An empirical comparison of character-based and coalescent-based approaches to species delimitation in a young avian complex BAILEY D. MCKAY,* HERMAN L. MAYS JR, † YUCHUN WU, ‡ HUI LI, ‡ CHENG-TE YAO, § ISAO NISHIUMI ¶ and FASHENG ZOU ‡ *Bell Museum of Natural History, Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA, †Cincinnati Museum Center, Cincinnati, OH 45203, USA, ‡Guangdong Entomological Institute/South China Institute of Endangered Animals, 105 Xingang Road West, Guangzhou 510260, China, §Endemic Species Research Institute, 1, Minsheng East Road, Jiji Township, Nantou County 552, Taiwan, ¶Department of Zoology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan Abstract 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 char- acter data sets produced conflicting species hypotheses with plumage data suggesting three species, mitochondrial data suggesting two species, and nuclear intron data sug- gesting 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 identi- fied 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 h priors had a dramatic impact on speciation proba- bilities, with lower values consistently favouring splitting and higher values consis- tently 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. Keywords: Bayesian Phylogenetics and Phylogeography, lineage delimitation, population aggregation analysis, Pycnonotus sinensis, Pycnonotus taivanus, species delimitation Received 5 February 2013; revision received 26 June 2013; accepted 2 July 2013 Introduction As fundamental units in biology, species are corner- stones in a diverse range of research programs. For example, ecologists study interactions among species, Correspondence: Bailey McKay, Department of Ornithology, American Museum of Natural History, Central Park West at 79th St., New York, NY 10024, USA, Fax: 1-212-769-5759; E-mail: bmckay@amnh.org; Fasheng Zou, Fax: 0086-020-84183704; E-mail: zoufs@gdei.gd.cn © 2013 John Wiley & Sons Ltd Molecular Ecology (2013) 22, 4943–4957 doi: 10.1111/mec.12446