A comparison of genomic islands of differentiation across three young avian species pairs

Irwin, Darren E.; Milá, Borja; Toews, David P. L.; Brelsford, Alan; Kenyon, Haley L.; Porter, Alison Nicole; Grossen, Christine; Delmore, Kira E.; Alcaide, Miguel; Irwin, Jessica H.

doi:10.1111/mec.14858

Cited by 101 publications

(182 citation statements)

References 85 publications

(188 reference statements)

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“…In addition, the presence of pronounced peaks of differentiation across the genome may indicate elevated selection within certain genomic regions, possibly related to the evolution of morphologically cryptic reproductive isolating mechanisms. Fewer peaks, on the other hand, may suggest a predominant role for neutral processes like genetic drift (Irwin et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Cryptic and extensive hybridization between ancient lineages of American crows

Slager

Epperly

et al. 2020

Molecular Ecology

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Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa that lack reliable traditional characters for identification. In this first population genomic study of Northwestern and American crows, we use genomic SNPs (nuDNA) and mtDNA to investigate the degree of genetic differentiation between these crows and the extent to which they may hybridize. Our results indicate that American and Northwestern crows have distinct evolutionary histories, supported by two nuDNA ancestry clusters and two 1.1%‐divergent mtDNA clades dating to the late Pleistocene, when glacial advances may have isolated crow populations in separate refugia. We document extensive hybridization, with geographic overlap of mtDNA clades and admixture of nuDNA across >900 km of western Washington and western British Columbia. This broad hybrid zone consists of late‐generation hybrids and backcrosses, but not recent (e.g., F1) hybrids. Nuclear DNA and mtDNA clines had concordant widths and were both centred in southwestern British Columbia, farther north than previously postulated. Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, perhaps due to recurring neutral expansion(s) from Pleistocene glacial refugia followed by lineage fusion(s). However, we do not rule out a contributing role for more recent potential drivers of hybridization, such as expansion into human‐modified habitats.

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Section: Introductionmentioning

confidence: 99%

Cryptic and extensive hybridization between ancient lineages of American crows

Slager

Epperly

et al. 2020

Molecular Ecology

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“…However, computer models suggest that the effects of background selection on the divergence landscape may be modest (Zeng and Charlesworth 2011;Matthey-Doret and Whitlock 2018;Zeng and Corcoran 2018). Additionally, background selection has failed to explain some empirical patterns (e.g., Irwin et al 2016Irwin et al , 2018, and it may be the case that there has not been sufficient time for drift and/or negative selection to influence differentiation in recently diverged species (Burri 2017;Delmore et al 2018). Given these differing theoretical and empirical results, we used a comparative approach to disentangle the contributions of background selection and parallel positive selection to the repeatability of genomic differentiation in a recently diverged species.…”

Section: Introductionmentioning

confidence: 99%

Shared Patterns of Genome-Wide Differentiation Are More Strongly Predicted by Geography Than by Ecology

Rennison

Delmore

Samuk

et al. 2020

The American Naturalist

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Closely related populations often display similar patterns of genomic differentiation, yet it remains an open question which ecological and evolutionary forces generate these patterns. The leading hypothesis is that this similarity in divergence is driven by parallel natural selection. However, several recent studies have suggested that these patterns may instead be a product of the depletion of genetic variation that occurs as result of background selection (i.e., linked negative selection). To date, there have been few direct tests of these competing hypotheses. To determine the relative contributions of background selection and parallel selection to patterns of repeated differentiation, we examined 24 independently derived populations of freshwater stickleback occupying a variety of niches and estimated genomic patterns of differentiation in each relative to their common marine ancestor. Patterns of genetic differentiation were strongly correlated across pairs of freshwater populations adapting to the same ecological niche, supporting a role for parallel natural selection. In contrast to other recent work, our study comparing populations adapting to the same niche produced no evidence signifying that similar patterns of genomic differentiation are generated by background selection. We also found that overall patterns of genetic differentiation were considerably more similar for populations found in closer geographic proximity. In fact, the effect of geography on the repeatability of differentiation was greater than that of parallel selection. Our results suggest that shared selective landscapes and ancestral variation are the key drivers of repeated patterns of differentiation in systems that have recently colonized novel environments. .ORCIDs: Rennison, https://orcid.org/0000-0002-5944-0743; Samuk, https:// orcid.org/0000-0003-0396-465X; Miller, https://orcid.org/0000-0002-9441-0101. v o l . 1 9 5 , n o . 2 t h e a m e r i c a n n a t u r a l i s t f e b r u a r y 2 0 2 0 This content downloaded from 169.228.123.

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“…Subsequent reinterpretation of these patterns, however, suggested that outlier peaks in FST could also be generated by reductions in within-population nucleotide diversity driven by "linked selection" (Noor and Bennett 2009;Cruickshank and Hahn 2014), either as a result of recent selective sweeps (Maynard Smith and Haigh 1974;Kaplan et al 1989;Stephan et al 1992;Braverman et al 1995;Gillespie 1997Gillespie , 2000Gillespie , 2001 or background selection (Charlesworth et al 1993;Charlesworth 1994;Hudson and Kaplan 1995;Gillespie 1997). Furthermore, some studies have demonstrated that genome-wide patterns in FST tend to be inversely correlated with both recombination rate and nucleotide diversity, suggesting that the search for the causal loci driving local adaptation may be obfuscated by the recombination and/or diversity landscapes across the genome (Burri et al 2015;Vijay et al 2017;Irwin et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Local adaptation can cause both peaks and troughs in nucleotide diversity within populations

Jasper

Yeaman

2020

Preprint

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Local adaptation is expected to cause high FST at sites linked to a causal locus, however this pattern can also be driven by background or positive selection. Within-population nucleotide diversity could provide a means to differentiate these scenarios, as both background and positive selection deplete diversity, whereas some theoretical studies have shown that local adaptation increases it. However, it is unclear whether such theoretical predictions generalize to more complicated models. Here, we explore how local adaptation shapes genome-wide patterns in nucleotide diversity and FST, extending previous work to study the effect of variable degrees of polygenicity and genotypic redundancy in an adaptive trait, and different levels of population structure. We show that local adaptation produces two very different patterns depending on the relative strengths of migration and selection, either markedly decreasing or increasing withinpopulation diversity at linked sites at equilibrium. When migration is low, regions of depleted diversity can extend large distances from the causal locus, with substantially more diversity eroded than expected with background selection. With higher migration, peaks occur over much smaller genomic distances but with much larger magnitude changes in diversity. In spatially extended clinal environments both patterns can be found within a single species, with increases in diversity at the center of the range and decreases towards the periphery. Our results demonstrate that there is no universal diagnostic signature of local adaptation based on nucleotide diversity, however, given that neither background nor positive selection inflate diversity, when peaks are found they strongly suggest local adaptation.

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A comparison of genomic islands of differentiation across three young avian species pairs

Cited by 101 publications

References 85 publications

Cryptic and extensive hybridization between ancient lineages of American crows

Cryptic and extensive hybridization between ancient lineages of American crows

Shared Patterns of Genome-Wide Differentiation Are More Strongly Predicted by Geography Than by Ecology

Local adaptation can cause both peaks and troughs in nucleotide diversity within populations

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