scholarly journals Fine scale population structure and extensive gene flow within an Eastern Nearctic snake complex (Pituophis melanoleucus)

2021 ◽  
Author(s):  
Zachary L Nikolakis ◽  
Richard Orton ◽  
Brian I Crother
Keyword(s):  
Gene Flow ◽  
Isolation By Distance ◽  
Genomic Structure ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Evolutionary Relationships ◽  
Population Genomic ◽  
Isolation By Environment ◽  
Pituophis Melanoleucus ◽  
Lineage Divergence

Understanding the processes and mechanisms that promote lineage divergence is a central goal in evolutionary biology. For instance, studies investigating the spatial distribution of genomic variation often highlight biogeographic barriers underpinning geographic isolation, as well as patterns of isolation by environment and isolation by distance that can also lead to lineage divergence. However, the patterns and processes that shape genomic variation and drive lineage divergence may be taxa-specific, even across closely related taxa co-occurring within the same biogeographic region. Here, we use molecular data in the form of ultra-conserved elements (UCEs) to infer the evolutionary relationships and population genomic structure of the Eastern Pinesnake complex (Pituophis melanoleucus) – a polytypic wide-ranging species that occupies much of the Eastern Nearctic. In addition to inferring evolutionary relationships, population genomic structure, and gene flow, we also test relationships between genomic diversity and putative barriers to dispersal, environmental variation, and geographic distance. We present results that reveal shallow population genomic structure and ongoing gene flow, despite an extensive geographic range that transcends geographic features found to reduce gene flow among many taxa, including other squamate reptiles within the Eastern Nearctic. Further, our results indicate that the observed genomic diversity is spatially distributed as a pattern of isolation by distance and suggest that the current subspecific taxonomy do not adhere to independent lineages, but rather, show a significant amount of admixture across the entire P. melanoleucus range.

scholarly journals Spatial, climate, and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra

2019 ◽  
Author(s):  
CW Ahrens ◽  
EA James ◽  
AD Miller ◽  
NC Aitken ◽  
JO Borevitz ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Isolation By Distance ◽  
Management Strategies ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
List Type ◽  
Themeda Triandra ◽  
Reduced Representation ◽  
Isolation By Environment ◽  
Susceptible Populations

SummaryFragmented grassland ecosystems, and the species that shape them, are under immense pressure. Restoration and management strategies should include genetic diversity and adaptive capacity to improve success but these data are generally unavailable. Therefore, we use the foundational grass, Themeda triandra, to test how spatial, environmental, and ploidy factors shape patterns of genetic variation.We used reduced-representation genome sequencing on 487 samples from 52 locations to answer fundamental questions about how the distribution of genomic diversity and ploidy polymorphism supports adaptation to harsher climates. We explicitly quantified isolation-by-distance (IBD), isolation-by-environment (IBE), and predicted population genomic vulnerability in 2070.We found that a majority (54%) of the genomic variation could be attributed to IBD, while 22% of the genomic variation could be explained by four climate variables showing IBE. Results indicate that heterogeneous patterns of vulnerability across populations are due to genetic variation, multiple climate factors, and ploidy polymorphism, which lessened genomic vulnerability in the most susceptible populations.These results indicate that restoration and management of T. triandra should incorporate knowledge of genomic diversity and ploidy polymorphisms to increase the likelihood of population persistence and restoration success in areas that will become hotter and more arid.

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

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Alexander B. Chase ◽  
Philip Arevalo ◽  
Eoin L. Brodie ◽  
Martin F. Polz ◽  
Ulas Karaoz ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Isolation By Distance ◽  
Dispersal Limitation ◽  
Genomic Diversity ◽  
Gene Content ◽  
Microbial Populations ◽  
Free Living ◽  
Phylogenetic Structure ◽  
Isolation By Environment

