Genetic and phenotypic differentiation in a Neotropical passerine with a disjunct distribution in the Andean and Atlantic forests (Thamnophilus ruficapillus)

The Andean and Atlantic forests are separated by the open vegetation corridor, which acts as a geographic barrier. However, these forests experienced cycles of connection and isolation in the past, which shaped the phylogeographic patterns of their biotas. We analysed the evolutionary history of the Rufous-capped Antshrike (Thamnophilus ruficapillus), a species with a disjunct distribution in the Atlantic and Andean forests and thus an appropriate model to study the effect of the open vegetation corridor and the Andes on the diversification of the Neotropical avifauna. We performed a phylogenetic/phylogeographic analysis, including the five subspecies, using mitochondrial and nuclear genomic DNA, and studied their differences in vocalizations and plumage coloration. Both the mitochondrial and nuclear DNA evidenced a marked phylogeographic structure with three differentiated lineages that diverged without signs of gene flow in the Pleistocene (1.0–1.7 Mya): one in the Atlantic Forest and..., We extracted genomic DNA from fresh tissue samples using DNeasy tissue extraction kit (Qiagen, CA, USA). To generate the genomic data we used double-digest restriction site-associated DNA sequencing (ddRADseq) following the protocol of Peterson et al. (2012) with modifications described in Thrasher et al. (2018). Briefly, for each sample we isolated ~500 ng of DNA, at a standardized concentration of 20 ng/µl, and digested it with the restriction enzymes SbfI High Fidelity (8 base bp recognition site; 5’-CCTGCAGG-3’) and MspI (4 base bp recognition site; 5’-CCGG-3’) (New England BioLabs, MA, USA). The digested DNA was ligated to P1 and P2 adapters on both ends (sequences are available in Peterson et al. 2012). We size-selected groups of 20 uniquely barcoded samples (index groups), retaining fragments between 400 and 700 bp using Blue Pippin (Sage Science, MA, USA). To incorporate the full Illumina TruSeq primer sequences and unique indexing primers into each library, we performed low cyc..., , Thamnophilus ruficapillus ddRAD data

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LOCI file containing the ddRAD data of 18 samples of the Rufous-capped Antshrike (*Thamnophilus ruficapillus*) collected in Bolivia, Argentina, and Uruguay.

Title of the manuscript: Genetic and phenotypic differentiation in a Neotropical passerine with a disjunct distribution in the Andean and Atlantic forests (Thamnophilus ruficapillus).

Authors: Belén Bukowski, Leonardo Campagna, Gustavo S. Cabanne, Pablo L. Tubaro and Darío A. Lijtmaer.