helpful discussions on the manuscript. This work was supported by the “Agence Nationale de la Recherche” (ANR, project ANR‐08‐BLAN‐0214‐03, ANR‐13‐JSV7‐0005), the “Centre National de la Recherche Scientifique” (CNRS), the “FR41 BioEnvironnement et Santé de l'Université de Lyon” and the “Earthwatch Institute”, the scholarship for postgraduate studies “Obra Social Fundació La Caixa” and Vetagro‐Sup.Sexual selection through female mate choice for genetic characteristics has been suggested to be an important evolutionary force maintaining genetic variation in animal populations. However, the genetic targets of female mate choice are not clearly identified and whether female mate choice is based on neutral genetic characteristics or on particular functional loci remains an open question. Here, we investigated the genetic targets of female mate choice in Alpine marmots (Marmota marmota), a socially monogamous mammal where extra‐pair paternity (EPP) occurs. We used 16 microsatellites to describe neutral genetic characteristics and two MHC loci belonging to MHC class I and II as functional genetic characteristics. Our results reveal that (1) neutral and MHC genetic characteristics convey different information in this species, (2) social pairs show a higher MHC class II dissimilarity than expected under random mate choice, and (3) the occurrence of EPP increases when social pairs present a high neutral genetic similarity or dissimilarity but also when they present low MHC class II dissimilarity. Thus, female mate choice is based on both neutral and MHC genetic characteristics, and the genetic characteristics targeted seem to be context dependent (i.e., the genes involved in social mate choice and genetic mate choice differ). We emphasize the need for empirical studies of mate choice in the wild using both neutral and MHC genetic characteristics because whether neutral and functional genetic characteristics convey similar information is not universal
Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant–folivore coevolutionary processes?

The debate whether the coevolution of plants and insects or macroevolutionary processes (phylogeny) is the main driver determining the arsenal of molecular defensive compounds of plants remains unresolved. Attacks by herbivorous insects affect not only the composition of defensive compounds in plants but also the entire metabolome. Metabolomes are the final products of genotypes and are constrained by macroevolutionary processes, so closely related species should have similar metabolomic compositions and may respond in similar ways to attacks by folivores. We analyzed the elemental compositions and metabolomes of needles from three closely related Pinus species with distant coevolutionary histories with the caterpillar of the processionary moth respond similarly to its attack. All pines had different metabolomes and metabolic responses to herbivorous attack. The metabolomic variation among the species and the responses to folivory reflected their macroevolutionary relationships, with P. pinaster having the most divergent metabolome. The concentrations of terpenes were in the attacked trees supporting the hypothesis that herbivores avoid plant individuals with higher concentrations. Our results suggest that macroevolutionary history plays important roles in the metabolomic responses of these pine species to folivory, but plant–insect coevolution probably constrains those responses. Combinations of different evolutionary factors and trade-offs are likely responsible for the different responses of each species to folivory, which is not necessarily exclusively linked to plant–insect coevolution
Dmrt1 polymorphism covaries with sex-determination patterns in Rana temporaria.

Patterns of sex-chromosome differentiation and gonadal development have been shown to vary among populations of Rana temporaria along a latitudinal transect in Sweden. Frogs from the northern-boreal population of Ammarnäs displayed well-differentiated X and Y haplotypes, early gonadal differentiation, and a perfect match between phenotypic and genotypic sex. In contrast, no differentiated Y haplotypes could be detected in the southern population of Tvedöra, where juveniles furthermore showed delayed gonadal differentiation. Here, we show that Dmrt1, a gene that plays a key role in sex determination and sexual development across all metazoans, displays significant sex differentiation in Tvedöra, with a Y-specific haplotype distinct from Ammarnäs. The differential segment is not only much shorter in Tvedöra than in Ammarnäs, it is also less differentiated and associates with both delayed gonadal differentiation and imperfect match between phenotypic and genotypic sex. Whereas Tvedöra juveniles with a local Y haplotype tend to ultimately develop as males, those without it may nevertheless become functional XX males, but with strongly female-biased progeny. Our findings suggest that the variance in patterns of sex determination documented in common frogs might result from a genetic polymorphism within a small genomic region that contains Dmrt1. They also substantiate the view that recurrent convergences of sex determination toward a limited set of chromosome pairs may result from the co-option of small genomic regions that harbor key genes from the sex-determination pathway
Carbon cycling in temperate grassland under elevated temperature

This study was funded by AGRI-I (RSF 10/SC/716), the LOEWE-excellence program FACE2FACE, and the Walsh Fellowship program.peer-reviewedAn increase in mean soil surface temperature has been observed over the last century, and it is predicted to further increase in the future. The effect of increased temperature on ecosystem carbon fluxes in a permanent temperate grassland was studied in a long-term (6 years) field experiment, using multiple temperature increments induced by IR lamps. Ecosystem respiration (R-eco) and net ecosystem exchange (NEE) were measured and modeled by a modified Lloyd and Taylor model including a soil moisture component for R-eco (average R2 of 0.78) and inclusion of a photosynthetic component based on temperature and radiation for NEE (R2 = 0.65). Modeled NEE values ranged between 2.3 and 5.3 kg CO2 m−2 year−1, depending on treatment. An increase of 2 or 3°C led to increased carbon losses, lowering the carbon storage potential by around 4 tonnes of C ha−1 year−1. The majority of significant NEE differences were found during night-time compared to daytime. This suggests that during daytime the increased respiration could be offset by an increase in photosynthetic uptake. This was also supported by differences in δ13C and δ18O, indicating prolonged increased photosynthetic activity associated with the higher temperature treatments. However, this increase in photosynthesis was insufficient to counteract the 24 h increase in respiration, explaining the higher CO2 emissions due to elevated temperature.This study was funded by AGRI-I (RSF 10/SC/716), the LOEWE-excellence program FACE2FACE, and the Walsh Fellowship program
A comparison between data requirements and availability for calibrating predictive ecological models for lowland UK woodlands: learning new tricks from old trees

