Speciation in mountain refugia: phylogeography and demographic history of the pine siskin and black‐capped siskin complex

Alvarez, Sofía; Salter, Jessie F.; McCormack, John E.; Milá, Borja

doi:10.1111/jav.00814

Cited by 16 publications

(6 citation statements)

References 67 publications

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“…18,000 years ago (Milá et al 2007; Friis et al 2016). Similar postglacial expansions have been reported for many other bird species (Seutin et al 1995; Milá et al 2000; 2006; Hansson et al 2008; Malpica and Ornelas 2014; Alvarez et al 2015). However, the population structure documented in this study reveals a variety of different spatial, selective and demographic factors not previously documented in other avian taxa.…”

Section: Discussionsupporting

confidence: 83%

Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird

Friis

Fandós

Zellmer

et al. 2018

Preprint

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The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified systems such as that of the Oregon junco (Aves: Emberizidae) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Genome-wide SNP loci analyses revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and more admixed recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (i) drift in geographic isolation, (ii) differentiation along continuous selective gradients, and (iii) isolation by adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation in several populations, driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation over short periods when acting over multiple independent loci.

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Section: Discussionsupporting

confidence: 83%

Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird

Friis

Fandós

Zellmer

et al. 2018

Preprint

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“…18,000 years ago (Friis et al, ; Milá et al, ). Similar postglacial expansions have been reported for many other bird species (Alvarez, Salter, McCormack, & Milá, ; Hansson, Hasselquist, Tarka, Zehtindjiev, & Bensch, ; Malpica & Ornelas, ; Milá, Girman, Kimura, & Smith, ; Milá, Smith, & Wayne, ; Seutin, Ratcliffe, & Boag, ). However, the population structure documented in this study reveals a variety of different spatial, selective and historical factors not previously documented in other avian taxa.…”

Section: Discussionsupporting

confidence: 80%

Genome‐wide signals of drift and local adaptation during rapid lineage divergence in a songbird

et al. 2018

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The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic‐environment association analyses (GEA) while controlling for population structure. Analysis of genome‐wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (a) drift in geographic isolation, (b) differentiation along continuous selective gradients and (c) isolation‐by‐adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci.

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“…Marked mtDNA genetic divergence between highland populations separated by the IT and molecular dating suggest that gene flow across the barrier has been interrupted for about 200 000 yr (Barber and Klicka 2010, Barrera-Guzmán et al 2012, Rodríguez-Gómez et al 2013, a period of time that corresponds approximately to two full glacial cycles in the late Pleistocene. Patterns of genetic diversity and haplotype networks are consistent with a scenario of recent population expansion on populations west side of the IT and, despite limited sample sizes, long-term isolation and small effective population sizes on those east of the IT (Barrera-Guzmán et al 2012, Malpica and Ornelas 2014, Álvarez et al 2016. In contrast, molecular dating with nSSRs for the amethyst-throated hummingbird Lampornis amethystinus indicates that gene flow across the IT has been interrupted since the Last Glacial Maximum (LGM), about 16 000 yr ago , supporting a scenario of postglacial isolation and divergence of L. amethystinus populations separated by the IT.…”

Section: Genetic Differentiation Across the Isthmus Of Tehuantepecmentioning

confidence: 57%

Genetic structuring and secondary contact in the white‐chestedAmaziliahummingbird species complex

Rodríguez‐Gómez

Ornelas

2018

Journal of Avian Biology

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Pleistocene climate cycles have been recognized to be a major driver of postglacial northward range expansion of North American bird populations. During glacial maxima, allopatric lineages that were reproductively isolated might have come into secondary contact with one another during expansion periods and the genetic signatures of past hybridization as a result of secondary contact events should produce detectable hybrid zones. The white‐chested hummingbirds Amazilia violiceps and A. viridifrons, constitute a species complex showing phenotypic similarity across its range. One exception is the subspecies found in the Central Depression of Chiapas (A. viridifrons villadai), which shares some plumage traits with the endemic but allopatric green‐fronted populations in Oaxaca. Phylogenetic relationships, taxonomy and species limits among violiceps, viridifrons and villadai have been controversial for decades. We assessed genetic structure of populations and introgression in this species complex by analysing 95 individuals at ten nuclear microsatellites and morphology. Bayesian analysis yielded four clusters. However, only two clusters generally match previously described mtDNA haplogroups, one parental taxon in the south (villadai) and a cluster with two admixed taxa (viridifrons and violiceps) that cannot be attributed to any pure parental population. High genetic admixture was recorded in the violiceps/viridifrons range, probably as a consequence of a postglacial northern expansion of violiceps. Signs of admixture and gene flow between violiceps/viridifrons and villadai were low. Historical and contemporary migration rates and Approximate Bayesian computations support a scenario of divergence with gene flow: a Pleistocene basal split separating A. violiceps and the other two clades are derived from a second split (villadai and viridifrons) or from a merger of violiceps and villadai into viridifrons due to gene flow.

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Speciation in mountain refugia: phylogeography and demographic history of the pine siskin and black‐capped siskin complex

Cited by 16 publications

References 67 publications

Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird

Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird

Genome‐wide signals of drift and local adaptation during rapid lineage divergence in a songbird

Genetic structuring and secondary contact in the white‐chestedAmaziliahummingbird species complex

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