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Open Access Highly Accessed Research article

Differential introgression among loci across a hybrid zone of the intermediate horseshoe bat (Rhinolophus affinis)

Xiuguang Mao12, Guangjian Zhu1, Libiao Zhang3, Shuyi Zhang1 and Stephen J Rossiter2*

Author Affiliations

1 Institute of Molecular Ecology and Evolution, East China Normal University, Shanghai 200062, China

2 School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK

3 Guangdong Entomological Institute, 105 Xingang Xilu, Haizhu Guangzhou, Guangdong Province 510260, China

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BMC Evolutionary Biology 2014, 14:154  doi:10.1186/1471-2148-14-154

Published: 9 July 2014



Hybrid zones formed by the secondary contact of divergent lineages represent natural laboratories for studying the genetic basis of speciation. Here we tested for patterns of differential introgression among three X-linked and 11 autosomal regions to identify candidate loci related to either reproductive isolation or adaptive introgression across a hybrid zone between two Chinese mainland subspecies of the intermediate horseshoe bat Rhinolophus affinis: R. a. himalayanus and R. a. macrurus.


Our results support the previous suggestion that macrurus formed when a third subspecies (R. a. hainanus) recolonized the mainland from Hainan Island, and that himalayanus is the ancestral taxon. However, this overall evolutionary history was not reflected in all loci examined, with considerable locus-wise heterogeneity seen in gene tree topologies, levels of polymorphism, genetic differentiation and rates of introgression. Coalescent simulations suggested levels of lineage mixing seen at some nuclear loci might result from incomplete lineage sorting. Isolation with migration models supported evidence of gene flow across the hybrid zone at one intronic marker of the hearing gene Prestin.


We suggest that phylogenetic discordance with respect to the species tree seen here is likely to arise via a combination of incomplete lineage sorting and a low incidence of introgression although we cannot rule out other explanations such as selection and recombination. Two X-linked loci and one autosomal locus were identified as candidate regions related to reproductive isolation across the hybrid zone. Our work highlights the importance of including multiple genomic regions in characterizing patterns of divergence and gene flow across a hybrid zone.

Phylogenetic discordance; Adaptive introgression; Speciation; Rhinolophus