☆ 4.5 Article

Past hybridization between two East Asian long-tailed tits (Aegithalos bonvaloti and A. fuliginosus)

FRONTIERS IN ZOOLOGY (2014)

Journal

FRONTIERS IN ZOOLOGY

Volume 11, Issue -, Pages -

Publisher

BMC

DOI: 10.1186/1742-9994-11-40

Keywords

Incomplete lineage sorting; Introgression; Isolation-with-migration; Multilocus analyses; Ecological niche modelling

Funding

State Key Program of National Natural Science of China [31330073]
Major International (Regional) Joint Research Project [31010103901]
Chinese Academy of Sciences Visiting Professorship for Senior International Scientists [2011T2S04]
CAS-IOZ Innovation Program [KSCX2-EW-J-2]
NSFC [J1210002]

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Abstract

Introduction: Incomplete lineage sorting and hybridization are two major nonexclusive causes of haplotype sharing between species. Distinguishing between these two processes is notoriously difficult as they can generate similar genetic signatures. Previous studies revealed that the mitochondrial DNA (mtDNA) differentiation between two East Asian long-tailed tits (Aegithalos bonvaloti and A. fuliginosus) was extremely low, even lower than intraspecific differentiation in some other long-tailed tits. Using a combination of multilocus and coalescent analyses, we explored the causes of the anomalous lack of mtDNA differentiation between the two species. Results: The mtDNA divergence between the two species was shallow, while the nuclear DNA (nuDNA) divergence was considerably deeper. The IMa analyses based on the mtDNA dataset suggested relatively high gene flow from A. fuliginosus to A. bonvaloti, while negligible gene flow in the opposite direction. In contrast to mtDNA, the migration rates at autosomal and Z-linked nuDNA loci were negligible or much lower. The NEWHYBRIDS analysis assigned all individuals except one to pure parental species with high posterior probability. The Bayesian skyline plot showed that both species underwent population expansions during the Last Glacial Maximum (LGM), and the ecological niche modelling suggested that their ranges overlapped more during the LGM than at present. Conclusions: We suggest that historical hybridization, in combination with selective sweep and/or genetic drift might be the main causes of the extremely low mtDNA differentiation between the two species. The hybridization probably occurred mainly between A. fuliginosus females and A. bonvaloti males. The LGM distribution expansion might have facilitated hybridization, while the post-LGM distribution contraction could have facilitated some mtDNA sorting. Ongoing hybridization between the two species might be very limited, but further studies with more samples from the contact zone are needed to test this conclusion.

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SINE-Based Phylogenomics Reveal Extensive Introgression and Incomplete Lineage Sorting in Myotis

Jennifer M. Korstian, Nicole S. Paulat, Roy N. Platt, Richard D. Stevens, David A. Ray

Summary: Using presence/absence data from over 10,000 Ves SINE insertions, the researchers reconstructed a phylogeny for 11 Myotis species. They found that phylogenetic conflict was rampant in this genus, with almost one-third of individual gene trees being discordant with the overall species tree. The study suggests that incomplete lineage sorting (ILS) is a major contributor to the discordance. The researchers also observed signs of introgression between Old and New World taxa, as well as within the New World Myotis species. The findings highlight the role of hybridization in the evolutionary history of Myotis.

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