Biology subjects

Douglas, M. R.

Publications and source records attributed to Douglas, M. R..

At least 19 recordsLinked to original sources

bioRxiv2023

autoStreamTree: Genomic variant data fitted to geospatial networks

SummaryLandscape genetics is a statistical framework that parses genetic variation within the context of spatial covariates, but current analytical methods typically fail to accommodate the unique topologies and autocorrelations inherent to network-configured habitats (e.g., streams or rivers). autoStreamTree analyzes and visualizes genome-wide variation across dendritic networks (i.e., riverscapes). Availability and ImplementationautoStreamTree is an open source workflow (https://github.com/tkchafin/autostreamtree) that automatically extracts a minimal graph representation of a geospatial network from a provided shapefile, then fits the components of genetic variation using a least-squares algorithm. To facilitate downstream population genomic analyses, genomic variation can be represented per-locus, per-SNP, or via microhaplotypes (i.e., phased data). We demonstrate the workflow by quantifying genetic variation in Speckled Dace (Rhinichthys osculus) versus environmental covariates, with putative adaptive variants subsequently identified. Contacttyler.chafin@bioss.ac.uk

bioinformatics↗

bioRxiv2022

A community genomics approach to natural hybridization

Hybridization is a complicated, oft-misunderstood process. Once deemed unnatural and uncommon, hybridization is now recognized as ubiquitous among species. But hybridization rates within and among communities are poorly understood despite the relevance to ecology, evolution, and conservation. To clarify, we examined hybridization across 75 freshwater fish communities within the Ozarks of the North American Interior Highlands (USA) by SNP genotyping 33 species (N=2,865 individuals; ddRAD). We found evidence of hybridization (70 putative hybrids; 2.4% of individuals) among 18 species-pairs involving 73% (24/33) of study species, with the majority being concentrated within one family (Leuciscidae/minnows; 15 species; 66 individuals). Interspecific genetic exchange-- or introgression-- was evident from 24 backcrossed individuals (10/18 species-pairs). Hybrids occurred within 42 of 75 communities (56%). Four selected environmental variables (species richness, protected area extent, precipitation [May and annually]) exhibited 73-78% accuracy in predicting hybrid occurrence via random forest classification. Our community-level assessment identified hybridization as spatially widespread and environmentally dependent (albeit predominantly within one large, diverse family). Our approach provides a more holistic survey of natural hybridization by testing a wide range of species-pairs, thus contrasting with more conventional evaluations.

evolutionary biology↗

bioRxiv2022

Trait-based predictors of genomic diversity within freshwater fish communities of the Ozarks

Phenotypic traits modulate the fate of species interactions with one another and the environment; thus, traits directly shape the past, present, and future evolutionary trajectories of populations. As such, distinct species-specific responses to a shifting environment are widely documented in the form of distinct genetic signatures, i.e., genetic diversity, reflecting differential responses over time. While the link between genetic diversity and phenotypic traits is seemingly fundamental, it has been challenging to establish unequivocally. Across an exemplar freshwater fish metacommunity, we employ phenotypic traits to test if they are significantly related to observed genetic patterns among species. Associated traits were then used to construct trait-based predictive models of genetic diversity. We collected representative constituents of a freshwater fish community (N=31 species) sampled across 75 sites within the White River Basin (Ozark Plateau, USA). For each species, we derived three genetic diversity indices (=HS/HT/G"ST) from SNP data (N=2,000 loci) and assessed 28 phenotypic traits related to morphology, life history, and ecology. We identified a series of traits (N=2-5, depending upon the index) strongly associated with facets of genetic diversity. These were subsequently applied in predictive models that explained 31-68% of the genetic variability across species, suggesting a potential utility as an imputation tactic for data-deficient species. Our approach effectively linked species-specific traits with genetic diversity within and among populations, thereby further clarifying correlations between contemporary ecological processes, as modulated by species traits, and long-term evolutionary trajectories.

evolutionary biology↗

bioRxiv2022

Riverscape community genomics: A comparative analytical framework to identify common drivers of spatial structure

