Biology subjects

Hancock, Z. B.

Publications and source records attributed to Hancock, Z. B..

6 recordsLinked to original sources

bioRxiv2025

sandwrm: an R package for estimating Wright's neighborhood size and species-level genetic diversity

In most natural populations, individuals in close proximity are more related on average than those at greater distances; this pattern gives rise to geographic population genetic structure. Despite extensive theoretical work on spatial population genetics, few empirical methods exist to estimate the components of theoretical models of genetic relatedness in continuous space. One classic model of relatedness in continuous space is the Wright-Malecot model, which predicts that the probability of identity-by-descent decays as a function of geographic distances. The shape of this decay curve is dictated by the dynamics of local dispersal and mating, as well as population density. This model can be reformulated to describe the probability of identity-by-state, in which case it decays to an asymptote, the value of which is determined by the historical demography of the population. Collectively, these features can be modeled in a likelihood-based framework to estimate neighborhood size and long-term diversity from pairwise genetic and geographic distance. In this article, we introduce the R package sandwrm Spatial Analysis of Neighborhood size and Diversity using WRight-Malecot), which takes a Bayesian approach to estimate key parameters of populations that are both dispersal-limited and distributed continuously across a landscape.

bioinformatics↗

bioRxiv2024

Investigating the Role of Management Decisions in Subspecies Hybridization Across the Wild Turkey's Range

The expanded geographic range and recovery to millions of wild turkeys across the country would not have been possible without management actions that included introducing and translocating individuals. However, the range-wide genetic impact of management decisions on one of North Americas greatest conservation success stories remains unknown despite the potential economic impact as hunters seek out easily identifiable subspecies for grand slams. In this study, we used DNA extracted from hunter-collected feathers from 29 states and Ontario to investigate genetic differences among turkeys in their historic and introduced ranges. Additionally, we compiled state-level management data to investigate how different management decisions are associated with the amount of admixture among subspecies. We found no difference in the amount of admixture in the turkeys historic range compared to the introduced range. However, management decisions like as the number of subspecies introduced and the number of unique source states resulted in an increased level of admixture detected, but there was no relationship in admixture and the number of unique relocated counties. This first investigation into the hybridization among subspecies of wild turkey provides evidence that individual states management actions have influenced the genetic makeup of subspecies in that state.

genomics↗

bioRxiv2024

Asymmetric gene flow maintains an abundant range center

Species are restricted to finite ranges, and when they are in demographic equilibrium with the environment this implies a failure to adapt at the range periphery. There are several competing evolutionary hypotheses for the maintenance and persistence of range edges. One hypothesis is gene swamping of edge populations, in which migrants from the center carrying alleles adapted to the range center but maladaptive along the edge hamper local adaptation. A competing explanation is dispersal limitation, in which reduced migration to the periphery keeps edge populations small, causing drift to dominate over selection. It has proven difficult to assess these potential generative scenarios due to the inherent complexity of species ranges. In this study, we leverage range-wide genomic sequencing data to investigate the evolution of range edges in an empirical system - Haustorius canadensis, the Canadian shovel bug. We find increased genetic drift and inbreeding on the range edges and detect signatures of asymmetric migration towards the range center. The inferred directionality of migration is consistent with the direction of the dominant current regimes in the North Atlantic. We conclude that anisotropic dispersal towards the range center leaves progressively fewer migrants to replenish peripheral populations, consistent with the migration limitation hypothesis, and generates the appearance of an abundant center.

evolutionary biology↗

bioRxiv2023

A spatial approach to jointly estimate Wright's neighborhood size and long-term effective population size

Spatially continuous patterns of genetic differentiation, which are common in nature, are often poorly described by existing population genetic theory or methods that assume panmixia or discrete, clearly definable populations. There is therefore a need for statistical approaches in population genetics that can accommodate continuous geographic structure, and that ideally use georeferenced individuals as the unit of analysis, rather than populations or subpopulations. In addition, researchers are often interested describing the diversity of a population distributed continuously in space, and this diversity is intimately linked to the dispersal potential of the organism. A statistical model that leverages information from patterns of isolation-by-distance to jointly infer parameters that control local demography (such as Wrights neighborhood size), and the long-term effective size (Ne) of a population would be useful. Here, we introduce such a model that uses individual-level pairwise genetic and geographic distances to infer Wrights neighborhood size and long-term Ne. We demonstrate the utility of our model by applying it to complex, forward-time demographic simulations as well as an empirical dataset of the Red Sea clownfish (Amphiprion bicinctus). The model performed well on simulated data relative to alternative approaches and produced reasonable empirical results given the natural history of clownfish. The resulting inferences provide important insights into the population genetic dynamics of spatially structure populations.

evolutionary biology↗

bioRxiv2021

Paths to annihilation: Genetic and demographic consequences of range contraction patterns

Species range contractions are important contributors to biological annihilation, yet typically do not receive the same attention as extinctions. Range contractions can lead to marked impacts on populations but are often only characterized by measurements of reduced extent. For effective conservation efforts, it is critical to recognize that not all range contractions are the same. We propose four distinct patterns of range contraction: shrinkage, amputation, hollow, and fragmentation. We tested their impact on populations of a generic generalist species using forward-time simulations. Results showed that all four patterns differentially reduced population abundance (declines of 60-80%) and significantly increased average relatedness, with differing patterns in nucleotide diversity ({pi}) declines relative to the contraction pattern. The fragmentation pattern resulted in the strongest effects on post-contraction genetic diversity and structure. Defining and quantifying range contraction patterns and their consequences for the planets biodiversity provides necessary information to combat biological annihilation in the Anthropocene.

ecology↗

bioRxiv2020

Ghosts of a structured past: Impacts of ancestral isolation by distance on divergence time estimation

Isolation by distance is a widespread pattern in nature that describes the reduction of genetic correlation between subpopulations with increased geographic distance. In the population ancestral to modern sister species, this pattern may hypothetically inflate population divergence time estimation due to the potential for allele frequency differences in subpopulations at the ends of the ancestral population. In this study, we analyze the relationship between the time to the most recent common ancestor and the population divergence time when the ancestral population model is a linear stepping-stone. Using coalescent simulations, we compare the coalescent time to the population divergence time for various ratios of the divergence time over the product of the population size and the deme number. Next, we simulate whole genomes to obtain SNPs, and use the Bayesian coalescent program SNAPP to estimate divergence times. We find that as the rate of migration between neighboring demes decreases, the coalescent time becomes significantly greater than the population divergence time when sampled from end demes. Divergence-time overestimation in SNAPP becomes severe when the divergence-to-population size ratio < 10 and migration is low. We conclude that studies estimating divergence times be cognizant of the potential ancestral population structure in an explicitly spatial context or risk dramatically overestimating the timing of population splits.

evolutionary biology↗