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

scholarly journals Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0259124
Author(s):  
Damian C. Lettoof ◽  
Vicki A. Thomson ◽  
Jari Cornelis ◽  
Philip W. Bateman ◽  
Fabien Aubret ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Drift ◽  
Urban Areas ◽  
Population Genomics ◽  
Genomic Structure ◽  
Genomic Diversity ◽  
Effective Population ◽  
Population Genomic ◽  
Population Sizes ◽  
Urban Matrix

Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant ‘islands’. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which ‘islands’ of habitat are most in need of management and protection.

scholarly journals Spatial population genomics of a recent mosquito invasion

2020 ◽  
Author(s):  
Thomas L Schmidt ◽  
T. Swan ◽  
Jessica Chung ◽  
Stephan Karl ◽  
Samuel Demok ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Nucleotide Polymorphisms ◽  
Discrete Events ◽  
Long Distance ◽  
Population Genomic ◽  
Asian Tiger ◽  
Study Designs

AbstractPopulation genomic approaches can characterise dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally-restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG), and 4 incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232–577. Close kin dyads revealed recent movement between islands 31–203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and non-adjacent islands. Private alleles and a coancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

scholarly journals Genomic Adaptations to Salinity Resist Gene Flow in the Evolution of Floridian Watersnakes

2020 ◽  
Author(s):  
Rhett M Rautsaw ◽  
Tristan D Schramer ◽  
Rachel Acuña ◽  
Lindsay N Arick ◽  
Mark DiMeo ◽  
...  
Keyword(s):  
Gene Flow ◽  
Isolation By Distance ◽  
Species Boundaries ◽  
Selective Pressures ◽  
Nerodia Fasciata ◽  
Isolation By Environment ◽  
Significant Gene ◽  
Candidate Loci ◽  
Osmoregulatory Function ◽  
Ecological Differences

Abstract The migration-selection balance often governs the evolution of lineages, and speciation with gene flow is now considered common across the tree of life. Ecological speciation is a process that can facilitate divergence despite gene flow due to strong selective pressures caused by ecological differences; however, the exact traits under selection are often unknown. The transition from freshwater to saltwater habitats provides strong selection targeting traits with osmoregulatory function. Several lineages of North American watersnakes (Nerodia spp.) are known to occur in saltwater habitat and represent a useful system for studying speciation by providing an opportunity to investigate gene flow and evaluate how species boundaries are maintained or degraded. We use double digest restriction-site associated DNA sequencing to characterize the migration-selection balance and test for evidence of ecological divergence within the Nerodia fasciata-clarkii complex in Florida. We find evidence of high intraspecific gene flow with a pattern of isolation-by-distance underlying subspecific lineages. However, we identify genetic structure indicative of reduced gene flow between inland and coastal lineages suggesting divergence due to isolation-by-environment. This pattern is consistent with observed environmental differences where the amount of admixture decreases with increased salinity. Furthermore, we identify significantly enriched terms related to osmoregulatory function among a set of candidate loci, including several genes that have been previously implicated in adaptation to salinity stress. Collectively, our results demonstrate that ecological differences, likely driven by salinity, cause strong divergent selection which promotes divergence in the N. fasciata-clarkii complex despite significant gene flow.

scholarly journals Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation

2014 ◽  
Vol 369 (1648) ◽  
pp. 20130342 ◽  
Author(s):  
Alexander S. T. Papadopulos ◽  
Maria Kaye ◽  
Céline Devaux ◽  
Helen Hipperson ◽  
Jackie Lighten ◽  
...  
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Plant Species ◽  
Environmental Gradients ◽  
Isolation By Distance ◽  
Model Averaging ◽  
Dispersal Limitation ◽  
Population Divergence ◽  
Environmental Pressures ◽  
Isolation By Environment