Genetic differentiation among local groups of individuals, i.e., genetic {beta}-diversity, is a key component of population persistence related to connectivity and isolation. However, most genetic investigations of natural populations focus on a single species, overlooking opportunities for multispecies conservation plans to benefit entire communities in an ecosystem. We present an approach to evaluate genetic {beta}-diversity within and among many species and demonstrate how this riverscape community genomics approach can be applied to identify common drivers of genetic structure. Our study evaluated genetic {beta}-diversity in 31 co-distributed native stream fishes sampled from 75 sites across the White River Basin (Ozarks, USA) using SNP genotyping (ddRAD). Despite variance among species in the degree of genetic divergence, general spatial patterns were identified corresponding to river network architecture. Most species (N=24) were partitioned into discrete sub-populations (K=2-7). We used partial redundancy analysis to compare species-specific genetic {beta}-diversity across four models of genetic structure: Isolation by distance (IBD), isolation by barrier (IBB), isolation by stream hierarchy (IBH), and isolation by environment (IBE). A significant proportion of intraspecific genetic variation was explained by IBH (x{square} =62%), with the remaining models generally redundant. We found evidence for consistent spatial modularity in that gene flow is higher within rather than between hierarchical units (i.e., catchments, watersheds, basins), supporting the generalization of the Stream Hierarchy Model. We discuss our conclusions regarding conservation and management and identify the 8-digit Hydrologic Unit (HUC) as the most relevant spatial scale for managing genetic diversity across riverine networks.

evolutionary biology↗

bioRxiv2022

Relictual Hybridization and Biogeography of Massasauga Rattlesnakes (Sistrurus spp.)

Climate change inevitably leaves behind a genetic footprint within phylogeographic legacies of affected species, as individuals are driven to either disperse to track suitable conditions or adapt in situ. One potential consequence is the possibility of hybridization among species, as both geographic ranges and adaptive landscapes shift. The admixture resulting from these newly formed contact zones has various outcomes, to include the creation of new lineages. Interpreting these within the context of historic climate change provides clues necessary to predict biotic responses (and thus evolutionary trajectories) as a function of contemporary shifts. Herein, we dissect historic contact zones for Massasaugas (Viperidae; Sistrurus spp.) within two distinct North American regions (southwestern United States and Central Great Plains) using ddRAD sequencing. We identified fine-scale but previously unrecognized population structure within the southwestern contact zone, where we detected contemporary intergradation between Prairie and Desert massasaugas (S. tergeminus tergeminus, and S. t. edwardsii, respectively), with primary divergence indicated by demographic model selection. Within the Central Great Plains, we found evidence for historic secondary contact via Quaternary climatic cycles, subsequently followed by range expansion at the suture zone separating S. tergeminus and S. catenatus. Extant Missouri populations represent ancestral/relictual vestiges of this earlier hybridization, isolated between the eastern terminus of S. t. tergeminus and the western edge of S. catenatus. Our results illustrate how abrupt climate change has driven ancestral hybridization, cryptic diversity, and range dynamism within Sistrurus.

evolutionary biology↗

bioRxiv2021

Putting pesticides on the map for pollinator research and conservation

Wild and managed pollinators are essential to food production and the function of natural ecosystems; however, their populations are threatened by multiple stressors including pesticide use. Because pollinator species can travel hundreds to thousands of meters to forage, recent research has stressed the importance of evaluating pollinator decline at the landscape scale. However, scientists and conservationists ability to do this has been limited by a lack of accessible data on pesticide use at relevant spatial scales and in toxicological units meaningful to pollinators. Here, we synthesize information from several large, publicly available datasets on pesticide use patterns, land use, and toxicity to generate novel datasets describing pesticide use by active ingredient (kg, 1997-2017) and aggregate insecticide load (kg and honey bee lethal doses, 1997-2014) for state-crop combinations in the contiguous U.S. Furthermore, by linking pesticide datasets with land-use data in the contiguous United States, we describe a method to map pesticide indicators at spatial scales relevant to pollinator research and conservation.

ecology↗

bioRxiv2021

Parallel adaptations to an altitudinal gradient persist in tetraploid snowtrout (Cyprinidae: Schizothorax), despite extensive genomic exchange within adjacent Himalayan rivers

