genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms

Genotyping-by-sequencing illuminates high levels of divergence among sympatric forms of coregonines in the Laurentian Great Lakes

Effective resource management depends on our ability to partition diversity into biologically meaningful units. Recent evolutionary divergence, however, can often lead to ambiguity in morphological and genetic differentiation, complicating the delineation of valid conservation units. Such is the case with the "coregonine problem," where recent postglacial radiations of coregonines into lacustrine habitats resulted in the evolution of numerous species flocks, often with ambiguous taxonomy. The application of genomics methods is beginning to shed light on this problem and the evolutionary mechanisms underlying divergence in these ecologically and economically important fishes. Here, we used restriction site-associated DNA (RAD) sequencing to examine genetic diversity and differentiation among sympatric forms in the Coregonus artedi complex in the Apostle Islands of Lake Superior, the largest lake in the Laurentian Great Lakes. Using 29,068 SNPs, we were able to clearly distinguish among the three most common forms for the first time, as well as identify putative hybrids and potentially misidentified specimens. Population assignment rates for these forms using our RAD data were 93%-100% with the only mis-assignments arising from putative hybrids, an improvement from 62% to 77% using microsatellites. Estimates of pairwise differentiation (F ST: 0.045-0.056) were large given the detection of hybrids, suggesting that reduced fitness of hybrid individuals may be a potential mechanism for the maintenance of differentiation. We also used a newly built C. artedi linkage map to look for islands of genetic divergence among forms and found widespread differentiation across the genome, a pattern indicative of long-term drift, suggesting that these forms have been reproductively isolated for a substantial amount of time. The results of this study provide valuable information that can be applied to develop well-informed management strategies and stress the importance of re-evaluating conservation units with genomic tools to ensure they accurately reflect species diversity.

Functional colour genes and signals of selection in colour-polymorphic salamanders

Coloration has been associated with multiple biologically relevant traits that drive adaptation and diversification in many taxa. However, despite the great diversity of colour patterns present in amphibians the underlying molecular basis is largely unknown. Here, we use insight from a highly colour-variable lineage of the European fire salamander (Salamandra salamandra bernardezi) to identify functional associations with striking variation in colour morph and pattern. The three focal colour morphs-ancestral black-yellow striped, fully yellow and fully brown-differed in pattern, visible coloration and cellular composition. From population genomic analyses of up to 4,702 loci, we found no correlations of neutral population genetic structure with colour morph. However, we identified 21 loci with genotype-phenotype associations, several of which relate to known colour genes. Furthermore, we inferred response to selection at up to 142 loci between the colour morphs, again including several that relate to coloration genes. By transcriptomic analysis across all different combinations, we found 196 differentially expressed genes between yellow, brown and black skin, 63 of which are candidate genes involved in animal coloration. The concordance across different statistical approaches and 'omic data sets provide several lines of evidence for loci linked to functional differences between colour morphs, including TYR, CAMK1 and PMEL. We found little association between colour morph and the metabolomic profile of its toxic compounds from the skin secretions. Our research suggests that current ecological and evolutionary hypotheses for the origins and maintenance of these striking colour morphs may need to be revisited.

Subspecies in the Sarus Crane Antigone antigone revisited; with particular reference to the Australian population

Subspecies are often less well-defined than species but have become one of the basic units for legal protection. Evidence for the erection or synonymy of subspecies therefore needs to be founded on the best science available. Here we show that there is clear genetic disjunction in the Sarus Crane Antigone antigone, where previously the variation had appeared to be clinal. Based on a total sample of 76 individuals, analysis of 10 microsatellite loci from 67 samples and 49 sequences from the mitochondrial control region, this research establishes that the Australian Sarus Crane A. a. gillae differs significantly from both A. a. antigone (South Asia) and A. a. sharpii (Myanmar and Indochina). A single sample from the extinct Philippine subspecies A. a luzonica clustered with A. a. gillae, hinting at the potential for a more recent separation between them than from A. a. antigone and A. a. sharpii, even though A. a. sharpii is closer geographically. The results demonstrate that failure to detect subspecies through initial genetic profiling does not mean discontinuities are absent and has significance for other cases where subspecies are dismissed based on partial genetic evidence. It could also be potentially important for sourcing birds for reintroduction to the Philippines.

Urbanization and Population Genetic Structure of the Panama City crayfish (Procambarus econfinae)

For species with geographically restricted distributions, the impacts of habitat loss and fragmentation on long-term persistence may be particularly pronounced. We examined the genetic structure of Panama City crayfish (PCC), Procambarus econfinae, whose historical distribution is limited to an area approximately 145 km2, largely within the limits of Panama City and eastern Bay County, FL. Currently, PCC occupy approximately 28% of its historical range, with suitable habitat composed of fragmented patches in the highly urbanized western portion of the range and managed plantations in the more contiguous eastern portion of the range. We used 1640 anonymous single-nucleotide polymorphisms to evaluate the effects of anthropogenic habitat modification on the genetic diversity and population structure of 161 PCC sampled from across its known distribution. First, we examined urban habitat patches in the west compared with less-developed habitat patches in the east. Second, we used approximate Bayesian computation to model inferences on the demographic history of eastern and western populations. We found anthropogenic habitat modifications explain the genetic structure of PCC range-wide. Clustering analyses revealed significant genetic structure between and within eastern and western regions. Estimates of divergence between east and west were consistent with urban growth in the mid-20th century. PCC have low genetic diversity and high levels of inbreeding and relatedness, indicating populations are small and isolated. Our results suggest that PCC have been strongly affected by habitat loss and fragmentation and management strategies, including legal protection, translocations, or reintroductions, may be necessary to ensure long-term persistence.

Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish

Understanding the extent to which ecological divergence is repeatable is essential for predicting responses of biodiversity to environmental change. Here we test the predictability of evolution, from genotype to phenotype, by studying parallel evolution in a salmonid fish, Arctic charr (Salvelinus alpinus), across eleven replicate sympatric ecotype pairs (benthivorous-planktivorous and planktivorous-piscivorous) and two evolutionary lineages. We found considerable variability in eco-morphological divergence, with several traits related to foraging (eye diameter, pectoral fin length) being highly parallel even across lineages. This suggests repeated and predictable adaptation to environment. Consistent with ancestral genetic variation, hundreds of loci were associated with ecotype divergence within lineages of which eight were shared across lineages. This shared genetic variation was maintained despite variation in evolutionary histories, ranging from postglacial divergence in sympatry (ca. 10-15kya) to pre-glacial divergence (ca. 20-40kya) with postglacial secondary contact. Transcriptome-wide gene expression (44,102 genes) was highly parallel across replicates, involved biological processes characteristic of ecotype morphology and physiology, and revealed parallelism at the level of regulatory networks. This expression divergence was not only plastic but in part genetically controlled by parallel cis-eQTL. Lastly, we found that the magnitude of phenotypic divergence was largely correlated with the genetic differentiation and gene expression divergence. In contrast, the direction of phenotypic change was mostly determined by the interplay of adaptive genetic variation, gene expression, and ecosystem size. Ecosystem size further explained variation in putatively adaptive, ecotype-associated genomic patterns within and across lineages, highlighting the role of environmental variation and stochasticity in parallel evolution. Together, our findings demonstrate the parallel evolution of eco-morphology and gene expression within and across evolutionary lineages, which is controlled by the interplay of environmental stochasticity and evolutionary contingencies, largely overcoming variable evolutionary histories and genomic backgrounds.

