Data from: Resolving evolutionary relationships in closely related species with whole-genome sequencing data

Using genetic data to resolve the evolutionary relationships of species is
of major interest in evolutionary and systematic biology. However,
reconstructing the sequence of speciation events, the so-called species
tree, in closely related and potentially hybridizing species is very
challenging. Processes such as incomplete lineage sorting and
interspecific gene flow result in local gene genealogies that differ in
their topology from the species tree, and analyses of few loci with a
single sequence per species are likely to produce conflicting or even
misleading results. To study these phenomena on a full phylogenomic scale,
we use whole-genome sequence data from 200 individuals of four
black-and-white flycatcher species with so far unresolved phylogenetic
relationships to infer gene tree topologies and visualize genome-wide
patterns of gene tree incongruence. Using phylogenetic analysis in
nonoverlapping 10-kb windows, we show that gene tree topologies are
extremely diverse and change on a very small physical scale. Moreover, we
find strong evidence for gene flow among flycatcher species, with distinct
patterns of reduced introgression on the Z chromosome. To resolve species
relationships on the background of widespread gene tree incongruence, we
used four complementary coalescent-based methods for species tree
reconstruction, including complex modeling approaches that incorporate
post-divergence gene flow among species. This allowed us to infer the most
likely species tree with high confidence. Based on this finding, we show
that regions of reduced effective population size, which have been
suggested as particularly useful for species tree inference, can produce
positively misleading species tree topologies. Our findings disclose the
pitfalls of using loci potentially under selection as phylogenetic markers
and highlight the potential of modeling approaches to disentangle species
relationships in systems with large effective population sizes and
post-divergence gene flow.