The recurrence of similar evolutionary patterns within different habitats often reflects parallel selective pressures acting upon either standing or independently occurring genetic variation to produce a convergence of phenotypes. This interpretation (i.e. parallel divergences within adjacent streams) has been hypothesized for drainage-specific morphological ecotypes observed in polyploid snowtrout (Cyprinidae: Schizothorax). However, parallel patterns of differential introgression during secondary contact is a viable alternative hypothesis. Here, we utilized ddRADseq (N=35,319 de-novo and N=10,884 transcriptome-aligned SNPs), as derived from Nepali/Bhutanese samples (N=48 each), to test these competing hypotheses. We first employed genome-wide allelic depths to derive appropriate ploidy models, then a Bayesian approach to yield genotypes statistically consistent under the inferred expectations. Elevational ecotypes were consistent in geometric-morphometric space, but with phylogenetic relationships at the drainage-level, sustaining an hypothesis of independent emergence. However, partitioned analyses of phylogeny and admixture identified subsets of loci under selection that retained genealogical concordance with morphology, suggesting instead that apparent patterns of morphological/phylogenetic discordance are driven by widespread genomic homogenization. Here, admixture occurring in secondary contact effectively masks previous isolation. Our results underscore two salient factors:1) Morphological adaptations are retained despite hybridization; and 2) The degree of admixture varies across tributaries, presumably concomitant with underlying environmental or anthropogenic factors.

evolutionary biology↗

bioRxiv2021

Quantifying diversity, connectivity, and environmental resistance in dendritic ecological networks

O_LIA central theme in landscape ecology is the translation of individual movements within a population by deconstructing/interpreting the components of its topographical environment. Most such endeavors rely heavily on the concept of landscape resistance - a composite of an arbitrary number of features/covariates that, when identified/compiled, yield a surface inversely related to net movement. However, the statistical methodologies underlying this compilation have limited applicability when applied to dendritic ecological networks (DENs), including riverscapes. C_LIO_LIHerein we provide an analytical framework (ResistNet) that more appropriately annotates DEN segments by first aligning individual genetic distances with environmental covariates within a graph structure, then employing a genetic algorithm to optimise a composite model. C_LIO_LIWe evaluated the efficacy of our method by first testing it in silico across an array of sampling designs, spatial trajectories, and levels of complexity, then applying it in an empirical case study involving 13,218 ddRAD loci from N=762 Speckled Dace (Leuciscidae: Rhinichthys osculus), sampled across N=78 Colorado River localities. By doing so, we underscored the utility of ResistNet within a large-scale conservation study, as well as identified prerequisites for its appropriate application. C_LIO_LIOur contemporary framework not only allows an interpretation of meta-population/meta-community structure across DENs, but also highlights several innovative applications. These are: (a) Expanding an ongoing study design, and thus its hypotheses, into yet unsampled temporal and/or spatial arenas, and; (b) Promoting multi-species management through comparative analyses that extend across species and/or drainages. C_LI

ecology↗

bioRxiv2020

Metapopulation Connectivity in Voles (Microtus sp.) as a Gauge for Tallgrass Prairie Restoration in Midwestern North America

Applying quantifiable metrics to validate the success of restoration efforts is crucial for ongoing management programs in anthropogenically fragmented habitats. Estimates of dispersal can provide such baseline data because they measure not only the extent to which restored patches are colonized and interconnected, but also their metapopulation source/sink dynamics. In this context, we estimated dispersal and population connectivity among prairie (Microtus ochrogaster; N=231) and meadow vole (M. pennsylvanicus; N=83), sampled from eight restored plots at five tallgrass prairie sites embedded within the agricultural matrix of midwestern North America. Our expectation was that extensive distances separating these restored habitats (i.e., 48-246 km) would spatially isolate vole metapopulations, resulting in significant genetic differentiation. We first used molecular taxonomy to validate the field-identifications of all sampled individuals, then used pairwise FST derived from 15 microsatellite DNA loci to estimate genetic connectivity among the species-delimited study populations. Metapopulation stability was gauged by assessing migration rates and deriving effective population sizes (Ne). We also calculated relatedness values (r) as a potential surrogate for contact in prairie vole, a primary vector for Lyme disease. Molecular species-assignments contravened field-identifications in 25% of samples (11 prairie/67 meadow) and identified two instances of species-hybridization (0.6%). Local effects (i.e., population crash/drought) were manifested at two sites, as documented by significant temporal declines in Ne and r. Overall, high migration rates and non-significant (10/15) pairwise FST values underscored elevated metapopulation connectivity. A single site that recorded five significant FST values also displayed significant r-values indicating the inadvertent sampling of closely related individuals. This highlights the close social groupings among cooperatively-breeding prairie vole that can exacerbate Lyme disease transmission. Thus, while elevated population connectivity aligns with prairie restoration goals, it also reinforces a need in adaptive management to evaluate environmental matrices for their permeability to vector-borne diseases.

