Genomic signals of selection predict climate-driven population declines in a migratory bird

Bay, Rachael A.; Harrigan, Ryan J.; Underwood, Vinh Le; Gibbs, H. Lisle; Smith, Thomas B.; Ruegg, Kristen

doi:10.1126/science.aan4380

Cited by 390 publications

(496 citation statements)

References 39 publications

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“…Ultimately, our nested elevational sampling design may prove useful for untangling effects of environment from those of space, and efforts to evaluate optimal approaches for modelling selection and better controlling for population structure in this system are underway. Together with the present results on factors influencing genetic structure and diversity, understanding the response to selection across this region will prove useful in predicting responses to climate change, including the relative importance of niche tracking and adaptation (Bay et al., ; Fitzpatrick & Keller, ).…”

Section: Discussionmentioning

confidence: 60%

Distance, elevation and environment as drivers of diversity and divergence in bumble bees across latitude and altitude

et al. 2018

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Identifying drivers of dispersal limitation and genetic differentiation is a key goal in biogeography. We examine patterns of population connectivity and genetic diversity using restriction site-associated DNA sequencing (RADseq) in two bumble bee species, Bombus vosnesenskii and Bombus bifarius, across latitude and altitude in mountain ranges from California, Oregon and Washington, U.S.A. Bombus vosnesenskii, which occurs across a broader elevational range at most latitudes, exhibits little population structure while B. bifarius, which occupies a relatively narrow higher elevation niche across most latitudes, exhibits much stronger population differentiation, although gene flow in both species is best explained by isolation with environmental niche resistance. A relationship between elevational habitat breadth and genetic diversity is also apparent, with B. vosnesenskii exhibiting relatively consistent levels of genetic diversity across its range, while B. bifarius has reduced genetic diversity at low latitudes, where it is restricted to high-elevation habitat. The results of this study highlight the importance of the intersect between elevational range and habitat suitability in influencing population connectivity and suggest that future climate warming will have a fragmenting effect even on populations that are presently well connected, as they track their thermal niches upward in montane systems.

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Section: Discussionmentioning

confidence: 60%

Distance, elevation and environment as drivers of diversity and divergence in bumble bees across latitude and altitude

et al. 2018

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“…Most of these MMEs occurred without forewarning; causes, mechanisms, and effects had to be inferred post hoc in the absence of information about pre‐MME conditions. While our abilities to reconstruct likely factors from genomic signatures (De Wit, Rogers‐Bennett, Kudela, & Palumbi, 2014) and infer longer‐term decline of vulnerable populations with genomic tools (Bay et al, 2018) are improving, we remain largely ignorant of genomic attributes that may elevate susceptibility or resilience to MMEs.…”

Section: Introductionmentioning

confidence: 99%

An initial comparative genomic autopsy of wasting disease in sea stars

et al. 2020

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Beginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as “asteroid idiopathic wasting syndrome” (AIWS) due to its elusive aetiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progression from morbidity to death was rapid, leaving few tell‐tale symptoms. Here, we take a forensic genomic approach to discover candidate genes that may help explain sea star wasting syndrome. We report the first genome and annotation for Pisaster ochraceus, along with differential gene expression (DGE) analyses in four size classes, three tissue types, and in symptomatic and asymptomatic individuals. We integrate nucleotide polymorphisms associated with survivors of the wasting disease outbreak, DGE associated with temperature treatments in P. ochraceus, and DGE associated with wasting in another asteroid Pycnopodia helianthoides. In P. ochraceus, we found DGE across all tissues, among size classes, and between asymptomatic and symptomatic individuals; the strongest wasting‐associated DGE signal was in pyloric caecum. We also found previously identified outlier loci co‐occur with differentially expressed genes. In cross‐species comparisons of symptomatic and asymptomatic individuals, consistent responses distinguish genes associated with invertebrate innate immunity and chemical defence, consistent with context‐dependent stress responses, defensive apoptosis, and tissue degradation. Our analyses thus highlight genomic constituents that may link suspected environmental drivers (elevated temperature) with intrinsic differences among individuals (age/size, alleles associated with susceptibility) that elicit organismal responses (e.g., coelomocyte proliferation) and manifest as sea star wasting mass mortality.

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“…how much gene c change is required for adapta on to climate change, we thus need to quan fy and model environment-driven natural selec on at the gene c level. Thanks to species-wide genome scans [7][8][9] , as well as genome associa ons with climate of origin [10][11][12][13][14] , we increasingly understand the genomic basis of past selec on and climate adapta on, which has been used to es mate future adapta on debt or "genomic vulnerability" 10,11 .…”

Section: Field-validated Predic Ons Across the Species Range Indicatementioning

confidence: 99%

“…Niche Models (ENMs), but instead of training them with presence/absence data of a gene c variant 10,11 , we trained them with our measured allelic selec on differen als. This provided a means to predict whether alleles should increase/decrease in frequency in a certain climate, instead of 6 .…”

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confidence: 99%

A map of climate change-driven natural selection in Arabidopsis thaliana

Expósito-Alonso

Burbano

Bossdorf

et al. 2018

Preprint

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Through the lens of evolution, climate change is an agent of natural selection that forces populations to change and adapt, or face extinction. Current assessments of the risk of biodiversity associated with climate change1, however, do not typically take into account the genetic makeup of populations and how natural selection impacts it2. We made use of the extensive genome information in Arabidopsis thaliana and measured how rainfall-manipulation affected the fitness of 517 natural lines grown in Spain and Germany. This allowed us to directly infer selection along the genome3. Natural selection was particularly strong in the hot-dry Spanish location, killing 63% of lines and significantly changing the frequency of ~5% of all genome-wide variants. A significant portion of this climate-driven natural selection over variants was predictable from signatures of local adaptation (R2=29-52%), as genetic variants found in geographic areas with climates more similar to the experimental sites were positively selected. Field-validated predictions across the species range indicated that Mediterranean and Western Siberian populations — at the edges of the species’ environmental limits — currently experience the strongest climate-driven selection. With more frequent droughts and rising temperatures in Europe4, we forecast an increase in directional natural selection moving northwards from the southern end, and putting many native A. thaliana populations at evolutionary risk.

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Genomic signals of selection predict climate-driven population declines in a migratory bird

Cited by 390 publications

References 39 publications

Distance, elevation and environment as drivers of diversity and divergence in bumble bees across latitude and altitude

Distance, elevation and environment as drivers of diversity and divergence in bumble bees across latitude and altitude

An initial comparative genomic autopsy of wasting disease in sea stars

A map of climate change-driven natural selection in Arabidopsis thaliana

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