Effective Population Size, Genetic Variation, and Their Relevance for Conservation: The Bighorn Sheep in Tiburon Island and Comparisons with Managed Artiodactyls

Gasca-Pineda, Jaime; Cassaigne, Ivonne; Alonso, Ricardo; Eguiarte, Luis E.

doi:10.1371/journal.pone.0078120

Cited by 22 publications

(11 citation statements)

References 76 publications

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“…Genetic compensation could maintain genetic variation in PBS if certain social behaviors are density dependent. Gasca-Pineda et al (2013) found similar levels of genetic diversity in a bighorn sheep population established from only 16 individuals. These authors suggested that decreased predation pressure may have resulted in less sexual segregation, allowing females to mate with non-dominant males within the herd.…”

Section: Population Bottlenecks and Genetic Diversitymentioning

confidence: 58%

Genetic population structure of Peninsular bighorn sheep (Ovis canadensis nelsoni) indicates substantial gene flow across US–Mexico border

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Boyce

et al. 2015

Biological Conservation

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Section: Population Bottlenecks and Genetic Diversitymentioning

confidence: 58%

Genetic population structure of Peninsular bighorn sheep (Ovis canadensis nelsoni) indicates substantial gene flow across US–Mexico border

Buchalski

Navarro

Boyce

et al. 2015

Biological Conservation

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“…Similarly, depressed genetic diversity can also be seen in island bighorn sheep populations when compared to that of mainland populations (Gasca‐Pineda et al . ). Contemporary observations in other alpine species also tend to find that small isolated populations possess less genetic diversity (Henry et al .…”

Section: Discussionmentioning

confidence: 97%

Genome‐wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate

et al. 2016

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Past glaciation events have played a major role in shaping the genetic diversity and distribution of wild sheep in North America. The advancement of glaciers can isolate populations in ice-free refugia, where they can survive until the recession of ice sheets. The major Beringian refugium is thought to have held thinhorn sheep (Ovis dalli) populations during times of glacial advance. While isolation in the major refugium can account for much of the genetic and morphological diversity seen in extant thinhorn sheep populations, mounting evidence suggests the persistence of populations in smaller minor refugia. We investigated the refugial origins of thinhorn sheep using ~10 000 SNPs obtained via a cross-species application of the domestic sheep ovine HD BeadChip to genotype 52 thinhorn sheep and five bighorn sheep (O. canadensis) samples. Phylogenetic inference revealed a distinct lineage of thinhorn sheep inhabiting British Columbia, which is consistent with the survival of a group of thinhorn sheep in a minor refugium separate from the Beringian refugium. Isolation in separate glacial refugia probably mediated the evolution of the two thinhorn sheep subspecies, the white Dall's sheep (O. d. dalli), which persisted in Beringia, and the dark Stone's sheep (O. d. stonei), which utilized the minor refugium. We also found the first genetic evidence for admixture between sheep from different glacial refugia in south-central Yukon as a consequence of post glacial expansion and recolonization. These results show that glaciation events can have a major role in the evolution of species inhabiting previously glaciated habitats and the need to look beyond established refugia when examining the evolutionary history of such species.

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“…Although effective population size and genetic diversity are typically associated, previous studies have shown that these two diversity estimates can become uncoupled due to differential gene flow and/or demographic processes (e.g., bottlenecking) acting through time (Gasca-Pineda, Cassaigne, Alonso, & Eguiarte, 2013;Lonsinger, Adams, & Waits, 2018;Miller & Waits, 2003). Given that our study deals with gene flow between wild and domestic lineages, we posit that gene flow from an inbred domestic lineage (e.g., game-farm mallards) can move "novel" variation into a population and thus create a signature of increased or similar effective population size as es- Similarly, we hypothesize that differential gene flow of loci across the genome from game-farm mallards into wild mallards may also explain the increased genomic differentiation observed across time between wild mallards and black ducks (Figure 3; Supplementary Materials Figure S2B Figure 4).…”

Section: Impact Of Differential Gene Flow On Genomic Diversity and mentioning

confidence: 99%

Assessing changes in genomic divergence following a century of human‐mediated secondary contact among wild and captive‐bred ducks

et al. 2020

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Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used worldwide to augment wildlife populations. We test between possible outcomes of human‐mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD‐seq loci for contemporary mallards (Anas platyrhynchos) throughout North America and two domestic mallard types (i.e., known game‐farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game‐farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait‐capture array targeting thousands of loci in century‐old (1842–1915) and contemporary (2009–2010) mallard and American black duck (Anas rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game‐farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game‐farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.

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Effective Population Size, Genetic Variation, and Their Relevance for Conservation: The Bighorn Sheep in Tiburon Island and Comparisons with Managed Artiodactyls

Cited by 22 publications

References 76 publications

Genetic population structure of Peninsular bighorn sheep (Ovis canadensis nelsoni) indicates substantial gene flow across US–Mexico border

Genetic population structure of Peninsular bighorn sheep (Ovis canadensis nelsoni) indicates substantial gene flow across US–Mexico border

Genome‐wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate

Assessing changes in genomic divergence following a century of human‐mediated secondary contact among wild and captive‐bred ducks

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