Supplemental data from: Genomic signatures of speciation in butterflies

Studies of life rely on classifying organisms into species. Contrary to a
frequent belief, simple and quantitative standards for species delineation
are lacking, and debates about species delimitation create obstacles for
conservation biology, agriculture, legislation, and education. To tackle
this key biological question, we have chosen butterflies as model
organisms. We sequenced and analyzed transcriptomes of 186 butterfly
specimens representing pairs of close but clearly distinct species,
conspecific populations, and taxa that are debated among experts. We find
that species are robustly separated from conspecific populations by the
combination of two measures computed on Z-linked genes: the fixation index
that detects hiatus between species, and the extent of gene flow that
quantifies reproductive isolation. These criteria suggest that all 9
butterfly pairs that caused experts' disagreement are distinct
species, not populations or subspecies. When applied to Homo, our criteria
agree that all modern humans are the same species, distinct from
Neanderthals, suggesting the relevance of this study beyond butterflies.
Furthermore, we found that divergence and positive selection in proteins
involved in interaction with DNA (including proteins encoded by
trans-regulatory elements), circadian clock, pheromone sensing,
development, and immune response recurrently correlate with speciation. A
significant fraction of these divergent proteins is encoded by the Z
chromosome, which appears to be more resistant to introgression than
autosomes. Taken together, we find possible common speciation mechanisms
in butterflies, present additional support for an important role of the Z
chromosome in speciation of butterflies, and suggest quantitative criteria
for butterfly species delimitation using genomic data, which is vital for
the exploration of biodiversity.