Data from: Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon)

Closely related marine species with large sympatric ranges provide
opportunities to study the mechanisms of speciation, particularly when
there is evidence of gene flow between the lineages. Here we focus on a
case of hybridization between the sympatric sister-species Haemulon
maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial
and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs)
obtained via Restriction-site Associated DNA Sequencing (RADSeq).
Mitochondrial markers revealed a shared haplotype for COI and low
divergence for CytB and CR between the sister species. On the other hand,
complete lineage sorting was observed at the nuclear loci and most of the
SNPs. Under neutral expectations, the smaller effective population size of
mtDNA should lead to fixation of mutations faster than nDNA. Thus, these
results suggest that hybridization in the recent past (0.174 to 0.263 Ma)
led to introgression of the mtDNA, with little effect on the nuclear
genome. Analyses of the SNP data revealed 28 loci potentially under
divergent selection between the two species. The combination of mtDNA
introgression and limited nuclear DNA introgression provides a mechanism
for the evolution of independent lineages despite recurrent hybridization
events. This study adds to the growing body of research that exemplifies
how genetic divergence can be maintained in the presence of gene flow
between closely related species.