Data from: Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon)
Bernal, Moises A., King Abdullah University of Science and Technology
Gaither, Michelle R., Durham University
Simison, Warren Brian, California Academy of Sciences
Rocha, Luiz A., California Academy of Sciences
Published Mar 09, 2017 on Dryad.
Cite this dataset
Bernal, Moises A.; Gaither, Michelle R.; Simison, Warren Brian; Rocha, Luiz A. (2017). Data from: Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon) [Dataset]. Dryad. https://doi.org/10.5061/dryad.b9482
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.
Alignments for the Sanger sequences of mitochondrial markers COI, CytB and CR, and nuclear markers TMO and RAG2. The names of the individuals include the respective collection sites. The abbreviation Hmacu corresponds to Haemulon maculicauda, and Hflav to Haemulon flaviguttatum.
Genotype data in STRUCTURE format
The analyses corresponding to the SNP dataset (obtained via RADSeq) are based on this genotype dataset in STRUCTURE format. The first column represents the sample name, second column corresponds to the "population" of origin (2 species and 2 locations), and the rest of the columns represent the genotypes for the specific loci. The names of the individuals contain the location site and the abbreviation Hmac corresponds to Haemulon maculicauda, and Hflav corresponds to Haemulon flaviguttatum.
Input file for Migrate-n
This text file contains the sequences that were used for the analysis of migration presented in the manuscript, which were performed with Migrate-n. Sequences of both species were separated, but there was no distinction made by collection site.