Data from: Phylogeography, population structure, and species delimitation in rockhopper penguins (Eudyptes chrysocome and Eudyptes moseleyi) ...

• Main Authors: Mays, Herman, Oehler, David, Morrison, Kyle, Morales, Ariadna, Lycans, Alyssa, Perdue, Justin, Battley, Phillip, Cherel, Yves, Chilvers, B, Crofts, Sarah, Demongin, Laurent, Fry, W, Hiscock, Jo, Kusch, Alejandro, Marin, Manuel, Poisbleau, Maud, Quillfeldt, Petra, Raya Rey, Andrea, Steinfurth, Antje, Thompson, David, Weakley, Leonard
• Format: Dataset
• Language: English
• Published: Dryad 2019
• Subjects: Antarctic Circumpolar Current; Southern Ocean; Eudyptes chrysocome filholi; Conservation genetics and biodiversity; Eudyptes chrysocome chrysocome; Population structure and phylogeography; Subtropical front; Eudyptes moseleyi; Subtropical front Subject area Population structure and phylogeography; Antarctic; Antarc*
• Online Access: https://dx.doi.org/10.5061/dryad.6c8d45m; https://datadryad.org/stash/dataset/doi:10.5061/dryad.6c8d45m

Rockhopper penguins are delimited as two species, the northern rockhopper (Eudyptes moseleyi) and the southern rockhopper (E. chrysocome), with the latter comprising two subspecies, the western rockhopper (E. c. chrysocome) and the eastern rockhopper (E. c. filholi). We conducted a phylogeographic study using multilocus data from 114 individuals sampled across 12 colonies from the entire range of the northern/southern rockhopper complex to assess potential population structure, gene flow and species limits. Bayesian and likelihood methods with nuclear and mitochondrial DNA, including model testing and heuristic approaches, support E. moseleyi and E. chrysocome as distinct species lineages with a divergence time of 0.97 Ma. However, these analyses also indicated the presence of gene flow between these species. Among southern rockhopper subspecies, we found evidence of significant gene flow and heuristic approaches to species delimitation based on the genealogical diversity index failed to delimit them as ... : IMa2p output fileOutput file from IMa2pIMa2_RH2_8.xlsxDNAsp outputOutput from DNAsp analysis for 6 nuclear intron loci and one mitochondrial locus (ND2)BEAST combined runsLog and tree files from combined three runs in BEAST.Phased nuclear intron and mtDNA alignmentsPhased nuclear intron DNA alignments, mitochondrial DNA (ND2) alignment, and BEAST taxon file.BPP analysisBPP analysis including summary of runs and parameters, BPP output and MCMC files, and R code for producing gdi figures.ML trees for PHRAPL inputMaximum likelihood trees for each of 6 nuclear intron loci and one mitochondrial locus (ND2) produced in RAxML for input in PHRAPL analysis. Each file is in newick format.Unphased DNA sequence alignments in FASTA formatUnphased DNA sequence alignments for 6 nuclear intron loci and one mitochondrial DNA sequence (ND2) in FASTA format.Nuclear intron DNA allele filesNuclear intron genotype files for input into STRUCTUREBEAST run 1BEAST replicate run 1 files including xml file, log file, and ...