Data from: Multilocus species trees show the recent adaptive radiation of the mimetic Heliconius butterflies

Müllerian mimicry among Neotropical Heliconiini butterflies is an
excellent example of natural selection, associated with the
diversification of a large continental-scale radiation. Some of the
processes driving the evolution of mimicry rings are likely to generate
incongruent phylogenetic signals across the assemblage, and thus pose a
challenge for systematics. We use a dataset of 22 mitochondrial and
nuclear markers from 92% of species in the tribe, obtained by Sanger
sequencing and de novo assembly of short read data, to re-examine the
phylogeny of Heliconiini with both supermatrix and multispecies coalescent
approaches, characterize the patterns of conflicting signal and compare
the performance of various methodological approaches to reflect the
heterogeneity across the data. Despite the large extent of reticulate
signal and strong conflict between markers, nearly identical topologies
are consistently recovered by most of the analyses, although the
supermatrix approach failed to reflect the underlying variation in the
history of individual loci. However, the supermatrix represents a useful
approximation where multiple rare species represented by short sequences
can be incorporated easily. The first comprehensive, time-calibrated
phylogeny of this group is used to test the hypotheses of a
diversification rate increase driven by the dramatic environmental changes
in the Neotropics over the past 23 million years, or changes caused by
diversity-dependent effects on the rate of diversification. We find that
the rate of diversification has increased on the branch leading to the
presently most species-rich genus Heliconius, but the change occurred
gradually and cannot be unequivocally attributed to a specific
environmental driver. Our study provides comprehensive comparison of
philosophically distinct species tree reconstruction methods and provides
insights into the diversification of an important insect radiation in the
most biodiverse region of the planet.