Canadian polar bear population structure using genome-wide markers

Predicting the consequences of environmental changes, including human-mediated climate change on species, requires that we quantify range-wide patterns of genetic diversity and identify the ecological, environmental, and historical factors that have contributed to it. Here, we generate baseline data on polar bear population structure across most Canadian subpopulations (n = 358) using 13,488 genome-wide single nucleotide polymorphisms (SNPs) identified with double-digest restriction site-associated DNA sequencing (ddRAD). Our ddRAD dataset showed three genetic clusters in the sampled Canadian range, congruent with previous studies based on microsatellites across the same regions; however, due to a lack of sampling in Norwegian Bay, we were unable to confirm the existence of a unique cluster in that subpopulation. These data on the genetic structure of polar bears using SNPs provide a detailed baseline against which future shifts in population structure can be assessed, and opportunities to develop new noninvasive tools for monitoring polar bears across their range.

Patterns of genetic diversity in North Africa: Moroccan-Algerian genetic split in Juniperus thurifera subsp. africana

Juniperus thurifera is a key element of the forest communities in arid and semi-arid areas of the western Mediterranean. Previous genetic and morphological investigations suggested that Algerian populations are genetically more similar to European than to Moroccan populations and advocated their recognition at the variety rank. We aimed to investigate the spatial genetic structure in J. thurifera to verify the distinct character of the Algerian population in terms of the genetic breaks reported among several North African taxa. We also modelled species distributions since the Eemian to recognise the impact of past climatic changes on the current pattern of diversity and predict possible changes in species distribution in the future. Species-specific microsatellites were used in the analysis of 11 populations from Algeria, Morocco and Europe. We revealed the significant genetic distinctiveness of the Algerian populations from the Moroccan and European stands that may have important taxonomic and conservation implications. The diversity pattern revealed for J. thurifera reflects the east-west genetic splits reported among some North African plant and animal taxa and suggests an impact of shared historical processes. Additionally, modelling of the distribution allowed us to identify possible glacial refugia and their impact on the modern pattern of differentiation in J. thurifera. Reduction of species occurrence, especially in the European domain, is likely according to the future projections of the species distribution.

genodive version 3.0: Easy-to-use software for the analysis of genetic data of diploids and polyploids

genodive version 3.0 is a user-friendly program for the analysis of population genetic data. This version presents a major update from the previous version and now offers a wide spectrum of different types of analyses. genodive has an intuitive graphical user interface that allows direct manipulation of the data through transformation, imputation of missing data, and exclusion and inclusion of individuals, population and/or loci. Furthermore, genodive seamlessly supports 15 different file formats for importing or exporting data from or to other programs. One major feature of genodive is that it supports both diploid and polyploid data, up to octaploidy (2n = 8x) for some analyses, but up to hexadecaploidy (2n = 16x) for other analyses. The different types of analyses offered by genodive include multiple statistics for estimating population differentiation (φ_ST , F_ST , F'_ST , G_ST , G'_ST , G''_ST , D_est , R_ST , ρ), analysis of molecular variance-based K-means clustering, Hardy-Weinberg equilibrium, hybrid index, population assignment, clone assignment, Mantel test, Spatial Autocorrelation, 23 ways of calculating genetic distances, and both principal components and principal coordinates analyses. A unique feature of genodive is that it can also open data sets with nongenetic variables, for example environmental data or geographical coordinates that can be included in the analysis. In addition, genodive makes it possible to run several external programs (lfmm, structure, instruct and vegan) directly from its own user interface, avoiding the need for data reformatting and use of the command line. genodive is available for computers running Mac OS X 10.7 or higher and can be downloaded freely from: http://www.patrickmeirmans.com/software.

Gene Flow in the Müllerian Mimicry Ring of a Poisonous Papuan Songbird Clade (Pitohui; Aves)

Müllerian mimicry rings are remarkable symbiotic species assemblages in which multiple members share a similar phenotype. However, their evolutionary origin remains poorly understood. Although gene flow among species has been shown to generate mimetic patterns in some Heliconius butterflies, mimicry is believed to be due to true convergence without gene flow in many other cases. We investigated the evolutionary history of multiple members of a passerine mimicry ring in the poisonous Papuan pitohuis. Previous phylogenetic evidence indicates that the aposematic coloration shared by many, but not all, members of this genus is ancestral and has only been retained by members of the mimicry ring. Using a newly assembled genome and thousands of genomic DNA markers, we demonstrate gene flow from the hooded pitohui (Pitohui dichrous) into the southern variable pitohui (Pitohui uropygialis), consistent with shared patterns of aposematic coloration. The vicinity of putatively introgressed loci is significantly enriched for genes that are important in melanin pigment expression and toxin resistance, suggesting that gene flow may have been instrumental in the sharing of plumage patterns and toxicity. These results indicate that interspecies gene flow may be a more general mechanism in generating mimicry rings than hitherto appreciated.

Geographical Gradients of Genetic Diversity and Differentiation among the Southernmost Marginal Populations of Abies sachalinensis Revealed by EST-SSR Polymorphism

Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background and Objectives: Genetic diversity among local populations of a plant species at its distributional margin has long been of interest in ecological genetics. Populations at the distribution center grow well in favorable conditions, but those at the range margins are exposed to unfavorable environments, and the environmental conditions at establishment sites might reflect the genetic diversity of local populations. This is known as the central-marginal hypothesis in which marginal populations show lower genetic variation and higher differentiation than in central populations. In addition, genetic variation in a local population is influenced by phylogenetic constraints and the population history of selection under environmental constraints. In this study, we investigated this hypothesis in relation to Abies sachalinensis, a major conifer species in Hokkaido. Materials and Methods: A total of 1189 trees from 25 natural populations were analyzed using 19 EST-SSR loci. Results: The eastern populations, namely, those in the species distribution center, showed greater genetic diversity than did the western peripheral populations. Another important finding is that the southwestern marginal populations were genetically differentiated from the other populations. Conclusions: These differences might be due to genetic drift in the small and isolated populations at the range margin. Therefore, our results indicated that the central-marginal hypothesis held true for the southernmost A. sachalinensis populations in Hokkaido.