ecology↗

bioRxiv2020

Did the Himalayan Uplift Drive Evolution of Aquatic Biodiversity Across Asia? Snowtrout (Cyprinidae: Schizothorax) as a Test Case

The Himalayan uplift, a tectonic event of global importance, seemingly disseminated aquatic biodiversity broadly across Asia. But surprisingly, this hypothesis has yet to be tested. We do so herein by sequencing 1,140 base-pair of mtDNA cytochrome-b for 72 tetraploid Nepalese/Bhutanese Snowtrout (Schizothorax spp.), combining those data with 67 GENBANK(R) sequences (59 ingroup/8 outgroup), then reconstructing phylogenetic relationships using maximum likelihood/ Bayesian analyses. Results indicate Snowtrout originated in Central Asia, dispersed across the Qinghai-Tibetan Plateau (QTP), then into Bhutan via south-flowing tributaries of the east-flowing Yarlung-Tsangpo River (YLTR). The headwaters of five large Asian rivers provided dispersal corridors into southeast Asia. South of the Himalaya, the YLTR transitions into a westward-flowing Brahmaputra River that facilitated successive colonization of Himalayan drainages: First Bhutan, then Nepal, followed by far-western drainages subsequently captured by the Indus River. We found greater species-divergences across rather than within-basins, implicating vicariant evolution as a driver. The Himalaya is a component of the "third-pole" [Earths largest (but rapidly shrinking) glacial reservoir outside the Arctic/Antarctic]. Its unique aquatic biodiversity must not only be recognized (as herein) but also conserved through broad, trans-national collaborations. Our results effectively contrast phylogeography with taxonomy as a necessary first step in this process. The Himalaya is the most extensive and recently evolved mountain system on Earth (length=2400km; width=240km; elevation=75-8800m), with a global significance underscored by its large-scale lithospheric, cryospheric, and atmospheric interactions [1]. These have not only driven global climate, but also defined the cultural and biological endemism of the region [2]. Massive, tectonically derived mountain chains such as the Alps and the Himalaya are hypothesized as being fundamental to the formation of global biodiversity gradients via vicariance and local adaptation, with a significantly stronger signal in terrestrial rather than aquatic systems [3]. Here we test how orogeny (the deformation and folding of Earths crust by lateral compression) has contributed to the diversification of freshwater fishes broadly across Asia. We do so by evaluating the phylogeography of an endemic high-elevation fish, the Snowtrout (Schizothorax: Cyprinidae).

evolutionary biology↗

bioRxiv2020

Taxonomic hypotheses and the biogeography of speciation in the Tiger Whiptail complex (Aspidoscelis tigris: Squamata, Teiidae)

