DOI: 10.5061/dryad.6c8d45m
title: Data from: Phylogeography, population structure, and species delimitation in rockhopper penguins (Eudyptes chrysocome and Eudyptes moseleyi)

description: 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.
description: 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 trees.BEAST_run_1.zipBEAST run 2BEAST replicate run 2 files including xml file, log file, and trees.BEAST_run_2.zipBEAST run 3BEAST replicate run 3 files including xml file, log file, and trees.BEAST_run_3.zipRockhopper Penguin sampling listList of sampling locations and collectors for Rockhopper Penguin samples.Sample list.xlsx