DOI: 10.5061/dryad.dd3qs
title: Data from: Speciation in mountain refugia: phylogeography and demographic history of the pine siskin and black-capped siskin complex

description: Following Pleistocene glacial maxima, species that adapted to temperate
 climates in low-latitude refugia had to modify their ranges as climate
 changed, expanding either latitudinally towards the poles, or
 altitudinally to higher elevations in mountainous regions. Within just a
 few thousand years, populations taking alternative routes during
 interglacials became isolated from each other and subjected to different
 selection pressures, often leading to lineage divergence and speciation.
 The pine siskin Spinus pinus is a common and widespread songbird showing
 relative phenotypic uniformity across the North American continent. One
 exception is the subspecies found in the highlands of northern Central
 America (S. p. perplexus), which shows marked differentiation in plumage
 color and shares some traits with the endemic and partly sympatric
 black-capped siskin S. atriceps, suggesting potential introgression or
 even a hybrid origin of perplexus. Relationships and species limits among
 pinus, perplexus and atriceps have been controversial for decades. We
 provide new molecular evidence to help resolve the evolutionary history of
 the group. Phylogenetic analysis of mitochondrial DNA and nuclear intron
 sequences revealed three distinct lineages within the complex,
 corresponding to: 1) S. pinus individuals from Canada through central
 Mexico (S. p. pinus and S. p. macropterus), 2) individuals from the
 highlands of Guatemala and Chiapas (S. p. perplexus), and 3) S. atriceps.
 Pine siskins across North America show evidence of a recent postglacial
 population expansion and extremely low levels of diversity and structure.
 In contrast, S. p. perplexus shows evidence of demographic stasis,
 reflecting long-term isolation and restricted dispersal. Marked and
 diagnostic genetic differences among the three lineages in mtDNA and at
 least one intron, suggest that a hybrid origin of S. p. perplexus is
 unlikely, yet some degree of introgression between S. p. perplexus and S.
 atriceps cannot be ruled out in localities where they occur in sympatry.
description: ND2 haplotype alignemt
 of the pine siskin and black-capped siskin complexSpinus pinus, Spinus
 atriceps and Spinus notatus haplotype alignment; NADH dehydrogenase
 subunit 2 (ND2) gene, partial cds; mitochondrialpisi nd2
 haps.fasATP haplotype alignemt
 of the pine siskin and black-capped siskin complexSpinus pinus, Spinus
 atriceps and Spinus notatus haplotype alignment; cytochrome c oxidase
 subunit II gene, partial cds; tRNA-Lys gene, complete sequence; ATP
 synthase 8 gene, complete cds; and ATP synthase 6 gene, partial cds;
 mitochondrialpisi atp
 haps.fasGAPDH haplotype alignemt
 of the pine siskin and black-capped siskin complexSpinus pinus, Spinus
 atriceps and Spinus notatus haplotype alignment;
 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, partial intron
 11pisi
 gapdh ph haps.fasBRM15 haplotype alignemt
 of the pine siskin and black-capped siskin complexSpinus pinus, Spinus
 atriceps and Spinus notatus haplotype alignment; brahma protein (BRM)
 gene, intron 15pisi brm ph
 haps.fasALDOB haplotype alignemt
 of the pine siskin and black-capped siskin complexSpinus pinus, Spinus
 atriceps and Spinus notatus haplotype alignment;aldolase B
 fructose-bisphosphate (ALDOB) gene, exons 5 and 6, partial
 cds.pisi
 aldo ph haps.fas