Data from: The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterfly

The Palearctic butterfly Melitaea didyma stands out as one of the most
striking cases of intraspecific genetic differentiation detected in
Lepidoptera: 11 partially sympatric mitochondrial lineages have been
reported, displaying levels of divergence of up to 7.4%. To better
understand the evolutionary processes underlying the diversity observed in
mtDNA, we compared mtDNA and genome-wide SNP data using double-digest
restriction site-associated DNA sequencing (ddRADseq) results from 93
specimens of M. didyma ranging from Morocco to eastern Kazakhstan. We
found that, between ddRADseq and mtDNA results, there is a match only in
populations that likely remained allopatric for long periods of time.
Other mtDNA lineages may have resulted from introgression events and were
probably affected by Wolbachia infection. The five main ddRADseq clades
supported by STRUCTURE were parapatric or allopatric and showed high
pairwise FST values, but some were also estimated to display various
levels of gene flow. Melitaea didyma represents one of the first cases of
deep mtDNA splits among European butterflies assessed by a genome-wide DNA
analysis and reveals that the interpretation of patterns remains
challenging even when a high amount of genomic data is available. These
findings actualize the ongoing debate of species delimitation in
allopatry, issue likely of relevance to a significant proportion of global
biodiversity.