Datasets of Diversification in Amazonian Hypocnemis antbirds (Aves: Thamnophilidae) inferred from Ultraconserved Elements (UCEs)

This dataset contains processed files with sequences of up to 2,222 Ultra-conserved Elements (UCEs) and 30 exons loci from 58 specimens belonging to all currently recognized Hypocnemis (Aves: Thamnophilidae) species and all but one subspecies. These files were generated based on raw Illumina sequencing reads deposited in the NBCI Sequence Read Archive under BioProject PRJNA1311538. The dataset contained herein was used to infer phylogenies, population structure, interspecific limits, and the genus’ biogeographic history, and is divided into 8 different subsets, as described below. Dataset 1 encompassed all sampled Hypocnemis individuals plus the outgroup belonging to the genus Drymophila, whereas dataset 2 contained only all Hypocnemis individuals sequenced (Table 1 in tps://doi.org/10.2139/ssrn.5215079). Datasets 3+5 and datasets 4+7 included, respectively, the same randomly selected individuals of the H. cantator and H. hypoxantha complexes, i.e., up to three specimens per lineage recovered by the ML phylogeny (Table 1 in tps://doi.org/10.2139/ssrn.5215079). Finally, dataset 6 contained all specimens sequenced of the H. cantator complex, whereas dataset 8 included only specimens belonging to H. striata and H. rondoni (Table 1 in tps://doi.org/10.2139/ssrn.5215079). Datasets 2, 3 and 4 were obtained through the selection of loci with highly informative sites. For this, we used the script “phyluce_allign_get_informative_sites” and retained only loci with more than 16 informative sites, which accounted for approximately 25% of all variable sites. See the table below for a short description of the different dataset subsets and the analyses employed with each of them. Dataset (n) samples Taxa (n) genetic markers Analyses (softwares) 1 59 Hypocnemis cantator complex, Hypocnemis hypoxantha complex and Drymophila genei (outgroup) 2,222 UCEs + 30 exons Likelihood phylogenetic tree (RaxML) 2 58 Hypocnemis cantator complex and Hypocnemis hypoxantha complex 93 UCEs + 7 exons Coalescent species tree (*Beast) and Biogeographic history (BioGeoBEARS – Rpackage) 3 28 Hypocnemis cantator complex 93 UCEs + 7 exons Species delimitation tree (STACEY–Beast2) 4 12 Hypocnemis hypoxantha complex 120 UCEs + 8 exons Species delimitation tree (STACEY–Beast2) 5 28 Hypocnemis cantator complex 1,069 SNPs Species delimitation tree (SNAPP–Beast2) 6 46 Hypocnemis cantator complex 1,069 SNPs Phylogenetic network (Splitstree), PcoA-1 (Past) and Populational structure-1 (sNMF) 7 12 Hypocnemis hypoxantha complex 1,242 SNPs Phylogenetic network (Splitstree), PcoA-1 (Past), Species delimitation tree (SNAPP–Beast2) and Populational structure-1 (sNMF) 8 20 Polytypic H. striata + H. rondoni 1,029 SNPs PcoA-1 (Past) and Populational structure-1 (sNMF)