ddRAD data-set of manuscript "Phylogeographic variation within the Buff-browed Foliage-gleaner (Aves: Furnariidae: Syndactyla rufosuperciliata) supports an Andean-Atlantic forests connection via the Cerrado", by Cabanne et al
Description
We evaluated whether the Andean and the Atlantic forests acted as refugia during the Quaternary, and tested biogeographic hypotheses about the regions involved in the connectivity between those biomes (through the Chaco or the Cerrado). To achieve these goals we selected the Buff-browed Foliage-gleaner Syndactyla rufosuperciliata (Aves, Furnariidae) as a study system, a taxon distributed between the Andean and Atlantic forest. We first explored the historical connectivity between regions through niche modeling. We subsequently used DNA sequences (n=71 individuals) and genomic analyses (ddRADseq, n=33 individuals) to evaluate population genetic structure and gene flow within this species. Finally, we performed population model selection using Approximate Bayesian Computation. Our findings indicate that the Andean and the Atlantic forests acted as refugia, and that the populations of the focal species from both regions contacted through the Cerrado region, thus suggesting that the historical dynamics of Andean and Atlantic forests are important for the evolution of forest birds in the region. The results are in agreement with studies of other organisms and may indicate a more general pattern of connectivity among biomes in the Neotropics. Finally, we recommend recognizing both the Andean and the Altantic forests lineages of S. rufosuperciliata as independent species. ### denovo_assembly_syndactyla.tar.gz ### Final STACKS assembly. Includes two population maps: 1) all samples; 2) samples with low missing data that are in the paper. Files in different formats (structure, vcf, genpop, etc) can be exported using the "populations" module from stacks. ### GPhoCS.zip ### GPhoCS input file and control files for the combined and small (gene flow restricted to one pair of populations) population models. ### 2883_SNPs.structure.tsv ### Structure input file for Syndactyla rufosuperciliata alone ### 2386_SNPs.structure.tsv ### Structure input file for Syndactyla rufosuperciliata and Syndactyla dimidiata