Chromosome and Genome Divergence between the Cryptic Eurasian Malaria Vector-Species Anopheles messeae and Anopheles daciae

Chromosomal inversions are important drivers of genome evolution. The Eurasian malaria vector Anophelesmesseae has five polymorphic inversions. A cryptic species, An. daciae, has been discriminated from An. messeae based on five fixed nucleotide substitutions in the internal transcribed spacer 2 (ITS2) of ribosomal DNA. However, the inversion polymorphism in An. daciae and the genome divergence between these species remain unexplored. In this study, we sequenced the ITS2 region and analyzed the inversion frequencies of 289 Anopheles larvae specimens collected from three locations in the Moscow region. Five individual genomes for each of the two species were sequenced. We determined that An. messeae and An. daciae differ from each other by the frequency of polymorphic inversions. Inversion X1 was fixed in An. messeae but polymorphic in An. daciae populations. The genome sequence comparison demonstrated genome-wide divergence between the species, especially pronounced on the inversion-rich X chromosome (mean Fst = 0.331). The frequency of polymorphic autosomal inversions was higher in An. messeae than in An. daciae. We conclude that the X chromosome inversions play an important role in the genomic differentiation between the species. Our study determined that An. messeae and An. daciae are closely related species with incomplete reproductive isolation.

Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq

To study the genetic structure of clonal plant populations, genotyping and genet detection using genetic markers are necessary to assign ramets to corresponding genets. Assignment is difficult as it involves setting a robust threshold of genetic distance for genet distinction as neighbouring genets in a plant population are often genetically related. Here, we used restriction site-associated DNA sequencing (RAD-seq) for a rhizomatous clonal herb, Cardamine leucantha [Brassicaceae] to accurately determine genet structure in a natural population. We determined a draft genome sequence of this species for the first time, which resulted in 66 617 scaffolds with N₅₀ = 6086 bp and an estimated genome size of approximately 253 Mbp. Using genetic distances based on the RAD-seq analysis, we successfully distinguished ramets that belonged to distinct genets even from a half-sib family. We applied these methods to 372 samples of C. leucantha collected at 1-m interval grids within a 20 × 20 m plot in a natural population in Hokkaido, Japan. From these samples, we identified 61 genets with high inequality in terms of genet size and patchy distribution. Spatial autocorrelation analyses indicated significant aggregation within 7 and 4 m at ramet and genet levels, respectively. An analysis of parallel DNA microsatellite loci (simple sequence repeats) suggested that RAD-seq can provide data that allows robust genet assignment. It remains unclear whether the large genets identified here became dominant stochastically or deterministically. Precise identification of genets will assist further study and characterization of dominant genets.

The Atoxigenic Biocontrol Product Aflasafe SN01 Is a Valuable Tool to Mitigate Aflatoxin Contamination of Both Maize and Groundnut Cultivated in Senegal

Aflatoxin contamination of groundnut and maize infected by Aspergillus section Flavi fungi is common throughout Senegal. The use of biocontrol products containing atoxigenic Aspergillus flavus strains to reduce crop aflatoxin content has been successful in several regions, but no such products are available in Senegal. The biocontrol product Aflasafe SN01 was developed for use in Senegal. The four active ingredients of Aflasafe SN01 are atoxigenic A. flavus genotypes native to Senegal and distinct from active ingredients used in other biocontrol products. Efficacy tests on groundnut and maize in farmers' fields were carried out in Senegal during the course of 5 years. Active ingredients were monitored with vegetative compatibility analyses. Significant (P < 0.05) displacement of aflatoxin producers occurred in all years, districts, and crops. In addition, crops from Aflasafe SN01-treated fields contained significantly (P < 0.05) fewer aflatoxins both at harvest and after storage. Most crops from treated fields contained aflatoxin concentrations permissible in both local and international markets. Results suggest that Aflasafe SN01 is an effective tool for aflatoxin mitigation in groundnut and maize. Large-scale use of Aflasafe SN01 should provide health, trade, and economic benefits for Senegal.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: A case study using the lake whitefish

Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth, as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these “simple” methodological decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) a larger number of loci at low sequencing depth based on a 9mer (library A); and (2) fewer loci at higher sequencing depth based on a 10mer (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (F_ST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters, largely due to retention of more loci in analyses. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for F_ST and ADMIXTURE, but not DAPC. When detecting fine population differentiation, the population map influenced the number of loci and missing data, which generated artefacts in all downstream analyses tested. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library construction and bioinformatics parameters can have important impacts on the interpretation of population subdivision. Although potentially more costly on a per-locus basis, early investment in striking a balance between the number of loci and sequencing effort is well worth the reduced genomic coverage for population genetics studies. More conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation. Overall, we recommend that researchers approach “simple” methodological decisions with caution, especially when working on non-model species for the first time.

Genetic structure of the European hedgehog (Erinaceus europaeus) in Denmark

OBJECTIVES

Low genetic diversity can lead to reduced average fitness in a population or even extinction. Preserving genetic connectivity across fragmented landscapes is therefore vital to counteract the negative consequences of genetic drift and inbreeding. This study aimed to assess the genetic composition and consequently the conservation status of a nationwide sample of European hedgehogs (Erinaceus europaeus) in Denmark.

METHODS

We applied an adaptation of the genotyping by sequencing (GBS) technique to 178 individuals from six geographically distinct populations. We used a Bayesian clustering method to subdivide individuals into genetically distinct populations. We estimated individual observed (iHO), observed (HO), and unbiased expected (uHE) heterozygosity, inbreeding coefficient (FIS), percentage of polymorphic loci (P%) and tested for deviations from Hardy-Weinberg equilibrium (HWE). We used linear models to test for potential anthropogenic effects on the genetic variability of hedgehogs with iHO, uHE, P% and FIS as response variables, and assessed the demographic history of the population.

RESULTS

The Danish hedgehog population is composed of three genetic clusters. We found a mean P% of 54.44-94.71, a mean uHE of 0.126-0.318 and a mean HO of 0.124-0.293 in the six populations. The FIS was found to be significantly positive for three of the six populations. We detected a large heterogeneity of iHO values within populations, which can be due to inbreeding and/or fragmentation. FIS values decreased with increasing farmland density, but there was no significant association with human population or road density.

CONCLUSIONS

We found a low level of genetic variability and evidence for genetic substructure and low effective population size, which are all consequences of habitat fragmentation. We failed to detect signs of a recent population bottleneck or population increase or decline. However, because the test only identifies recent changes in population size, we cannot reject the possibility of a longer-term decline in the Danish hedgehog population.