© 2016 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.Woodlands provide valuable ecosystem services, and it is important to understand their dynamics. To predict the way in which these might change, we need process-based predictive ecological models, but these are necessarily very data intensive. We tested the ability of existing datasets to provide the parameters necessary to instantiate a well-used forest model (SORTIE) for a well-studied woodland (Wytham Woods). Only five of SORTIE's 16 equations describing different aspects of the life history and behavior of individual trees could be parameterized without additional data collection. One age class – seedlings – was completely missed as they are shorter than the height at which Diameter at Breast Height (DBH) is measured. The mensuration of trees has changed little in the last 400 years (focussing almost exclusively on DBH) despite major changes in the nature of the source of value obtained from trees over this time. This results in there being insufficient data to parameterize process-based models in order to meet the societal demand for ecological prediction. We do not advocate ceasing the measurement of DBH, but we do recommend that those concerned with tree mensuration consider whether additional measures of trees could be added to their data collection protocols. We also see advantages in integrating techniques such as ground-based LIDAR or remote sensing techniques with long-term datasets to both preserve continuity with what has been performed in the past and to expand the range of measurements made.published_or_final_versio
The role of endosymbionts in the evolution of haploid-male genetic systems in scale insects (Coccoidea)

There is an extraordinary diversity in genetic systems across species, but this variation remains poorly understood. In part, this is because the mechanisms responsible for transitions between systems are often unknown. A recent hypothesis has suggested that conflict between hosts and endosymbiotic microorganisms over transmission could drive the transition from diplodiploidy to systems with male haploidy (haplodiploidy, including arrhenotoky and paternal genome elimination [PGE]). Here, we present the first formal test of this idea with a comparative analysis across scale insects (Hemiptera: Coccoidea). Scale insects are renowned for their large variation in genetic systems, and multiple transitions between diplodiploidy and haplodiploidy have taken place within this group. Additionally, most species rely on endosymbiotic microorganisms to provide them with essential nutrients lacking in their diet. We show that species harboring endosymbionts are indeed more likely to have a genetic system with male haploidy, which supports the hypothesis that endosymbionts might have played a role in the transition to haplodiploidy. We also extend our analysis to consider the relationship between endosymbiont presence and transitions to parthenogenesis. Although in scale insects there is no such overall association, species harboring eukaryote endosymbionts were more likely to be parthenogenetic than those with bacterial symbionts. These results support the idea that intergenomic conflict can drive the evolution of novel genetic systems and affect host reproduction.Publisher PDFPeer reviewe
Ecosystem size matters: The dimensionality of intralacustrine diversification in Icelandic stickleback is predicted by lake size

Cases of evolutionary diversification can be characterized along a continuum from weak to strong genetic and phenotypic differentiation. Several factors may facilitate or constrain the differentiation process. Comparative analyses of replicates of the same taxon at different stages of differentiation can be useful to identify these factors. We estimated the number of distinct phenotypic groups in threespine stickleback populations from nine lakes in Iceland and in one marine population. Using the inferred number of phenotypic groups in each lake, genetic divergence from the marine population, and physical lake and landscape variables, we tested if ecosystem size, approximated by lake size and depth, or isolation from the ancestral marine gene pool predict the occurrence and the extent of phenotypic and genetic diversification within lakes. We find intralacustrine phenotypic diversification to be the rule rather than the exception, occurring in all but the youngest lake population and being manifest in ecologically important phenotypic traits. Neutral genetic data further indicates non-random mating in four out of nine studied lakes, and restricted gene flow between sympatric phenotypic groups in two. Although neither the phenotypic variation nor the number of intralacustrine phenotypic groups were associated with any of our environmental variables, the number of phenotypic traits that were differentiated was significantly positively related to lake size, and evidence for restricted gene flow between sympatric phenotypic groups was only found in the largest lakes where trait specific phenotypic differentiation was highest
Multitrophic diversity effects of network degradation

Predicting the functional consequences of biodiversity loss in realistic, multitrophic communities remains a challenge. No existing biodiversity–ecosystem function study to date has simultaneously incorporated information on species traits, network topology, and extinction across multiple trophic levels, while all three factors are independently understood as critical drivers of post-extinction network structure and function. We fill this gap by comparing the functional consequences of simulated species loss both within (monotrophic) and across (bitrophic) trophic levels, in an ecological interaction network estimated from spatially explicit field data on tropical fecal detritus producer and consumers (mammals and dung beetles). We simulated trait-ordered beetle and mammal extinction separately (monotrophic extinction) and the coextinction of beetles following mammal loss (bitrophic extinction), according to network structure. We also compared the diversity effects of bitrophic extinction models using a standard monotrophic function (the daily production or consumption of fecal detritus) and a unique bitrophic functional metric (the proportion of daily detritus production that is consumed). We found similar mono- and bitrophic diversity effects, regardless of which species traits were used to drive extinctions, yet divergent predictions when different measures of function were used. The inclusion of information on network structure had little apparent effect on the qualitative relationship between diversity and function. These results contribute to our growing understanding of the functional consequences of biodiversity from real systems and underscore the importance of species traits and realistic functional metrics to assessments of the ecosystem impacts of network degradation through species loss