The Effect of Balancing Selection on Population Differentiation: A Study with HLA Genes

Brandt, Débora Y. C.; Cesar, Jonatas; Goudet, Jérôme; Meyer, Diogo

doi:10.1534/g3.118.200367

Cited by 40 publications

(37 citation statements)

References 68 publications

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“…These results suggest that HLA loci show high levels of variation, deviations from neutrality-equilibrium and relatively high levels of population differentiation, even though under balancing selection. This scenario is consistent with that described by Brandt et al [ 47 ], in which populations of the same geographic region tend to show higher F ST values for HLA SNPs, while populations of distinct geographic regions have lower F ST values. Suggesting that local adaptation of HLA alleles may contribute to population differentiation on a regional scale, however, without erasing signatures of long-term balancing selection.…”

Section: Resultssupporting

confidence: 93%

Demographic history and selection at HLA loci in Native Americans

et al. 2020

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The American continent was the last to be occupied by modern humans, and native populations bear the marks of recent expansions, bottlenecks, natural selection, and population substructure. Here we investigate how this demographic history has shaped genetic variation at the strongly selected HLA loci. In order to disentangle the relative contributions of selection and demography process, we assembled a dataset with genome-wide microsatellites and HLA-A , -B , -C , and - DRB1 typing data for a set of 424 Native American individuals. We find that demographic history explains a sizeable fraction of HLA variation, both within and among populations. A striking feature of HLA variation in the Americas is the existence of alleles which are present in the continent but either absent or very rare elsewhere in the world. We show that this feature is consistent with demographic history (i.e., the combination of changes in population size associated with bottlenecks and subsequent population expansions). However, signatures of selection at HLA loci are still visible, with significant evidence selection at deeper timescales for most loci and populations, as well as population differentiation at HLA loci exceeding that seen at neutral markers.

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Section: Resultssupporting

confidence: 93%

Demographic history and selection at HLA loci in Native Americans

et al. 2020

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“…Signatures of low and high genetic differentiation between populations can be the result of purifying or positive selection. However, balancing selection, a mechanism that could maintain polymorphism above the expected genetic diversity, could also in part result in genetic differentiation ( Brandt et al, 2018 ). To account for balancing selection, we compared the pairwise genetic diversity (π) among populations and we could not find signatures of elevated genetic diversity within the investigated regions under strong selection.…”

Section: Resultsmentioning

confidence: 99%

Intra-species differences in population size shape life history and genome evolution

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Reichard

et al. 2020

eLife

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The evolutionary forces shaping life history divergence within species are largely unknown. Turquoise killifish display differences in lifespan among wild populations, representing an ideal natural experiment in evolution and diversification of life history. By combining genome sequencing and population genetics, we investigate the evolutionary forces shaping lifespan among wild turquoise killifish populations. We generate an improved reference genome assembly and identify genes under positive and purifying selection, as well as those evolving neutrally. Short-lived populations from the outer margin of the species range have small population size and accumulate deleterious mutations in genes significantly enriched in the WNT signaling pathway, neurodegeneration, cancer and the mTOR pathway. We propose that limited population size due to habitat fragmentation and repeated population bottlenecks, by increasing the genome-wide mutation load, exacerbates the effects of mutation accumulation and cumulatively contribute to the short adult lifespan.

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“…We also found that adaptive F ST values were generally lower than neutral values for Washington herds (Fig. 6D), which is expected in cases of balancing selection, especially when populations experience similar selective pressures, such as pathogenmediated selective regimes (Aguilar et al 2004, Brandt et al 2018. We did not observe this pattern in British Columbia, likely as a result of a high proportion of Rocky Mountain ancestry in sampled animals from some herds alone (Figs.…”

Section: Discussionmentioning

confidence: 61%

Genetic Diversity and Divergence among Bighorn Sheep from Reintroduced Herds in Washington and Idaho

et al. 2021

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Bighorn sheep (Ovis canadensis) populations in the western United States have undergone widespread declines and extirpations since the late nineteenth century as a consequence of introduced diseases, competition with livestock, and unregulated hunting. Washington, Idaho, USA, and British Columbia, Canada were historically thought to be occupied by 2 bighorn lineages or subspecies: Rocky Mountain (O. c. canadensis) and California (O. c. californiana). The putative California lineage was completely extirpated in the United States, and reintroductions to reestablish populations were sourced directly or indirectly from a single region in southern British Columbia. Restoration efforts have attempted to maintain the diversity and divergence of these 2 lineages, sometimes referred to as subspecies although taxonomic classifications have changed over time. In this study we describe genetic variation in a subset of native and reintroduced herds of California and Rocky Mountain bighorn sheep. We examined genetic diversity and divergence between bighorn sheep herds using 15 microsatellite loci, including 4 loci linked to genes involved in immune function. We analyzed 504 samples from reintroduced herds in Washington (n = 10 California herds, n = 4 Rocky Mountain herds) and Idaho (n = 5 California), and source herds in Oregon (n = 1 Rocky Mountain) and British Columbia (n = 5 California, 1 Rocky Mountain). Genetic structure reflected known reintroduction history, and geographic proximity also was associated with decreased genetic divergence. Herds in Washington and Idaho sourced from California bighorn sheep were less genetically diverse than those sourced from Rocky Mountain herds. Also, levels of relatedness within and across California herds were higher than in Rocky Mountain herds and similar to what would be expected for full and half siblings. Lower diversity and higher relatedness among California herds is a concern for long-term fitness and likely related to past population bottlenecks, fewer source populations, and management history, such as entirely sourcing California herds from British Columbia. Genetic divergence of neutral loci between California and Rocky Mountain herds was greater than that of adaptive loci, potentially indicating that balancing selection has maintained similar genetic diversity across lineages in loci associated with immune and other adaptive functions. Thus, we recommend future reintroductions and augmentations should continue to use source populations from the appropriate California or Rocky Mountain lineage to avoid potential outbreeding depression and maintain possible adaptive differences. This could be accomplished by obtaining sheep from ≥1 source within the genetic lineage, while avoiding sourcing from admixed herds. Future work encompassing a broader geographic sampling of populations and a greater portion of the genome is necessary to better evaluate the degree to which contemporary divergence between lineages is associated with recent founder effects and genetic isolation or evol...

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The Effect of Balancing Selection on Population Differentiation: A Study with HLA Genes

Cited by 40 publications

References 68 publications

Demographic history and selection at HLA loci in Native Americans

Demographic history and selection at HLA loci in Native Americans

Intra-species differences in population size shape life history and genome evolution

Genetic Diversity and Divergence among Bighorn Sheep from Reintroduced Herds in Washington and Idaho

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