Biology subjects

Zbinden, Z. D.

Publications and source records attributed to Zbinden, Z. D..

7 recordsLinked to original sources

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↗

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

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

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↗

bioRxiv2019

Spatiotemporal Dynamics of Stream Fish Assemblages Over Four Decades

Fish assemblage structure was compared between 1974 and 2014 at 33 sampling locations in the Muddy Boggy River drainage, OK. The two main objectives for this comparison were to first quantify change in assemblage structure, and, second, to test for a relationship between compositional change and spatial scale. Spatial scale was manipulated by pooling assemblage data into groups ranging from K=33 pairs (i.e., local scale) to K=1 pair (i.e., global scale). Local assemblages varied in the degree of assemblage change over 4 decades (range=10-99% dissimilarity; mean=66%). The global assemblage remained quantitatively and qualitatively similar: most species persisted through time and those that did not were rare, and several diversity measures were not significantly different between time periods. Pooling assemblage data into consecutively larger groups and assessing the resultant compositional change revealed interesting patterns indicative of domains of spatial scaling. A discontinuity in the relationship between compositional change and spatial scale occurred at K=15, and this grouping is roughly the size of the headwater/tributary drainages of the Muddy Boggy system. This result suggests assemblages are more predictable when defined at scales larger than a stream reach, and a domain of higher predictability exists at a scale smaller than the entire drainage.

ecology↗