10.5061/DRYAD.HK45M
McKay, Bailey D.
University of Minnesota
Mays Jr., Herman L.
Guangdong Entomological Institute/South China Institute of Endangered
Animals; 105 Xingang Road West Guangzhou 510260 China
Wu, Yuchun
Guangdong Entomological Institute/South China Institute of Endangered
Animals; 105 Xingang Road West Guangzhou 510260 China
Li, Hui
Guangdong Entomological Institute/South China Institute of Endangered
Animals; 105 Xingang Road West Guangzhou 510260 China
Yao, Cheng-te
Endemic Species Research Institute; 1 Minsheng East Road, Jiji Township;
Nantou County 552 Taiwan
Nishiumi, Isao
National Museum
Zou, Fasheng
Guangdong Entomological Institute/South China Institute of Endangered
Animals; 105 Xingang Road West Guangzhou 510260 China
Mays, Herman L.
Cincinnati Museum Center
Data from: An empirical comparison of a character-based and a
coalescent-based approach to species delimitation in a young avian complex
Dryad
dataset
2013
Pycnonotus taivanus
Pycnonotus sinensis hainanus
Pycnonotus sinensis sinensis
Pycnonotus sinensis
Pycnonotus sinensis orii
Pycnonotus sinensis formosae
2013-07-16T17:09:16Z
2013-07-16T17:09:16Z
en
https://doi.org/10.1111/mec.12446
1573423 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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
China
Japan
Taiwan
East Asia