Genomic and Fitness Consequences of Genetic Rescue in Wild Populations

Gene flow is an enigmatic evolutionary force because it can limit adaptation but may also rescue small populations from inbreeding depression [1-3]. Several iconic examples of genetic rescue-increased population growth caused by gene flow [4, 5]-have reversed population declines [6, 7]. However, concerns about outbreeding depression and maladaptive gene flow limit the use of human-mediated gene flow in conservation [8, 9]. Rescue effects of immigration through demographic and/or genetic mechanisms have received theoretical and empirical support, but studies that monitor initial and long-term effects of gene flow on individuals and populations in the wild are lacking. Here, we used individual-based mark-recapture, multigenerational pedigrees, and genomics to test the demographic and evolutionary consequences of manipulating gene flow in two isolated, wild Trinidadian guppy populations. Recipient and source populations originated from environments with different predation, flow, and resource regimes [10]. We documented 10-fold increases in population size following gene flow and found that, on average, hybrids lived longer and reproduced more than residents and immigrants. Despite overall genomic homogenization, alleles potentially associated with local adaptation were not entirely swamped by gene flow. Our results suggest that genetic rescue was caused not just by increasing individual genetic diversity, rather new genomic variation from immigrants combined with alleles from the recipient population resulted in highly fit hybrids and subsequent increases in population size. Contrary to the classic view of maladaptive gene flow, our study reveals conditions under which immigration can produce long-term fitness benefits in small populations without entirely swamping adaptive variation.

So Closely Related and Yet So Different: Strong Contrasts Between the Evolutionary Histories of Species of the Cardamine pratensis Polyploid Complex in Central Europe

Recurrent polyploid formation and weak reproductive barriers between independent polyploid lineages generate intricate species complexes with high diversity and reticulate evolutionary history. Uncovering the evolutionary processes that formed their present-day cytotypic and genetic structure is a challenging task. We studied the species complex of Cardamine pratensis, composed of diploid endemics in the European Mediterranean and diploid-polyploid lineages more widely distributed across Europe, focusing on the poorly understood variation in Central Europe. To elucidate the evolution of Central European populations we analyzed ploidy level and genome size variation, genetic patterns inferred from microsatellite markers and target enrichment of low-copy nuclear genes (Hyb-Seq), and environmental niche differentiation. We observed almost continuous variation in chromosome numbers and genome size in C. pratensis s.str., which is caused by the co-occurrence of euploid and dysploid cytotypes, along with aneuploids, and is likely accompanied by inter-cytotype mating. We inferred that the polyploid cytotypes of C. pratensis s.str. are both of single and multiple, spatially and temporally recurrent origins. The tetraploid Cardamine majovskyi evolved at least twice in different regions by autopolyploidy from diploid Cardamine matthioli. The extensive genome size and genetic variation of Cardamine rivularis reflects differentiation induced by the geographic isolation of disjunct populations, establishment of triploids of different origins, and hybridization with sympatric C. matthioli. Geographically structured genetic lineages identified in the species under study, which are also ecologically divergent, are interpreted as descendants from different source populations in multiple glacial refugia. The postglacial range expansion was accompanied by substantial genetic admixture between the lineages of C. pratensis s.str., which is reflected by diffuse borders in their contact zones. In conclusion, we identified an interplay of diverse processes that have driven the evolution of the species studied, including allopatric and ecological divergence, hybridization, multiple polyploid origins, and genetic reshuffling caused by Pleistocene climate-induced range dynamics.

Genetic monogamy despite frequent extrapair copulations in "strictly monogamous" wild jackdaws

"Monogamy" refers to different components of pair exclusiveness: the social pair, sexual partners, and the genetic outcome of sexual encounters. Avian monogamy is usually defined socially or genetically, whereas quantifications of sexual behavior remain scarce. Jackdaws (Corvus monedula) are considered a rare example of strict monogamy in songbirds, with lifelong pair bonds and little genetic evidence for extrapair (EP) offspring. Yet jackdaw copulations, although accompanied by loud copulation calls, are rarely observed because they occur visually concealed inside nest cavities. Using full-day nest-box video surveillance and on-bird acoustic bio-logging, we directly observed jackdaw sexual behavior and compared it to the corresponding genetic outcome obtained via molecular parentage analysis. In the video-observed nests, we found genetic monogamy but frequently detected forced EP sexual behavior, accompanied by characteristic male copulation calls. We, thus, challenge the long-held notion of strict jackdaw monogamy at the sexual level. Our data suggest that male mate guarding and frequent intrapair copulations during the female fertile phase, as well as the forced nature of the copulations, could explain the absence of EP offspring. Because EP copulation behavior appeared to be costly for both sexes, we suggest that immediate fitness benefits are an unlikely explanation for its prevalence. Instead, sexual conflict and dominance effects could interact to shape the spatiotemporal pattern of EP sexual behavior in this species. Our results call for larger-scale investigations of jackdaw sexual behavior and parentage and highlight the importance of combining social, sexual, and genetic data sets for a more complete understanding of mating systems.

Speciation and subsequent secondary contact in two edaphic endemic primroses driven by Pleistocene climatic oscillation

Climatic perturbation during the Pleistocene era has played a major role in plant evolutionary history by altering species distribution range. However, the relative roles of climatic and geographic factors in the distribution dynamics remain poorly understood; in particular, the edaphic endemics. In this paper, we examine the evolutionary history of two ultramafic primroses, Primula hidakana and Primula takedana. These species are ecologically and morphologically distinct with disjunct distributions on Hokkaido Island, Japan. Primula hidakana is found on various rocks in southern Hokkaido and P. takedana in serpentine areas in northern Hokkaido. We performed population genetics analyses on nuclear and chloroplast data sets and tested alternative phylogenetic models of divergence using approximate Bayesian computation (ABC) analyses. Nuclear microsatellite loci clearly distinguished the two sister taxa. In contrast, chloroplast sequence variations were shared between P. takedana and P. hidakana. ABC analyses based on nuclear data supported a secondary contact scenario involving asymmetrical gene flow from P. hidakana to P. takedana. Paleodistribution modeling also supported the divergence model, and predicted their latitudinal range shifts leading to past secondary contact. Our findings highlight the importance of the distribution dynamics during the Pleistocene climatic oscillations in the evolution of serpentine plants, and demonstrate that tight species cohesion between serpentine and nonserpentine sister taxa has been maintained despite past interspecific gene flow across soil boundaries.

Going with the flow: Intraspecific variation may act as a natural ally to counterbalance the impacts of global change for the riparian species Populus deltoides

The speed and magnitude of global change will have major impacts on riparian ecosystems, thereby leading to greater forest vulnerability. Assessing species' adaptive capacities to provide relevant information for vulnerability assessments remains challenging, especially for nonmodel species like the North American Populus deltoides W. Bartram ex Marshall. The objective of this study was to understand how genomic diversity of this foundation species was shaped by its environment (climate, soil, and biotic interactions) to gauge its adaptive capacity. We used two complementary approaches to get a full portrait of P. deltoides genetic diversity at both the species and whole-genome ranges. First, we used a set of 93 nuclear and three chloroplastic SNP markers in 946 individuals covering most of the species' natural distribution. Then, to measure the degree of intraspecific divergence at the whole-genome level and to support the outlier and genomic-environment association analyses, we used a sequence capture approach on DNA pools. Three distinct lineages for P. deltoides were detected, and their current distribution was associated with abiotic and biotic variations. The comparison between both cpDNA and ncDNA patterns showed that gene flow between the lineages is unbalanced. The southern and northeastern populations may benefit from the input, through river flow, of novel alleles located upstream to their local gene pools. These alleles could migrate from populations that are already adapted to conditions that fit the predicted climates in the receiving local populations, hotter at the northeastern limit and drier in the Central United States. These "preadapted" incoming alleles may help to cope with maladaptation in populations facing changing conditions.

