DOI: 10.5061/dryad.bg79cnpfr
title: Data from: Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation

description: 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 phylogenetic relationships within this group, with a special
 emphasis on characterizing the extent of gene tree heterogeneity and its
 underlying causes. We first used multispecies coalescent methods to
 generate a “complete evidence” phylogenetic hypothesis based on
 genome-wide variants, while accounting for incomplete lineage sorting and
 introgression. We then investigated the variation in phylogenetic signal
 across the genome, to quantify the extent of discordance across genomic
 regions, and test its underlying causes. We found that wagtail genomes are
 mosaics of regions supporting variable genealogies, because of ILS and
 inter-specific introgression. The most common topology across the genome,
 supporting M. alba and M. aguimp as sister species, appears to be
 influenced by ancient introgression. Additionally, we inferred another
 ancient introgression event, between M. alba and M. grandis. By combining
 results from multiple analyses, we propose a phylogenetic network for the
 black-and-white wagtails that confirms that similar phenotypes evolved in
 non-sister lineages, supporting parallel plumage evolution. Furthermore,
 the inferred reticulations do not connect species with similar plumage
 coloration, suggesting that introgression does not underlie parallel
 plumage evolution in this group. Our results demonstrate the importance of
 investigation of genome-wide patterns of gene tree heterogeneity to help
 understanding the mechanisms underlying phenotypic evolution.
description: # Data from: Introgression underlies phylogenetic uncertainty but not
 parallel plumage evolution in a recent songbird radiation *** 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: --&gt; 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. --&gt;
 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 the latter with a subset of 4 species. Theses files were used
 to infer phylogenetic trees with SNAPPER and phylogenetic networks with
 SNaQ!. --&gt; SNPs_chr*_topology_weighting.geno: 31 variant files (1
 per chromosome) containing all genome wide variants for the focal species.
 These files are in the geno format, which is similar to vcf and
 generated/used by the genomics general package
 (https://github.com/simonhmartin/genomics_general). These files were used
 for topology weighting and calculations of Dxy in sliding windows. In
 addition, the file Rancilhac_2023_wagtail_phylogeny_supplements.docx
 contains the supplementary material for the manuscript.