(225)Biodiversity in southwestern North America has a complex biogeographic history involving tectonism interspersed with climatic fluctuations. This yields a contemporary pattern replete with historic idiosyncrasies often difficult to interpret when viewed from through the lens of modern ecology. The Aspidoscelis tigris (Tiger Whiptail) complex (Squamata: Teiidae) is one such group in which potential taxonomic boundaries have been confounded by a series of complex biogeographic processes that have defined the evolution of the clade. To clarify this situation, we first generated multiple taxonomic hypotheses, which were subsequently tested using mitochondrial DNA sequences (ATPase 8 and 6) evaluated across 239 individuals representing five continental members of this complex. To do so, we evaluated the manner by which our models parsed phylogenetic and biogeographic patterns. We found considerable variation among species hypotheses, which we suggest in part reflects inflated levels of inter-population genetic divergence caused by historical demographic expansion and contraction cycles. Inter-specific boundaries with A. marmoratus juxtaposed topographically with the Cochise Filter Barrier that separates Sonoran and Chihuahuan deserts (interpreted herein as case of soft allopatry). Patterns of genetic divergence were consistent across the Cochise Filter Barrier, regardless of sample proximity. Surprisingly, this also held true for intraspecific comparisons that spanned the Colorado River. These in turn suggest geomorphic processes as a driver of speciation in the tigris complex, with intraspecific units governed locally by demographic processes. HIGHLIGHTSO_LIPhylogeographies of vertebrates within the southwestern deserts of North America have been shaped by climatic fluctuations imbedded within broad geomorphic processes. C_LIO_LIThe resulting synergism drives evolutionary processes, such as an expansion of within-species genetic divergence over time. Taxonomic inflation often results (i.e., an increase in recognized taxa due to arbitrary delineations), such as when morphological divergences fail to juxtapose with biogeographic hypotheses. C_LIO_LIHowever, isolated groups can be discriminated within-species by mapping genetic variability onto geographic distances. This approach can often diagnose hard barriers to dispersal, or alternatively, strong selection acting against hybridization. On the other hand, elevated genetic divergences among groups less-isolated would underscore isolation-by-distance (i.e., an increase in genetic differentiation concomitant with geographic distance). C_LIO_LIThe biogeographic patterns we identified in Tiger Whiptail are largely synonymous with those found in other regional species, particularly given the geomorphic separation of Mohave and Sonoran deserts by the Colorado River, and Sonoran/ Chihuahuan deserts by the Cochise Filter Barrier. C_LIO_LIOur results for the Tiger Whiptail complex broaden and extend the context within which polytypic species are conserved and managed, particularly those that reflect an incongruence among molecular and morphological standards. C_LI

evolutionary biology↗

bioRxiv2020

Population Genomic Analyses Separate Historic Translocations from Contemporary Gene Flow in Arkansas White-tailed Deer (Odocoileus virginianus)

Approximately 100 years ago, unregulated harvest nearly eliminated white-tailed deer (Odocoileus virginianus) from eastern North America, which subsequently served to catalyze wildlife management as a national priority. An extensive stock-replenishment effort soon followed, with deer broadly translocated among states as a means of re-establishment. However, an unintended consequence was that natural patterns of gene flow became obscured and pre-translocation signatures of population structure were replaced. We applied cutting-edge molecular and biogeographic tools to disentangle genetic signatures of historical management from those reflecting spatially heterogeneous dispersal by evaluating 35,099 single nucleotide polymorphisms (SNPs) derived via reduced-representation genomic sequencing from 1,143 deer sampled state-wide in Arkansas. We then employed Simpsons diversity index to summarize ancestry assignments and visualize spatial genetic transitions. Using sub-sampled transects across these transitions, we tested clinal patterns across loci against theoretical expectations of their response under scenarios of recolonization and restricted dispersal. Two salient results emerged: (A) Genetic signatures from historic translocations are demonstrably apparent; and (B) Geographic filters (major rivers; urban centers; highways) now act as inflection points for the distribution of this contemporary ancestry. These results yielded a state-wide assessment of contemporary population structure in deer as driven by historic translocations as well as ongoing processes. In addition, the analytical framework employed herein to effectively decipher extant/historic drivers of deer distribution in Arkansas are also applicable for other biodiversity elements with similarly complex demographic histories.

evolutionary biology↗

bioRxiv2020

ClinePlotR: Visualizing genomic clines and detecting outliers in R

Patterns of multi-locus differentiation (i.e., genomic clines) often extend broadly across hybrid zones and their quantification can help diagnose how species boundaries are shaped by adaptive processes, both intrinsic and extrinsic. In this sense, the transitioning of loci across admixed individuals can be contrasted as a function of the genome-wide trend, in turn allowing an expansion of clinal theory across a much wider array of biodiversity. However, computational tools that serve to interpret and consequently visualize genomic clines are limited. Here, we introduce the CO_SCPLOWLINEC_SCPLOWPO_SCPLOWLOTC_SCPLOWR R-package for visualizing genomic clines and detecting outlier loci using output generated by two popular software packages, O_SCPLOWBGCC_SCPLOW and IO_SCPLOWNTROGRESSC_SCPLOW. CO_SCPLOWLINEC_SCPLOWPO_SCPLOWLOTC_SCPLOWR bundles both input generation (i.e, filtering datasets and creating specialized file formats) and output processing (e.g., MCMC thinning and burn-in) with functions that directly facilitate interpretation and hypothesis testing. Tools are also provided for post-hoc analyses that interface with external packages such as ENMO_SCPLOWEVALC_SCPLOW and RIO_SCPLOWDEOGRAMC_SCPLOW. Our package increases the reproducibility and accessibility of genomic cline methods, thus allowing an expanded user base and promoting these methods as mechanisms to address diverse evolutionary questions in both model and non-model organisms.