Population Genomics of an Anadromous Hilsa Shad Tenualosa ilisha Species across Its Diverse Migratory Habitats: Discrimination by Fine-Scale Local Adaptation

The migration of anadromous fish in heterogenic environments unceasingly imposes a selective pressure that results in genetic variation for local adaptation. However, discrimination of anadromous fish populations by fine-scale local adaptation is challenging because of their high rate of gene flow, highly connected divergent population, and large population size. Recent advances in next-generation sequencing (NGS) have expanded the prospects of defining the weakly structured population of anadromous fish. Therefore, we used NGS-based restriction site-associated DNA (NextRAD) techniques on 300 individuals of an anadromous Hilsa shad (Tenualosa ilisha) species, collected from nine strategic habitats, across their diverse migratory habitats, which include sea, estuary, and different freshwater rivers. The NextRAD technique successfully identified 15,453 single nucleotide polymorphism (SNP) loci. Outlier tests using the F_ST OutFLANK and pcadapt approaches identified 74 and 449 SNPs (49 SNPs being common), respectively, as putative adaptive loci under a divergent selection process. Our results, based on the different cluster analyses of these putatively adaptive loci, suggested that local adaptation has divided the Hilsa shad population into two genetically structured clusters, in which marine and estuarine collection sites were dominated by individuals of one genetic cluster and different riverine collection sites were dominated by individuals of another genetic cluster. The phylogenetic analysis revealed that all the riverine populations of Hilsa shad were further subdivided into the north-western riverine (turbid freshwater) and the north-eastern riverine (clear freshwater) ecotypes. Among all of the putatively adaptive loci, only 36 loci were observed to be in the coding region, and the encoded genes might be associated with important biological functions related to the local adaptation of Hilsa shad. In summary, our study provides both neutral and adaptive contexts for the observed genetic divergence of Hilsa shad and, consequently, resolves the previous inconclusive findings on their population genetic structure across their diverse migratory habitats. Moreover, the study has clearly demonstrated that NextRAD sequencing is an innovative approach to explore how dispersal and local adaptation can shape genetic divergence of non-model anadromous fish that intersect diverse migratory habitats during their life-history stages.

The roles of vicariance and dispersal in the differentiation of two species of the Rhinella marina species complex

The high levels of Neotropical biodiversity are commonly associated with the intense Neogene-Quaternary geological events and climate dynamics. Here, we investigate the evolutionary history of two species of Neotropical closely related amphibians (R. horribilis and R. marina). We combine published data with new mitochondrial DNA sequences and multiple nuclear markers, including 12 microsatellites. The phylogenetic analyses showed support for grouping the samples in two main clades; R. horribilis (Central America and Mexico) and R. marina (South America east of the Andes). However, the phylogenetic inferences also show an evident mito-nuclear discordance. We use Approximate Bayesian Computation (ABC) to test the role of different events in the diversification between the two groups recovered. We found that both species were affected primarily by a recent Pleistocene divergence, which was similar to the divergence estimate revealed by the Isolation-with-Migration model, under persistent bidirectional gene flow through time. We provide the first evidence that R. horribilis is differentiated from the South American R. marina at the nuclear level supporting the taxonomic status of R. horribilis, which has been controversial for more than a century.

Genome-wide profiles indicate wolf population connectivity within the eastern Carpathian Mountains

The Carpathian Mountains provide critical wildlife habitat in central Europe, and previous genome-wide studies have found western Carpathian Mountain wolves (Canis lupus) to be a separate population. Whereas differentiation to the north may be explained by a lowland-mountain transition and habitat fragmentation, the eastern Carpathian Mountains extending through Romania appear to offer continuous wildlife habitat southward. Our objective was to assess gene flow patterns and population connectivity among wolves in Romania, western Ukraine, and the Republic of Moldova. We sought to determine if the Carpathian Mountain region is best described by a north-south gradient in genetic profiles, or whether Romanian wolves show population structure with northern individuals clustering with western Ukraine. We genotyped 48 individuals with 170 000 single nucleotide polymorphism markers, and successful profiles from Romania (n = 27) and Moldova (n = 2) were merged with existing data from western Ukraine (n = 10). Expected heterozygosity was 0.234 (SE 0.001) for Romania and 0.229 (SE 0.001) for western Ukraine, whereas observed heterozygosity values were 0.230 (SE 0.001) versus 0.231 (SE 0.001). Population structure analyses with a maximum likelihood method supported K = 1 population, followed by K = 2 where Romania formed one cluster, and western Ukraine and Moldova formed another. Principal component analysis results were broadly consistent with K = 2. Pairwise F_ST between western Ukraine and Romania was 0.042 (p = 0.001). Our findings indicated weak population differentiation, and future research may clarify whether the spatial distribution of genetic diversity in the region is associated with environmental and ecological factors such as terrain ruggedness and the distribution of prey species.

Transferability and Polymorphism of SSR Markers Located in Flavonoid Pathway Genes in Fragaria and Rubus Species

Strawberry (Fragaria) and raspberry (Rubus) are very popular crops, and improving their nutritional quality and disease resistance are important tasks in their breeding programs that are becoming increasingly based on use of functional DNA markers. We identified 118 microsatellite (simple sequence repeat-SSR) loci in the nucleotide sequences of flavonoid biosynthesis and pathogenesis-related genes and developed 24 SSR markers representing some of these structural and regulatory genes. These markers were used to assess the genetic diversity of 48 Fragaria and Rubus specimens, including wild species and rare cultivars, which differ in berry color, ploidy, and origin. We have demonstrated that a high proportion of the developed markers are transferable within and between Fragaria and Rubus genera and are polymorphic. Transferability and polymorphism of the SSR markers depended on location of their polymerase chain reaction (PCR) primer annealing sites and microsatellite loci in genes, respectively. High polymorphism of the SSR markers in regulatory flavonoid biosynthesis genes suggests their allelic variability that can be potentially associated with differences in flavonoid accumulation and composition. This set of SSR markers may be a useful molecular tool in strawberry and raspberry breeding programs for improvement anthocyanin related traits.

