Fitness costs associated with ancestry to isolated populations of an endangered species

Wilder, Aryn P.; Navarro, Asako Y.; King, Shauna N. D.; Miller, William B.; Thomas, Steven; Steiner, Cynthia C.; Ryder, Oliver A.; Shier, Debra M.

doi:10.1007/s10592-020-01272-8

Cited by 22 publications

(22 citation statements)

References 52 publications

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“…Therefore, using migrants from a population that underwent drastic bottlenecking can introduce high genetic load as well as little genetic diversity and adaptive potential, bringing together the worst of both worlds. This seems to have been the case with one of the donor populations used to rescue the endangered Pacific pocket mouse (Wilder et al 2020). Fortunately, analysis of genomic data can provide inferences on the demographic history (Santiago et al 2020, and references therein) that may allow the election of a donor population with a record of moderate size allowing for efficient purging.…”

Section: Genetic Purging In the Donor Populationmentioning

confidence: 99%

Reviewing the consequences of genetic purging on the success of rescue programs

2021

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Genetic rescue is increasingly considered a promising and underused conservation strategy to reduce inbreeding depression and restore genetic diversity in endangered populations, but the empirical evidence supporting its application is limited to a few generations. Here we discuss on the light of theory the role of inbreeding depression arising from partially recessive deleterious mutations and of genetic purging as main determinants of the medium to long-term success of rescue programs. This role depends on two main predictions: (1) The inbreeding load hidden in populations with a long stable demography increases with the effective population size; and (2) After a population shrinks, purging tends to remove its (partially) recessive deleterious alleles, a process that is slower but more efficient for large populations than for small ones. We also carry out computer simulations to investigate the impact of genetic purging on the medium to long term success of genetic rescue programs. For some scenarios, it is found that hybrid vigor followed by purging will lead to sustained successful rescue. However, there may be specific situations where the recipient population is so small that it cannot purge the inbreeding load introduced by migrants, which would lead to increased fitness inbreeding depression and extinction risk in the medium to long term. In such cases, the risk is expected to be higher if migrants came from a large non-purged population with high inbreeding load, particularly after the accumulation of the stochastic effects ascribed to repeated occasional migration events. Therefore, under the specific deleterious recessive mutation model considered, we conclude that additional caution should be taken in rescue programs. Unless the endangered population harbors some distinctive genetic singularity whose conservation is a main concern, restoration by continuous stable gene flow should be considered, whenever feasible, as it reduces the extinction risk compared to repeated occasional migration and can also allow recolonization events.

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Section: Genetic Purging In the Donor Populationmentioning

confidence: 99%

Reviewing the consequences of genetic purging on the success of rescue programs

2021

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“…Deliberate translocations of small numbers of individuals from one population to another has been advocated as a conservation tool to rescue genetically depauperate populations from the most severe fitness effects of genetic erosion (Frankham 2015 ; Whiteley et al 2015 ; Ralls et al 2018 ). However, doing so without sufficient understanding of evolutionary relationships or demographic history could potentially thwart evolutionary trajectories, risk outbreeding depression, or, depending on the genetic load of donor populations, exacerbate inbreeding depression (Edmands 2007 ; Bell et al 2019 ; Wilder et al 2020 ; Kyriazis et al 2021 ). Targeting conservation measures to specific populations therefore requires detailed knowledge of population structure, both to identify populations of conservation need and value as well as to assess the suitability of potential donor populations (e.g., Frankham et al 2011 ).…”

Section: Introductionmentioning

confidence: 99%

Contrasting genetic trajectories of endangered and expanding red fox populations in the western U.S

Quinn

Preckler‐Quisquater

Akins³

et al. 2022

Heredity

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As anthropogenic disturbances continue to drive habitat loss and range contractions, the maintenance of evolutionary processes will increasingly require targeting measures to the population level, even for common and widespread species. Doing so requires detailed knowledge of population genetic structure, both to identify populations of conservation need and value, as well as to evaluate suitability of potential donor populations. We conducted a range-wide analysis of the genetic structure of red foxes in the contiguous western U.S., including a federally endangered distinct population segment of the Sierra Nevada subspecies, with the objectives of contextualizing field observations of relative scarcity in the Pacific mountains and increasing abundance in the cold desert basins of the Intermountain West. Using 31 autosomal microsatellites, along with mitochondrial and Y-chromosome markers, we found that populations of the Pacific mountains were isolated from one another and genetically depauperate (e.g., estimated Ne range = 3–9). In contrast, red foxes in the Intermountain regions showed relatively high connectivity and genetic diversity. Although most Intermountain red foxes carried indigenous western matrilines (78%) and patrilines (85%), the presence of nonindigenous haplotypes at lower elevations indicated admixture with fur-farm foxes and possibly expanding midcontinent populations as well. Our findings suggest that some Pacific mountain populations could likely benefit from increased connectivity (i.e., genetic rescue) but that nonnative admixture makes expanding populations in the Intermountain basins a non-ideal source. However, our results also suggest contact between Pacific mountain and Intermountain basin populations is likely to increase regardless, warranting consideration of risks and benefits of proactive measures to mitigate against unwanted effects of Intermountain gene flow.

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“…2022 ), the subspecies persists in three small, isolated populations in Orange and San Diego counties with very low effective population sizes ( N e = 3.3, 25.0, and 50.6; Swei et al . 2003 ; Wilder et al . 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…Microsatellite and mitochondrial markers have provided estimates of population differentiation, diversity, N e , and relatedness, but genomic data would give additional resolution needed to address remaining questions relevant to population management. For example, a fitness analysis suggested that inbreeding and genetic load may play a role in limiting reproductive success ( Wilder et al . 2020 ), and evidence of karyotype variation within P. longimembris ( Patton 1967 ; McKnight and Lee 1992 ) and within PPM ( King et al .…”

Section: Introductionmentioning

confidence: 99%

A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population

Wilder

Dudchenko

Curry

et al. 2022

Genome Biology and Evolution

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High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of runs of homozygosity, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load.

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Fitness costs associated with ancestry to isolated populations of an endangered species

Cited by 22 publications

References 52 publications

Reviewing the consequences of genetic purging on the success of rescue programs

Reviewing the consequences of genetic purging on the success of rescue programs

Contrasting genetic trajectories of endangered and expanding red fox populations in the western U.S

A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population

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