Data from: Phylogeography, population structure, and species delimitation in rockhopper penguins (Eudyptes chrysocome and Eudyptes moseleyi)
Raya Rey, Andrea
Published Aug 16, 2019 on Dryad.
Cite this dataset
Mays, Herman et al. (2019). Data from: Phylogeography, population structure, and species delimitation in rockhopper penguins (Eudyptes chrysocome and Eudyptes moseleyi) [Dataset]. Dryad. https://doi.org/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 species. The best-supported population models for the southern rockhoppers were those where E. c. chrysocome and E. c. filholi were combined into a single lineage or two lineages with bidirectional gene flow. Additionally, we found that E. c. filholi has the highest effective population size while E. c. chrysocome showed similar effective population size to that of the endangered E. moseleyi. We suggest that the current taxonomic definitions within rockhopper penguins be upheld and that E. chrysocome populations, all found south of the subtropical front, should be treated as a single taxon with distinct management units for E. c. chrysocome and E. c. filholi.
IMa2p output file
Output file from IMa2p
Output from DNAsp analysis for 6 nuclear intron loci and one mitochondrial locus (ND2)
BEAST combined runs
Log and tree files from combined three runs in BEAST.
Phased nuclear intron and mtDNA alignments
Phased nuclear intron DNA alignments, mitochondrial DNA (ND2) alignment, and BEAST taxon file.
BPP analysis including summary of runs and parameters, BPP output and MCMC files, and R code for producing gdi figures.
ML trees for PHRAPL input
Maximum 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 format
Unphased DNA sequence alignments for 6 nuclear intron loci and one mitochondrial DNA sequence (ND2) in FASTA format.
Nuclear intron DNA allele files
Nuclear intron genotype files for input into STRUCTURE
BEAST run 1
BEAST replicate run 1 files including xml file, log file, and trees.
BEAST run 2
BEAST replicate run 2 files including xml file, log file, and trees.
BEAST run 3
BEAST replicate run 3 files including xml file, log file, and trees.
Rockhopper Penguin sampling list
List of sampling locations and collectors for Rockhopper Penguin samples.