Phylogeographic evidence that the distribution of cryptic euryhaline species in the Gambusia punctata species group in Cuba was shaped by the archipelago geological history

The main drivers of diversification of freshwater fishes in Cuba are not yet well understood. For example, salt tolerance was thought as the main factor involved in the diversification of Gambusia punctata species group in this archipelago. However, evidence from a recent DNA barcoding survey suggested the presence of cryptic species and no correlation between species delimitation and level of salinity. In this study, we analyzed the cryptic diversification of G. punctata species group in Cuba, based on a comprehensive sampling of its distribution and including habitats with different salinity levels. We evaluated the patterns of molecular divergence of the samples by sequencing a set of mitochondrial DNA (mtDNA) regions and genotyping nine nuclear microsatellite loci. We also used cytochrome b gene (cytb) partial sequences and these microsatellite loci to analyze population structure inside putative species. Five mtDNA well-differentiated haplogroups were found, four of them also identified by the analysis of the microsatellite polymorphism which corresponds to two already recognized species, G. punctata, and G. rhizophorae, and three putative new species. The extent of hybrid zones between these groups is also described. In each group, populations inhabiting environments with contrasting salinity levels were identified, indicating a generalized trait not specific to G. rhizophorae. The geographic distribution of the groups suggested a strong association with major relict territories of the Cuban Archipelago that was periodically joined or split-up by changes in seawater levels and land uplifts. Salinity tolerance might have facilitated sporadic and long-distance oversea dispersal but did not prevent speciation in the Cuban archipelago.

The origins and evolutionary history of feral apples in southern Canada

Feral populations of domesticated crops can establish through two nonmutually exclusive pathways: hybridization with native relatives and recruitment of and recombination between known cultivars. The extent and relative importance of these pathways is not known, especially for woody fruit crops. Here, we examined the evolutionary origins of feral populations of Malus domestica (domestic apple) in southern Canada using a population genetic analysis. We characterized genotypes of 578 putative feral apple trees and evaluated them in relation to genotypes of 156 commercial cultivars, 28 non-native, ornamental crabapples and 47 native Malus coronaria trees using 14 microsatellite markers. No feral trees were genetic admixtures between domestic and native Malus; however, a minority of trees were admixed with introduced ornamental Malus. Feral trees and commercial cultivars both occurred in two major genetic groups and seven subgroups distributed throughout all commercial growing regions. A total of 42 cultivars, both heritage and currently grown, occurred in probable parental pairs for feral trees, with nine heritage varieties accounting for 72% of parental assignments. We conclude that feral apples in southern Canada are not products of hybridization with native M. coronaria but we cannot exclude ornamental apple species as contributing to the naturalization process. Nonhybrid feral domestic apples have multiple origins, with a prominent signature of early heritage cultivars. These lineages have spread and coexist throughout Ontario, rather than being derived strictly from local sources.

Identification of winter moth (Operophtera brumata) refugia in North Africa and the Italian Peninsula during the last glacial maximum

Numerous studies have shown that the genetic diversity of species inhabiting temperate regions has been shaped by changes in their distributions during the Quaternary climatic oscillations. For some species, the genetic distinctness of isolated populations is maintained during secondary contact, while for others, admixture is frequently observed. For the winter moth (Operophtera brumata), an important defoliator of oak forests across Europe and northern Africa, we previously determined that contemporary populations correspond to genetic diversity obtained during the last glacial maximum (LGM) through the use of refugia in the Iberian and Aegean peninsulas, and to a lesser extent the Caucasus region. Missing from this sampling were populations from the Italian peninsula and from North Africa, both regions known to have played important roles as glacial refugia for other species. Therefore, we genotyped field-collected winter moth individuals from southern Italy and northwestern Tunisia-the latter a region where severe oak forest defoliation by winter moth has recently been reported-using polymorphic microsatellite. We reconstructed the genetic relationships of these populations in comparison to moths previously sampled from the Iberian and Aegean peninsulas, the Caucasus region, and western Europe using genetic distance, Bayesian clustering, and approximate Bayesian computation (ABC) methods. Our results indicate that both the southern Italian and the Tunisian populations are genetically distinct from other sampled populations, and likely originated in their respective refugium during the LGM after diverging from a population that eventually settled in the Iberian refugium. These suggest that winter moth populations persisted in at least five Mediterranean LGM refugia. Finally, we comment that outbreaks by winter moth in northwestern Tunisia are not the result of a recent introduction of a nonnative species, but rather are most likely due to land use or environmental changes.

Genetic diversity of laboratory strains and implications for research: The case of Aedes aegypti

The yellow fever mosquito (Aedes aegypti), is the primary vector of dengue, Zika, and chikungunya fever, among other arboviral diseases. It is also a popular laboratory model in vector biology due to its ease of rearing and manipulation in the lab. Established laboratory strains have been used worldwide in thousands of studies for decades. Laboratory evolution of reference strains and contamination among strains are potential severe problems that could dramatically change experimental outcomes and thus is a concern in vector biology. We analyzed laboratory and field colonies of Ae. aegypti and an Ae. aegypti-derived cell line (Aag2) using 12 microsatellites and ~20,000 SNPs to determine the extent of divergence among laboratory strains and relationships to their wild relatives. We found that 1) laboratory populations are less genetically variable than their field counterparts; 2) colonies bearing the same name obtained from different laboratories may be highly divergent; 3) present genetic composition of the LVP strain used as the genome reference is incompatible with its presumed origin; 4) we document changes in two wild caught colonies over ~16 generations of colonization; and 5) the Aag2 Ae. aegypti cell line has experienced minimal genetic changes within and across laboratories. These results illustrate the degree of variability within and among strains of Ae. aegypti, with implications for cross-study comparisons, and highlight the need of a common mosquito repository and the implementation of strain validation tools.

Contrasting effects of host tree isolation on population connectedness in two tropical epiphytic bromeliads

PREMISE

Conversion of primary forests to pastures is a major cause of habitat fragmentation in the tropics. Fragmentation is expected to impede gene flow for many plant species that are restricted to remaining forest fragments. Epiphytes may be especially vulnerable to this effect of forest fragmentation because they depend on host trees. However, trees that remain in pastures may enhance connectivity across the landscape for epiphyte species that can thrive on such trees. To investigate this possibility, we studied the genetic structures of two such species on isolated pasture trees and surrounding forest, in relation to their local abundances in different habitat types and aspects of their reproductive biology including pollen and seed dispersal agents, and looked for evidence of increased or diminished gene flow.

METHODS

We used microsatellite markers to assess geographic patterns of genetic diversity and differentiation in two epiphytic bromeliads, Catopsis nitida and Werauhia tonduziana, in the Monteverde region of Costa Rica.

RESULTS

About 85% of the F_ST value for Catopsis nitida was found among pastures within regions, while for Weruahia tonduziana, about 80% of the F_ST value was contributed by differences between regions, indicating much more gene flow within regions, relative to C. nitida.

CONCLUSIONS

Although there was substantial genetic differentiation among epiphyte populations, those on isolated pasture trees were not substantially less diverse than those in adjacent forests, suggesting that pasture trees may serve as "stepping stones" that help these species maintain their genetic connectedness and diversity at larger geographic scales.

