Repeated divergent selection on pigmentation genes in a rapid finch radiation

Campagna, Leonardo; Repenning, Márcio; Silveira, Luís Fábio; Fontana, Carla Suertegaray; Tubaro, Pablo L.; Lovette, Irby J.

doi:10.1126/sciadv.1602404

Cited by 166 publications

(177 citation statements)

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“…Thus, genetic differentiation is prevalent throughout the genome, which differs from a suite of recent studies that have found patterns of widespread genomic homogeneity with a small number of loci likely underlying phenotypic differentiation in other avian taxa (Mason & Taylor, 2015;Poelstra et al, 2014;. Indeed, the deep evolutionary split that we documented between S. torqueola and S. morelleti is in stark contrast to the shallow evolutionary history that characterizes the southern capuchino radiation in the same genus, in which rapid and recent phenotypic differentiation and speciation are driven by a few loci of large effect (Campagna et al, 2017).…”

Section: Diversification Of the Sporophila Torqueola Complexcontrasting

confidence: 99%

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Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White‐collared Seedeater complex (Thraupidae: Sporophila torqueola)

Mason

Olvera-Vital

Lovette

et al. 2018

Ecology and Evolution

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Phenotypic and genetic variation are present in all species, but lineages differ in how variation is partitioned among populations. Examining phenotypic clustering and genetic structure within a phylogeographic framework can clarify which biological processes have contributed to extant biodiversity in a given lineage. Here, we investigate genetic and phenotypic variation among populations and subspecies within a Neotropical songbird complex, the White‐collared Seedeater (Sporophila torqueola) of Central America and Mexico. We combine measurements of morphology and plumage patterning with thousands of nuclear loci derived from ultraconserved elements (UCEs) and mitochondrial DNA to evaluate population differentiation. We find deep levels of molecular divergence between two S. torqueola lineages that are phenotypically diagnosable: One corresponds to S. t. torqueola along the Pacific coast of Mexico, and the other includes S. t. morelleti and S. t. sharpei from the Gulf Coast of Mexico and Central America. Surprisingly, these two lineages are strongly differentiated in both nuclear and mitochondrial markers, and each is more closely related to other Sporophila species than to one another. We infer low levels of gene flow between these two groups based on demographic models, suggesting multiple independent evolutionary lineages within S. torqueola have been obscured by coarse‐scale similarity in plumage patterning. These findings improve our understanding of the biogeographic history of this lineage, which includes multiple dispersal events out of South America and across the Isthmus of Tehuantepec into Mesoamerica. Finally, the phenotypic and genetic distinctiveness of the range‐restricted S. t. torqueola highlights the Pacific Coast of Mexico as an important region of endemism and conservation priority.

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Section: Diversification Of the Sporophila Torqueola Complexcontrasting

confidence: 99%

“…The genus Sporophila has a remarkably high speciation rate that is similar to Darwin's Finches (Burns et al, 2014;Campagna et al, 2017).…”

Section: Diversification Of the Sporophila Torqueola Complexmentioning

confidence: 99%

Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White‐collared Seedeater complex (Thraupidae: Sporophila torqueola)

Mason

Olvera-Vital

Lovette

et al. 2018

Ecology and Evolution

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“…However, this study along with other recent findings in finches (Campagna et al. ), fresh water sticklebacks (Marques et al. ), and cichlids (Malinksy et al.…”

Section: Discussionsupporting

confidence: 72%

Demography and selection shape transcriptomic divergence in field crickets

et al. 2018

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Gene flow, demography, and selection can result in similar patterns of genomic variation and disentangling their effects is key to understanding speciation. Here, we assess transcriptomic variation to unravel the evolutionary history of Gryllus rubens and Gryllus texensis, cryptic field cricket species with highly divergent mating behavior. We infer their demographic history and screen their transcriptomes for footprints of selection in the context of the inferred demography. We find strong support for a long history of bidirectional gene flow, which ceased during the late Pleistocene, and a bottleneck in G. rubens consistent with a peripatric origin of this species. Importantly, the demographic history has likely strongly shaped patterns of genetic differentiation (empirical F distribution). Concordantly, F -based selection detection uncovers a large number of outliers, likely comprising many false positives, echoing recent theoretical insights. Alternative genetic signatures of positive selection, informed by the demographic history of the sibling species, highlighted a smaller set of loci; many of these are candidates for controlling variation in mating behavior. Our results underscore the importance of demography in shaping overall patterns of genetic divergence and highlight that examining both demography and selection facilitates a more complete understanding of genetic divergence during speciation.

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“…These observations highlight an additional implication of the speciation sieve: ancestral polymorphism may persist through multiple speciation events, especially rapid radiations, before it is sieved. As a result, multiple species pairs will share sieved regions and may appear as if they had undergone repeated local adaptation (e.g., Campagna et al., ).…”

Section: Relevance Of Sieved Polymorphisms During Recent Genomic Divementioning

confidence: 99%

Speciation as a sieve for ancestral polymorphism

Guerrero

Hahn

2017

Molecular Ecology

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Because they are considered rare, balanced polymorphisms are often discounted as crucial constituents of genome-wide variation in sequence diversity. Despite its perceived rarity, however, long-term balancing selection can elevate genetic diversity and significantly affect observed divergence between species. Here, we discuss how ancestral balanced polymorphisms can be "sieved" by the speciation process, which sorts them unequally across descendant lineages. After speciation, ancestral balancing selection is revealed by genomic regions of high divergence between species.This signature, which resembles that of other evolutionary processes, can potentially confound genomic studies of population divergence and inferences of "islands of speciation."

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Repeated divergent selection on pigmentation genes in a rapid finch radiation

Abstract: Selection acted repeatedly on regions that may regulate the expression of genes underlying coloration differences in seedeaters.

Cited by 166 publications

References 64 publications

Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White‐collared Seedeater complex (Thraupidae: Sporophila torqueola)

Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White‐collared Seedeater complex (Thraupidae: Sporophila torqueola)

Demography and selection shape transcriptomic divergence in field crickets

Speciation as a sieve for ancestral polymorphism

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