Testing hypotheses of mitochondrial gene-tree paraphyly: unravelling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (Pomatorhinus musicus)

• Published in: Molecular ecology Vol. 23; no. 23; pp. 5855 - 5867
• Main Authors: Dong, Feng, Zou, Fa-Sheng, Lei, Fu-Min, Liang, Wei, Li, Shou-Hsien, Yang, Xiao-Jun
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01-12-2014
• Subjects: Animals; approximate Bayesian computation; Bayes Theorem; Birds; Cell Nucleus - genetics; DNA, Mitochondrial - genetics; Evolution, Molecular; Gene Flow; Genes, Mitochondrial; Genetic Speciation; incomplete lineage sorting; introgressive hybridization; Mitochondrial DNA; mitochondrial gene-tree paraphyly; Models, Genetic; Passeriformes - genetics; Population genetics; predictive coalescent simulations; Sequence Analysis, DNA; mitochondrial gene-tree paraphyly; incomplete lineage sorting; approximate Bayesian computation; introgressive hybridization; predictive coalescent simulations
• ISSN: 0962-1083; 1365-294X
• DOI: 10.1111/mec.12981

Species‐level paraphyly inferred from mitochondrial gene trees is a prevalent phenomenon in taxonomy and systematics, but there are several potential causes that are not easily explained by currently used methods. This study aimed to test the underlying causes behind the observed paraphyly of Streak‐breasted Scimitar Babbler (Pomatorhinus ruficollis) via statistical analyses of four mitochondrial (mtDNA) and nine nuclear (nuDNA) genes. Mitochondrial gene trees show paraphyly of P. ruficollis with respect to the Taiwan Scimitar Babbler (Pomatorhinus musicus), but nuclear genealogies support a sister‐group relationship. Predictive coalescent simulations imply several hypothetical explanations, the most likely being mitochondrial capture of P. ruficollis by P. musicus for the observed cyto‐nuclear incongruence. Further approximate Bayesian computation suggests a unidirectional introgression model with substantial level of gene flow from P. ruficollis to P. musicus during their initial divergence during the Late Pleistocene. This specific observation frames several potential causes for incongruent outcomes of mitochondrial and nuclear introgression in general, and on the whole, our results underscore the strength of multiple independent loci for species delimitation and importance of testing hypotheses that explain disparate causes of mitochondrial gene‐tree paraphyly.