Spatial population genetics in heavily managed species: Separating patterns of historical translocation from contemporary gene flow in white‐tailed deer

Abstract

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 pretranslocation 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 1143 deer sampled statewide in Arkansas. We then employed Simpson's 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 re‐colonization 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 statewide 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 is also applicable for other biodiversity elements with similarly complex demographic histories.

Population genomics of free‐ranging Great Plains white‐tailed and mule deer reflects a long history of interspecific hybridization

“…Our study, along with other recent related work (Chafin et al, 2021;Russell et al, 2019), constitutes a relatively new chapter in deer genetics research that can now address an old observation of interspecific hybridization with more powerful analytical methods. Yet, the results we have presented pose as many new questions and problems as they address and undoubtedly will precipitate productive future research avenues with broader geographic scope.…”

“…Also, given that extralimital WTD samples (from east-central Kansas and Wisconsin) were likewise genetically divergent from WTD from western Kansas, it is evident that comprehensive SNP data may be informative for recognizing regional genetic populations and potentially for resolving the regional origins of transplanted or dispersing individuals (Chafin et al, 2021).…”

Speciation without gene-flow in hybridising deer

“…To detect islands of divergence between WTD & MD, we used the python script popgenWindows.py (Martin 2021) to estimate individual heterozygosity, FST, Dxy and p in 50Kbp windows (note we filtered out scaffolds shorter than 50kb). The accurate computation of Dxy and p require a dataset including the invariant sites, we performed this analysis on the DeerALL dataset.…”

“…The fd statistic, proposed by Martin et al (2015), is less dependent on diversity than D and therefore allows to detect potentially introgressed regions of the genome. We used the python script ABBABABAwindows.py (Martin 2021) to estimate in D and fd in 50Kbp windows to detect potentially introgressed loci in our DeerCAR dataset on two comparisons: 1) P1 = WTD allopatry, P2 = WTD sympatry, P3 = MD sympatry and 2) P1 = MD allopatry, P2 = MD sympatry, P3 = WTD sympatry, both with the caribou as outgroup. We then identified potentially introgressed windows as those having a fd value higher than the 97.5% quantile.…”

Genome-wide SNP analysis of three moose subspecies at the southern range limit in the contiguous United States

“…Our analysis indicated that A. a. shirasi samples from NMT share a notable proportion of SNPs with A. a. andersoni samples (Figs. 2,3B,4), potentially indicating recent or ongoing gene flow, divergence within A. a. shirasi, or clinal variation (sensu Chafin et al 2021) between the two subspecies. DeCesare et al (2020) recently characterized the last century of moose populations in Montana using microsatellite and mtDNA markers, and found evidence that hunting pressure in the middle of the state locally extirpated moose, dividing the moose into northern and southern subpopulations that persisted through the twentieth century, even as moose populations recovered.…”