Nuclear locus divergence at the early stages of speciation in the Orchard Oriole complex

Abstract

As two lineages diverge from one another, mitochondrial DNA should evolve fixed differences more rapidly than nuclear DNA due to its smaller effective population size and faster mutation rate. As a consequence, molecular systematists have focused on the criteria of reciprocal monophyly in mitochondrial DNA for delimiting species boundaries. However, mitochondrial gene trees do not necessarily reflect the evolutionary history of the taxa in question, and even mitochondrial loci are not expected to be reciprocally monophyletic when the speciation event happened very recently. The goal of this study was to examine mitochondrial paraphyly within the Orchard Oriole complex, which is composed of Icterus spurius (Orchard Oriole) and Icterus fuertesi (Fuertes' Oriole). We increased the geographic sampling, added four nuclear loci, and used a range of population genetic and coalescent methods to examine the divergence between the taxa. With increased taxon sampling, we found evidence of clear structure between the taxa for mitochondrial DNA. However, nuclear loci showed little evidence of population structure, indicating a very recent divergence between I. spurius and I. fuertesi. Another goal was to examine the genetic variation within each taxon to look for evidence of a past founder event within the I. fuertesi lineage. Based on the high amounts of genetic variation for all nuclear loci, we found no evidence of such an event – thus, we found no support for the possible founding of I. fuertesi through a change in migratory behavior, followed by peripheral isolates speciation. Our results demonstrate that these two taxa are in the earliest stages of speciation, at a point when they have fixed differences in plumage color that are not reflected in monophyly of the mitochondrial or nuclear DNA markers in this study. This very recent divergence makes them ideal for continued studies of species boundaries and the earliest stages of speciation.

Genetic and morphological support for possible sympatric origin of fish from subterranean habitats

“…The mtDNA phylogeny shows deeper genetic divergence between the two cave barb species (3.6% K2P) compared to the genomic divergence (0.14% K2P). The deeper mtDNA in face of a shallow nuclear genomic divergence between the cave barbs can be justified by the 5–10 times higher mutation rate and smaller effective population sizes of mtDNA compared to nucDNA 25 , 39 . The higher mutation rate and the lower effective population size of mtDNA in combination with behavioural and ecological characters like differential habitat dependence of male and female cave barbs, in which females show philopatry while males disperse more 25 , 40 , may magnify the divergence depth difference observed between the maternally inherited genome and the nuclear genome.…”