It is now recognized that speciation can proceed even when divergent natural selection is opposed by gene flow. Understanding the extent to which environmental gradients and geographical distance can limit gene flow within species can shed light on the relative roles of selection and dispersal limitation during the early stages of population divergence and speciation. On the remote Lord Howe Island (Australia), ecological speciation with gene flow is thought to have taken place in several plant genera. The aim of this study was to establish the contributions of isolation by environment (IBE) and isolation by community (IBC) to the genetic structure of 19 plant species, from a number of distantly related families, which have been subjected to similar environmental pressures over comparable time scales. We applied an individual-based, multivariate, model averaging approach to quantify IBE and IBC, while controlling for isolation by distance (IBD). Our analyses demonstrated that all species experienced some degree of ecologically driven isolation, whereas only 12 of 19 species were subjected to IBD. The prevalence of IBE within these plant species indicates that divergent selection in plants frequently produces local adaptation and supports hypotheses that ecological divergence can drive speciation in sympatry.

scholarly journals Landscape drivers of genomic diversity and divergence in woodland Eucalyptus

2019 ◽  
Author(s):  
Kevin Murray ◽  
Jasmine Janes ◽  
Helen Bothwell ◽  
Ashley Jones ◽  
Rose Andrew ◽  
...  
Keyword(s):  
Geographic Distance ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
High Genetic Diversity ◽  
Genome Wide ◽  
Isolation By Environment ◽  
Genetic Patterns ◽  
Discrete Population ◽  
Eucalyptus Albens ◽  
Eucalyptus Sideroxylon

AbstractSpatial genetic patterns are influenced by numerous factors, and they can vary even among coexisting, closely related species due to differences in dispersal and selection. Eucalyptus (L’Héritier 1789; the “eucalypts”) are foundation tree species that provide essential habitat and modulate ecosystem services throughout Australia. Here we present a study of landscape genomic variation in two woodland eucalypt species, using whole genome sequencing of 388 individuals of Eucalyptus albens and Eucalyptus sideroxylon. We found exceptionally high genetic diversity (π ≈ 0.05) and low genome-wide, inter-specific differentiation (FST = 0.15). We found no support for strong, discrete population structure, but found substantial support for isolation by geographic distance (IBD) in both species. Using generalised dissimilarity modelling, we identified additional isolation by environment (IBE). Eucalyptus albens showed moderate IBD, and environmental variables have a small but significant amount of additional predictive power (i.e., IBE). Eucalyptus sideroxylon showed much stronger IBD, and moderate IBE. These results highlight the vast adaptive potential of these species, and set the stage for testing evolutionary hypotheses of interspecific adaptive differentiation across environments.

scholarly journals Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

2019 ◽  
Author(s):  
Nikki Leanne Phair ◽  
Robert John Toonen ◽  
Ingrid Knapp ◽  
Sophie von der Heyden
Keyword(s):  
Ecosystem Engineer ◽  
Environmental Gradients ◽  
Keystone Species ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Eastern Africa ◽  
Seagrass Habitat ◽  
Temperature And Precipitation ◽  
Outlier Loci ◽  
Isolation By Environment

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ~9600km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.

scholarly journals Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations 

2020 ◽  
Author(s):  
Eeva Jansson ◽  
Francois Besnier ◽  
Ketil Malde ◽  
Carl André ◽  
Geir Dahle ◽  
...  
Keyword(s):  
Genetic Divergence ◽  
De Novo ◽  
Genomic Structure ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Full Genome Sequencing ◽  
Population Genomic ◽  
Genome Wide ◽  
Ctenolabrus Rupestris ◽  
Goldsinny Wrasse

Abstract Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse ( Ctenolabrus rupestris ) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33 235 genome wide SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global F ST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~1% within Scandinavia. SNPs showing large divergence ( F ST >0.15) were picked as candidate diagnostic markers for population assignment. 173 of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. 69 of these SNPs were significantly ( p <0.05) differentiated (mean F ST_173_loci = 0.065, F ST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

scholarly journals Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Eeva Jansson ◽  
Francois Besnier ◽  
Ketil Malde ◽  
Carl André ◽  
Geir Dahle ◽  
...  
Keyword(s):  
Genetic Divergence ◽  
De Novo ◽  
Genomic Structure ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Full Genome Sequencing ◽  
Population Genomic ◽  
Cost Efficient ◽  
Ctenolabrus Rupestris ◽  
Goldsinny Wrasse

Abstract Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

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