Population genetics of Anopheles koliensis through Papua New Guinea: New cryptic species and landscape topography effects on genetic connectivity

New Guinea is a topographically and biogeographically complex region that supports unique endemic fauna. Studies describing the population connectivity of species through this region are scarce. We present a population and landscape genetic study on the endemic malaria-transmitting mosquito, Anopheles koliensis (Owen). Using mitochondrial and nuclear sequence data, as well as microsatellites, we show the evidence of geographically discrete population structure within Papua New Guinea (PNG). We also confirm the existence of three rDNA ITS2 genotypes within this mosquito and assess reproductive isolation between individuals carrying different genotypes. Microsatellites reveal the clearest population structure and show four clear population units. Microsatellite markers also reveal probable reproductive isolation between sympatric populations in northern PNG with different ITS2 genotypes, suggesting that these populations may represent distinct cryptic species. Excluding individuals belonging to the newly identified putative cryptic species (ITS2 genotype 3), we modeled the genetic differences between A. koliensis populations through PNG as a function of terrain and find that dispersal is most likely along routes with low topographic relief. Overall, these results show that A. koliensis is made up of geographically and genetically discrete populations in Papua New Guinea with landscape topography being important in restricting dispersal.

Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach

The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned and distributed. This study investigates the role of spatial, environmental and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide single nucleotide polymorphisms, in conjunction with landscape variables derived from Geographic Information Systems, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-resistance (IBR) and isolation-by-colonization (IBC). Our results demonstrated that IBR contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.

Conservation genomics in the fight to help the recovery of the critically endangered Siamese crocodile Crocodylus siamensis

Endangered species are often characterized by low genetic diversity and it is imperative for conservation efforts to incorporate the knowledge obtained from genetic studies for effective management. However, despite the promise of technological advances in sequencing, application of genome-wide data to endangered populations remains uncommon. In the present study we pursued a holistic conservation-genomic approach to inform a field-based management programme of a Critically Endangered species, the Siamese crocodile Crocodylus siamensis. Using thousands of single nucleotide polymorphisms from throughout the genome, we revealed signals of introgression from two other crocodile species within our sample of both wild and captive-bred Siamese crocodiles from Cambodia. Our genetic screening of the Siamese crocodiles resulted in the subsequent re-introduction of 12 individuals into the wild as well as the selection of four individuals for captive breeding programmes. Comparison of intraspecific genetic diversity revealed an alarmingly low contemporary effective population size in the wild (<50) with evidence of a recent bottleneck around Tonle Sap Lake. We also projected a probable future extinction in the wild (within fewer than five generations) in this population in the absence of re-introduction efforts. However, an increase in the number of potential breeders through re-introductions, including the one resulting from this project, could counter this trend. Our results have been implemented in ongoing re-introduction and captive breeding programmes, with major implications for the conservation management of Siamese crocodiles, and provide a blueprint for the rescue effort of other "terminally ill" populations of critically endangered species.

Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish

Little empirical work in nature has quantified how wild populations with varying effective population sizes and genetic diversity perform when exposed to a gradient of ecologically important environmental conditions. To achieve this, juvenile brook trout from 12 isolated populations or closed metapopulations that differ substantially in population size and genetic diversity were transplanted to previously fishless ponds spanning a wide gradient of ecologically important variables. We evaluated the effect of genome-wide variation, effective population size (N_e), pond habitat, and initial body size on two fitness correlates (survival and growth). Genetic variables had no effect on either fitness correlate, which was determined primarily by habitat (pond temperature, depth, and pH) and initial body size. These results suggest that some vertebrate populations with low genomic diversity, low N_e, and long-term isolation can represent important sources of variation and are capable of maintaining fitness in, and ultimately persisting and adapting to, changing environments. Our results also reinforce the paramount importance of improving available habitat and slowing habitat degradation for species conservation.

The complex evolutionary history of apricots: Species divergence, gene flow and multiple domestication events

Domestication is an excellent model to study diversification and this evolutionary process can be different in perennial plants, such as fruit trees, compared to annual crops. Here, we inferred the history of wild apricot species divergence and of apricot domestication history across Eurasia, with a special focus on Central and Eastern Asia, based on microsatellite markers and approximate Bayesian computation. We significantly extended our previous sampling of apricots in Europe and Central Asia towards Eastern Asia, resulting in a total sample of 271 cultivated samples and 306 wild apricots across Eurasia, mainly Prunus armeniaca and Prunus sibirica, with some Prunus mume and Prunus mandshurica. We recovered wild Chinese species as genetically differentiated clusters, with P. sibirica being divided into two clusters, one possibly resulting from hybridization with P. armeniaca. Central Asia also appeared as a diversification centre of wild apricots. We further revealed at least three domestication events, without bottlenecks, that gave rise to European, Southern Central Asian and Chinese cultivated apricots, with ancient gene flow among them. The domestication event in China possibly resulted from ancient hybridization between wild populations from Central and Eastern Asia. We also detected extensive footprints of recent admixture in all groups of cultivated apricots. Our results thus show that apricot is an excellent model for studying speciation and domestication in long-lived perennial fruit trees.

Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline

The blue swimming crab (Portunus pelagicus Linnaeus, 1758) is one of the commercially exploited crab fishery resources in Vietnam. This is the first study to provide a broad survey of genetic diversity, population structure and migration patterns of P. pelagicus along the Vietnamese coastline. The crab samples were collected from northern, central and southern Vietnam. Here, we used a panel of single nucleotide polymorphisms (SNPs) generated from restriction site-associated DNA sequencing (RADseq). After removing 32 outlier loci, 306 putatively neutral SNPs from 96 individuals were used to assess fine-scale population structure of blue swimming crab. The mean observed heterozygosity (Ho) and expected heterozygosity (He) per locus was 0.196 and 0.223, respectively. Pairwise Fst and hierarchical AMOVA supported significant differentiation of central and northern from southern populations (P<0.01). Population structure analyses revealed that P. pelagicus in the south is a separate fisheries unit from the north and center. Contemporary migration patterns supported high migration between northern and central populations and restricted genetic exchange within the southern population. In contrast, historic gene flow provides strong evidence for single panmictic population. The results are useful for understanding current status of P. pelagicus in the wild under an environment changing due to natural and anthropogenic stresses, with implications for fisheries management.

Evidence for adaptive introgression of exons across a hybrid swarm in deer

Background

Secondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study, we examined genetic population structure, extent of introgression, and selection pressures in freely interbreeding populations of mule deer and black-tailed deer using mitochondrial DNA sequences, 9 microsatellite loci, and 95 SNPs from protein-coding genes.

