期刊
MOLECULAR PHYLOGENETICS AND EVOLUTION
卷 163, 期 -, 页码 -出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2021.107239
关键词
Incomplete lineage sorting; Species tree approach; Paraphyly; Quartet support; Hybridization; Branch length discordance
资金
- Second Tibetan Plateau Scientific Expedition and Research Program [2019QZKK0501]
- National Natural Science Foundation of China [31572243]
The study on Asian mountain salamanders revealed challenges in examining hybridization and species-level paraphyly due to incomplete lineage sorting. The results indicated potential hybridization events and paraphyly at the species level in the studied species of the genus Batrachuperus.
The prevalence of incomplete lineage sorting complicates the examination of hybridization and species-level paraphyly with gene trees of a small number of loci. In Asian mountain salamanders of the genus Batrachuperus, possible hybridization and species paraphyly had been identified by utilizing mitochondrial genealogy and fixed allozyme differences. Here we sampled 2909 UCEs in 44 local populations from all six Batrachuperus species, inferred gene and species trees, compared them with mitochondrial and allozyme results, and examined the potential hybridization and species paraphyly. The clustering pattern of single-locus trees, increased proportion of heterozygous SNPs, allele frequency-based migration edge estimation, and intrapopulation long branches (as expected from an increase of genetic lineage and nucleotide diversity) support that an eastern B. karlschmidti population has experienced admixture with B. tibetanus. On the 2909-UCE concatenated and species trees, lower nodal supports were observed when similar proportions of loci agreed with alternative topologies, i.e., a reciprocal monophyly between a Pengxian lineage and the remainder of B. pinchonii (0.379) or a paraphyly of the latter with respect to Pengxian (0.362). The UCE phylogenomics agreed with the relatively recent groupings in the allozyme dendrogram. Despite incomplete lineage sorting, the mitochondrial trees were similar to the UCE trees for deeper relationships of the genus. However, one significant branch-length level discordance was identified. The branch between the common ancestor of B. daochengensis and B. yenyuanensis and common ancestor of the genus was approximately three times shorter on the mitochondrial tree than on the UCE tree, suggesting that the split of the mitochondrial lineages was likely a few million years earlier than the split of species. This finding supports considering possible ancestral polymorphism when interpreting different divergence dates estimated from mitochondrial and genome-wide data.
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