DOI: 10.5061/dryad.hk45m
title: Data from: An empirical comparison of a character-based and a coalescent-based approach to species delimitation in a young avian complex

description: The process of discovering species is a fundamental responsibility of
 systematics. Recently, there has been a growing interest in
 coalescent-based methods of species delimitation aimed at objectively
 identifying species early in the divergence process. However, few
 empirical studies have compared these new methods with character-based
 approaches for discovering species. In this study, we applied both a
 character-based and a coalescent-based approaches to delimit species in a
 closely related avian complex, the light-vented/Taiwan bulbul (Pycnonotus
 sinensis/Pycnonotus taivanus). Population aggregation analyses of plumage,
 mitochondrial and 13 nuclear intron character data sets produced
 conflicting species hypotheses with plumage data suggesting three species,
 mitochondrial data suggesting two species, and nuclear intron data
 suggesting one species. Such conflict is expected among recently diverged
 species, and by integrating all sources of data, we delimited three
 species verified with independently congruent character evidence as well
 as a more weakly supported fourth species identified by a single
 character. Attempts to validate species hypothesis using Bayesian
 Phylogenetics and Phylogeography (BPP), a coalescent-based method of
 species delimitation, revealed several issues that can seemingly affect
 statistical support for species recognition. We found that θ priors had a
 dramatic impact on speciation probabilities, with lower values
 consistently favouring splitting and higher values consistently favouring
 lumping. More resolved guide trees also resulted in overall higher
 speciation probabilities. Finally, we found suggestive evidence that BPP
 is sensitive to the divergent effects of nonrandom mating caused by
 intraspecific processes such as isolation-with-distance, and therefore,
 BPP may not be a conservative method for delimiting independently evolving
 population lineages. Based on these concerns, we questioned the
 reliability of BPP results and based our conclusions about species limits
 exclusively on character data.
description: Input and output from
 BPP analysesCompressed file
 containing input and output files from BPP analyses of the
 light-vented/Taiwan bulbul (Pycnonotus sinensis/P. taivanus) complex.
 Analyses include 4 taxa analyses, 5 taxa analyses, 5 taxa analyses using
 two alternative tree topologies, and geographic cluster analyses.
 Geographic cluster analyses include seperate analyses for sinensis,
 hainanus, and taivanus. All analyses were run using low, middle, and high
 theta priors.BPP_files.zip12630 locus phased alignment12630 locus phased alignment in fasta format12630 Align Phased.fas13403 locus phased alignment13403 locus phased alignment in fasta format13403 Align Phased.fas14572 locus phased alignment14572 locus phased alignment in fasta format14572 Align Phased.fas15463 locus phased alignment15463 locus phased alignment in fasta format15463 Align Phased.fas17898 locus phased alignment17898 locus phased alignment in fasta format17898 Align Phased.fas22187 locus phased alignment22187 locus phased alignment in fasta format22187 Align Phased.fas23361 locus phased alignment23361 locus phased alignment in fasta format23361 Align Phased.fas24972 locus phased alignment24972 locus phased alignment in fasta format24972 Align Phased.fas25442 locus phased alignment25442 locus phased alignment in fasta format25442 Align Phased.fas25613 locus phased alignment25613 locus phased alignment in fasta format25613 Align Phased.fas27331 locus phased alignment27331 locus phased alignment in fasta format27331 Align Phased.fas27818 locus phased alignment27818 locus phased alignment in fasta format27818 Align Phased.fasMUSK locus phased alignmentMUSK locus phased alignment in fasta formatMUSK Align Phased.fasND2 locus alignmentND2 locus alignment in fasta formatND2 Align Full.phyND2 locus alignment-trimmedND2 locus alignment that has been trimmed to include only the 25 individuals sequenced for nuclear introns. The full (1041 bp) ND2 gene was sequenced for these individuals.ND2 Align Trimmed.fastaMorphological data matrixA table described the four observed plumage character states for all scored individuals.CHBU Plumage.xlsx