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

Abstract

Closely related marine species with large overlapping ranges provide opportunities to study mechanisms of speciation, particularly when there is evidence of gene flow between such 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 (0.174-0.263 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.

Distinct patterns of hybridization across a suture zone in a coral reef fish (Dascyllus trimaculatus)

“…The opposite is also true (i.e., predominant Pacific SNPs with Indian Ocean mitochondria; Figure ), which further suggests there is rampant hybridization in the suture zone at CHR, but not at CKE. This has been previously reported in marine fishes, where hybridization can lead to different mitonuclear combinations across closely related groups (Bernal, Gaither, Simison, & Rocha, ). These events will continue until there is some selective advantage maintaining certain combinations of mitochondrial haplotypes with specific nuclear backgrounds (Hill, ), which could already be happening at CKE.…”

Genomic, ecological, and morphological approaches to investigating species limits: A case study in modern taxonomy from Tropical Eastern Pacific surgeonfishes

“…However, a low, but significant, F ST was found between spotted and nonspotted individuals. This value was comparable to F ST estimates of different collection sites (e.g., Mexico vs. Central American localities), and these results suggest a possible signature of isolation by distance, which has been previously reported for other fishes of the TEP (Bernal, Gaither, Simison, & Rocha, ; Lessios & Baums, ). It would be tempting to suggest that SNPs gathered from UCEs lack sufficient signal to detect differentiation at this time scale given the conserved nature of these genomic regions.…”

Austrian gudgeons of the genusGobio(Teleostei: Gobionidae): A mixture of divergent lineages

“…obtusirostris , 2.0%; G. gobio —Balkan lineage, 2.2%; G. obtusirostris —Balkan lineage, 1.3%). Assuming a general substitution rate of 0.5%–2% per million years for the COI gene (Bermingham et al, ; Bernal et al, ; Brown et al, ; Lessios, ), the lineages diverged 0.65–1.2 to 2.6–4.8 million years ago. No clear phylogeographic structure became evident within the G. gobio and Balkan lineages, with haplotypes shared across river systems and different countries, especially in G. gobio .…”

“…Past population size trajectories for these mitochondrial lineages were inferred by means of a Bayesian coalescent approach (Bayesian skyline plot [BSP] tree prior) as implemented in BEAST 1.8.4 (Drummond, Suchard, Xie, & Rambaut, ), employing the TN93 model as the best fitting model of molecular evolution and assuming a strict molecular clock. As there is no Gobionidae specific substitution rate available for COI , we assumed a general rate of 0.5%–2% per million years for the COI gene in fishes (Bermingham, McCafferty, & Martin, ; Bernal, Gaither, Simison, & Rocha, ; Brown, George, & Wilson, ; Lessios, ). Two independent MCMC runs of 15 million generations each were conducted, with a sampling frequency of 1,000 steps and a burn‐in of the first 10% of sampled generations.…”