Results

We observed bi-directional hybridization and classified approximately one third of the 172 individuals as hybrids, almost all of which were beyond the F1 generation. High genetic differentiation between black-tailed deer and mule deer at protein-coding genes suggests that there is positive divergent selection, though selection on these loci is relatively weak. Contrary to predictions, there was not greater selection on protein-coding genes thought to be associated with immune function and mate choice. Geographic cline analyses were consistent across genetic markers, suggesting long-term stability (over hundreds of generations), and indicated that the center of the hybrid swarm is 20-30 km to the east of the Cascades ridgeline, where there is a steep ecological transition from wet, forested habitat to dry, scrub habitat.

Conclusions

Our data are consistent with a genetic boundary between mule deer and black-tailed deer that is porous but maintained by many loci under weak selection having a substantial cumulative effect. The absence of clear reproductive barriers and the consistent centering of geographic clines at a sharp ecotone suggests that ecology is a driver of hybrid swarm dynamics. Adaptive introgression in this study (and others) promotes gene flow and provides valuable insight into selection strength on specific genes and the evolutionary trajectory of hybridizing taxa.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1497-x) contains supplementary material, which is available to authorized users.

Ecotypic differentiation, hybridization and clonality facilitate the persistence of a cold-adapted sedge in European bogs

Recent research has shown that many cold-adapted species survived the last glacial maximum (LGM) in northern refugia. Whether this evolutionary history has had consequences for their genetic diversity and adaptive potential remains unknown. We sampled 14 populations of Carex limosa, a sedge specialized to bog ecosystems, along a latitudinal gradient from its Scandinavian core to the southern lowland range-margin in Germany. Using microsatellite and experimental common-garden data, we evaluated the impacts of global climate change along this gradient and assessed the conservation status of the southern marginal populations. Microsatellite data revealed two highly distinct genetic groups and hybrid individuals. In our common-garden experiment, the two groups showed divergent responses to increased nitrogen/phosphorus (N/P) availability, suggesting ecotypic differentiation. Each group formed genetically uniform populations at both northern and southern sampling areas. Mixed populations occurred throughout our sampling area, an area that was entirely glaciated during the LGM. The fragmented distribution implies allopatric divergence at geographically separated refugia that putatively differed in N/P availability. Molecular data and an observed low hybrid fecundity indicate the importance of clonal reproduction for hybrid populations. At the southern range-margin, however, all populations showed effects of clonality, lowered fecundity and low competitiveness, suggesting abiotic and biotic constraints to population persistence.

Host genetics and geography influence microbiome composition in the sponge Ircinia campana

Marine sponges are hosts to large, diverse communities of microorganisms. These microbiomes are distinct among sponge species and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiome variability are underexplored and may shed light on the evolutionary and ecological relationships between host and microbiome. Here, we examined the influence of genetic variation and geographic location on the composition of the Ircinia campana microbiome. We developed new microsatellite markers to genotype I. campana from two locations in the Florida Keys, USA, and characterized their microbiomes using V4 16S rRNA amplicon sequencing. We show that microbial community composition and diversity is influenced by host genotype, with more genetically similar sponges hosting more similar microbial communities. We also found that although I. campana was not genetically differentiated between sites, microbiome composition differed by location. Our results demonstrate that both host genetics and geography influence the composition of the sponge microbiome. Host genotypic influence on microbiome composition may be due to stable vertical transmission of the microbial community from parent to offspring, making microbiomes more similar by descent. Alternatively, sponge genotypic variation may reflect variation in functional traits that influence the acquisition of environmental microbes. This study reveals drivers of microbiome variation within and among locations, and shows the importance of intraspecific variability in mediating eco-evolutionary dynamics of host-associated microbiomes.

The Lesser Antillean Iguana (Iguana delicatissima) on St. Eustatius: Genetically Depauperate and Threatened by Ongoing Hybridization

The Lesser Antillean Iguana (Iguana delicatissima) is an endangered species threatened by habitat loss and hybridization with non-native Green Iguanas (Iguana iguana). Iguana delicatissima has been extirpated on several islands, and the Green Iguana has invaded most islands with extant populations. Information is essential to protect this species from extinction. We collected data on 293 iguanas including 17 juveniles from St. Eustasius, one of the few remaining I. delicatissima strongholds. Genetic data were leveraged to test for hybridization presence with the Green Iguana using both mitochondrial and nuclear genes, including 16 microsatellite loci. The microsatellites were also analyzed to estimate genetic diversity, population structure, and effective population size. Using molecular and morphological data, we identified 286 I. delicatissima individuals captured during our first fieldwork effort, and 7 non-native iguanas captured during a second effort, showing hybridization occurs within this population. Comparing homologous microsatellites used in studies on Dominica and Chancel, the I. delicatissima population on St. Eustatius has extremely low genetic diversity (HO = 0.051; HE = 0.057), suggesting this population is genetically depauperate. Furthermore, there is significant evidence for inbreeding (FIS = 0.12) and weak spatial genetic structure (FST = 0.021, P = 0.002) within this population. Besides immediate threats including hybridization, this population's low genetic diversity, presence of physiological abnormalities and low recruitment could indicate presence of inbreeding depression that threatens its long-term survival. We conclude there is a continued region-wide threat to I. delicatissima and highlight the need for immediate conservation action to stop the continuing spread of Green Iguanas and to eliminate hybridization from St. Eustatius.

Clonal diversity and spatial genetic structure in the long-lived herb, Prairie trillium

Combining population genetic studies with demographic surveys in long-lived clonal herbs can yield insight into the population dynamics of clonal plant populations. In this study, we assayed clonal diversity and spatial genetic structure in a population of a long-lived understory herb, Trillium recurvatum, that has been the focus of a demographic study spanning 26 years at the Meeman Biological Station in Memphis, Tennessee, USA. Using a set of five newly developed simple sequence repeat markers first reported here, we assessed 1) the extent of clonal diversity within the Meeman site, 2) the degree to which genetic diversity varies with stage class (juvenile, non-flowering, and flowering adults) at this site, 3) whether there is spatial genetic structure at the Meeman site, and 4) how measures of genetic diversity and inbreeding at the Meeman site compare to two additional nearby populations. Along with these analyses, we calculated and compared traditional population genetic metrics with information theory-based diversity indices. Although clonal propagation was present, the focal population displayed moderate levels of clonal diversity comprising 81 genets from the 174 individuals sampled. In the focal site, we also found that genetic diversity was highest in the flowering stage class when compared to the non-flowering and juvenile classes. We report that genets exhibited spatial genetic structure in the focal site exhibiting values for the Sp statistic of 0.00199 for linear distance and 0.0271 for log distance. Measures of unbiased gene diversity and the inbreeding coefficient were comparable across the sampled populations. Our results provide complementary genetic data to previous demographic studies in T. recurvatum, and these findings provide data for future studies aimed at integrating the degree of clonality, genetic variation, and population dynamics in this species. Our findings suggest that T. recurvatum at the focal Meeman site displays higher levels of sexual reproduction than were previously suggested, and spatial genetic structure estimates were comparable to other plant species with mixed and outcrossing mating strategies.