Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient.

Identifying the genetic basis of phenotypic variation and its relationship with the environment is key to understanding how local adaptations evolve. Such patterns are especially interesting among populations distributed across habitat gradients, where genetic structure can be driven by isolation by distance (IBD) and/or isolation by environment (IBE). Here, we used variation in ~1,600 high-quality SNPs derived from paired-end sequencing of double-digest restriction site-associated DNA (ddRAD-Seq) to test hypotheses related to IBD and IBE in the Yucatan jay (Cyanocorax yucatanicus), a tropical bird endemic to the Yucatán Peninsula. This peninsula is characterized by a precipitation and vegetation gradient-from dry to evergreen tropical forests-that is associated with morphological variation in this species. We found a moderate level of nucleotide diversity (π = .008) and little evidence for genetic differentiation among vegetation types. Analyses of neutral and putatively adaptive SNPs (identified by complementary genome-scan approaches) indicate that IBD is the most reliable explanation to account for frequency distribution of the former, while IBE has to be invoked to explain those of the later. These results suggest that selective factors acting along a vegetation gradient can promote local adaptation in the presence of gene flow in a vagile, nonmigratory and geographically restricted species. The putative candidate SNPs identified here are located within or linked to a variety of genes that represent ideal targets for future genomic surveys.

Phylogeography of the white-crowned parrot (Pionus senilis) / Filogeografia do maitaca-de-testa-branca (Pionus senilis)

Abstract The white-crowned parrot Pionus senilis (von Spix, 1824) is distributed throughout Middle America, inhabiting the Gulf of Mexico coastal area from Tamaulipas (Mexico) to northern Panama. We used mitochondrial data (COI, ND2 and ND4) from 55 specimens to infer phylogenetic relationships, and analyzed the phylogeographic structure, genetic diversity, divergence periods, and historical demography to explore phylogeographic patterns. We found three divergent lineages: two geographically separated by the Isthmus of Tehuantepec, and the third, in Costa Rica by the Nicaragua Depression. The analysis of molecular variance and statistical analyses were consistent with genetically distinct populations. The Central American lineage diverged 1.33 million years ago, whereas the other two lines branched off 1.19 million years ago. This phylogenetic pattern has been reported in other species of Middle American birds.

Resumo A curica-de-testa-branca Pionus senilis (von Spix, 1824) está distribuída por toda a América Central, habitando a área costeira do Golfo do México de Tamaulipas (México) ao norte do Panamá. Usamos dados mitocondriais (COI, ND2 e ND4) de 55 espécimes para inferir relações filogenéticas e analisamos a estrutura filogeográfica, diversidade genética, períodos de divergência e demografia histórica para explorar padrões filogeográficos. Encontramos três linhagens divergentes: duas geograficamente separadas pelo Istmo de Tehuantepec, e a terceira, na Costa Rica pela Depressão da Nicarágua. A análise de variância molecular e as análises estatísticas foram consistentes com populações geneticamente distintas. A linhagem da América Central divergiu há 1.33 milhão de anos, enquanto as outras duas linhas se ramificaram há 1.19 milhão de anos. Este padrão filogenético foi relatado em outras espécies de aves da América Central.