Data from: Most genomic loci misrepresent the phylogeny of an avian radiation because of ancient gene flow

Phylogenetic trees based on genome-wide sequence data may not always
represent the true evolutionary history for a variety of reasons. One
process that can lead to incorrect reconstruction of species phylogenies
is gene flow, especially if interspecific gene flow has affected large
parts of the genome. We investigated phylogenetic relationships within a
clade comprising eight species of passerine birds
(Phylloscopidae, Phylloscopus, leaf warblers) using
one de novo genome assembly and 78 resequenced genomes.
On the basis of hypothesis-exclusion trials based on D-statistics,
phylogenetic network analysis, and demographic inference analysis, we
identified ancient gene flow affecting large parts of the genome between
one species and the ancestral lineage of a sister species pair. This
ancient gene flow consistently caused erroneous reconstruction of the
phylogeny when using large amounts of genome-wide sequence data. In
contrast, the true relationships were captured when smaller parts of the
genome were analyzed, showing that the “winner-takes-all democratic
majority tree” is not necessarily the true species tree. Under this
condition, smaller amounts of data may sometimes avoid the effects of gene
flow due to stochastic sampling, as hidden reticulation histories are more
likely to emerge from the use of larger data sets, especially whole-genome
data sets. In addition, we also found that genomic regions affected by
ancient gene flow generally exhibited higher genomic differentiation but a
lower recombination rate and nucleotide diversity. Our study highlights
the importance of considering reticulation in phylogenetic reconstructions
in the genomic era.