bioinformatics↗

bioRxiv2020

Age structuring and spatial heterogeneity in prion protein gene (PRNP) polymorphism in white-tailed deer

Chronic-wasting disease (CWD) is a prion-derived fatal neurodegenerative disease that has affected wild cervid populations on a global scale. Susceptibility has been linked unambiguously to several amino acid variants within the prion protein gene (PRNP). Quantifying their distribution across landscapes can provide critical information for agencies attempting to adaptively manage CWD. Here we attempt to further define management implications of PRNP polymorphism by quantifying the contemporary geographic distribution (i.e., phylogeography) of PRNP variants in hunter-harvested white-tailed deer (WTD; Odocoileus virginianus, N=1433) distributed across Arkansas (USA), including a focal spot for CWD since detection of the disease in February 2016. Of these, PRNP variants associated with the well-characterized 96S non-synonymous substitution showed a significant increase in relative frequency among older CWD-positive cohorts. We interpreted this pattern as reflective of a longer life expectancy for 96S genotypes in a CWD-endemic region, suggesting either decreased probabilities of infection or reduced disease progression. Other variants showing statistical signatures of potential increased susceptibility, however, seemingly do so as an artefact of population structure. We also showed marked heterogeneity across the landscape in the prevalence of reduced susceptibility genotypes. This may indicate, in turn, that differences in disease susceptibility among WTD in Arkansas are an innate, population-level characteristic that is detectable through phylogeographic analysis.

genetics↗

bioRxiv2020

ADMIXPIPE: Population analyses in ADMIXTURE for non-model organisms

Background: Research on the molecular ecology of non-model organisms, while previously constrained, has now been greatly facilitated by the advent of reduced-representation sequencing protocols. However, tools that allow these large datasets to be efficiently parsed are often lacking, or if indeed available, then limited by the necessity of a comparable reference genome as an adjunct. This, of course, can be difficult when working with non-model organisms. Fortunately, pipelines are currently available that avoid this prerequisite, thus allowing data to be a priori parsed. An oft-used molecular ecology program (i.e., STRUCTURE), for example, is facilitated by such pipelines, yet they are surprisingly absent for a second program that is similarly popular and computationally more efficient (i.e., ADMIXTURE). The two programs differ in that ADMIXTURE employs a maximum-likelihood framework whereas STRUCTURE uses a Bayesian approach, yet both produce similar results. Given these issues, there is an overriding (and recognized) need among researchers in molecular ecology for bioinformatic software that will not only condense output from replicated ADMIXTURE runs, but also infer from these data the optimal number of population clusters (K). Results: Here we provide such a program (i.e., ADMIXPIPE) that (a) filters SNPs to allow the delineation of population structure in ADMIXTURE, then (b) parses the output for summarization and graphical representation via CLUMPAK. Our benchmarks effectively demonstrate how efficient the pipeline is for processing large, non-model datasets generated via double digest restriction-site associated DNA sequencing (ddRAD). Outputs not only parallel those from STRUCTURE, but also visualize the variation among individual ADMIXTURE runs, so as to facilitate selection of the most appropriate K-value. Conclusions: ADMIXPIPE successfully integrates ADMIXTURE analysis with popular variant call format (VCF) filtering software to yield file types readily analyzed by CLUMPAK. Large population genomic datasets derived from non-model organisms are efficiently analyzed via the parallel-processing capabilities of ADMIXTURE. ADMIXPIPE is distributed under the GNU Public License and freely available for Mac OSX and Linux platforms at: https://github.com/stevemussmann/admixturePipeline.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗

bioRxiv2020

Defining Relictual Biodiversity: Conservation Units in Speckled Dace (Cyprinidae: Rhinichthys osculus) of the Greater Death Valley Ecosystem

The tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species-population interface. Analyses using thousands of nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective [e.g., DPS (distinct population segments); DUs (Diagnosable Units-Canada); MUs (management units); SSP (subspecies); Evolutionarily Significant Units (ESUs)]. One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates this approach in speckled dace (Cyprinidae: Rhinichthys osculus) endemic to two basins (Owens and Amargosa) in the Death Valley ecosystem (DVE). These fish persist in the Mojave Desert as isolated Pleistocene-relicts and are of conservation concern, but lack formal taxonomic descriptions/designations. Double-digest RAD (ddRAD) methods identified 14,355 SNP loci across 10 populations (N=140). Species delimitation analyses [multispecies coalescent (MSC) and unsupervised machine learning (UML)] delineated four putative ESUs. FST outlier loci (N=106) were juxtaposed to uncover the potential for localized adaptations. We detected one hybrid population that resulted from upstream reconnection of habitat following contemporary pluvial periods, whereas remaining populations represent relics of ancient tectonism within geographically-isolated springs and groundwater-fed streams. Our study offers three salient conclusions: A blueprint for a multi-faceted delimitation of conservation units; a proposed mechanism by which criteria for intraspecific biodiversity can be potentially standardized; and a strong argument for the proactive management of critically-endangered DVE fishes.

genetics↗

bioRxiv2020

Machine learning substantiates biologically meaningful species delimitations in the phylogenetically complex North American box turtle genus Terrapene

Model-based approaches that attempt to delimit species are hampered by computational limitations as well as the unfortunate tendency by users to disregard algorithmic assumptions. Alternatives are clearly needed, and machine-learning (M-L) is attractive in this regard as it functions without the need to explicitly define a species concept. Unfortunately, its performance will vary according to which (of several) bioinformatic parameters are invoked. Herein, we gauge the effectiveness of M-L-based species-delimitation algorithms by parsing 64 variably-filtered versions of a ddRAD-derived SNP dataset collected from North American box turtles (Terrapene spp.). Our filtering strategies included: (A) minor allele frequencies (MAF) of 5%, 3%, 1%, and 0% (=none), and (B) maximum missing data per-individual/per-population at 25%, 50%, 75%, and 100% (=no filtering). We found that species-delimitation via unsupervised M-L impacted the signal-to-noise ratio in our data, as well as the discordance among resolved clades. The latter may also reflect biogeographic history, gene flow, incomplete lineage sorting, or combinations thereof (as corroborated from previously observed patterns of differential introgression). Our results substantiate M-L as a viable species-delimitation method, but also demonstrate how commonly observed patterns of phylogenetic discordance can seriously impact M-L-classification.

evolutionary biology↗

bioRxiv2020

Genome-wide local ancestries discriminate homoploid hybrid speciation from secondary introgression in the red wolf (Canidae: Canis rufus)

Hybridization is well recognized as a driver of speciation, yet it often remains difficult to parse phylogenomically in that post-speciation gene flow frequently supersedes an ancestral signal. Here we examined how interactions between recombination and gene flow shaped the phylogenomic landscape of red wolf to create non-random retention of introgressed ancestry. Our re-analyses of genomic data recapitulate fossil evidence by demonstrating red wolf was indeed extant and isolated prior to more recent admixture with other North American canids. Its more ancient divergence, now sequestered within low-recombinant regions on the X-chromosome (i.e., chromosomal refugia), is effectively masked by multiple, successive waves of secondary introgression that now dominate its autosomal ancestry. These interpretations are congruent with more theoretical explanations that describe the manner by which introgression can be localized within the genome through recombination and selection. They also tacitly support the large-X effect, i.e., the manner by which loci that contribute to reproductive isolation can be enriched on the X-chromosome. By contrast, similar, high recombinant regions were also found as enriched within very shallow gene trees, thus reflecting post-speciation gene flow and a compression of divergence estimates to 1/20th of that found in recombination cold spots. Our results effectively reconcile conflicting hypotheses regarding the impact of hybridization on evolution of North American canids and support an emerging framework within which the analysis of a phylogenomic landscape structured by recombination can be used to successfully address the macroevolutionary implications of hybridization.

evolutionary biology↗