Data from: Evidence for hybridisation-driven heteroplasmy maintained across generations in a ricefish endemic to a Wallacean ancient lake

Heteroplasmy, the presence of multiple mitochondrial DNA (mtDNA)
haplotypes within cells of an individual, is caused by mutation or
paternal leakage. However, heteroplasmy is usually resolved to homoplasmy
within a few generations because of germ-line bottlenecks; therefore,
instances of heteroplasmy are limited in nature. Here, we report
heteroplasmy in the ricefish species Oryzias matanensis, endemic to Lake
Matano, an ancient lake in Sulawesi Island, in which one individual was
known to have many heterozygous sites in the mitochondrial NADH
dehydrogenase subunit 2 (ND2) gene. In this study, we cloned the ND2 gene
for some additional individuals with heterozygous sites and demonstrated
that they are truly heteroplasmic. Phylogenetic analysis revealed that the
extra haplotype within the heteroplasmic O. matanensis individuals
clustered with haplotypes of O. marmoratus, a congeneric species
inhabiting adjacent lakes. This indicated that the heteroplasmy originated
from paternal leakage due to interspecific hybridisation. The extra
haplotype was unique and contained two nonsynonymous substitutions. These
findings demonstrate that this hybridisation-driven heteroplasmy was
maintained across generations for a long time to the extent that the extra
mitochondria evolved within the new host.