Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation

Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the “black-and-white wagtails”, a group of five species in the songbird genus Motacilla: one species, the White Wagtail (M. alba), shows wide intra-specific plumage variation, while the four others form two pairs of very similar-looking species (African Pied Wagtail M. aguimp + Mekong Wagtail M. samveasnae and Japanese Wagtail M. grandis + White-browed Wagtail M. maderaspatensis, respectively). However, the two species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the p..., , , # Data from: Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation

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This data contains genome-wide variants from 29 individuals of six species of wagtails (Motacilla), derived from whole-genome resequencing data. Variants were called based on a White Wagtail (Motacilla alba) reference genome. This data was used to perform a variety of phylogenetic analyses.

## Description of the data and file structure

The repository contains three types of data files:
--> ASTRAL_*sp_trees.trees: two files containing phylogenetic trees inferred in non-overlapping 50kb sliding windows, with all species (5sp) or a subset of four species (4sp). These files were used to perform species tree inference with ASTRAL.
--> SNAPPER_*_snps_*.vcf: three vcf files containing genome-wide variants thinned to 5kb for the autosomes and chromosome Z separately. For the autosomes, two files are provided (5sp and 4sp), the former with all species and ...