3Genetic structure
We reconstructed the phylogenetic relationships between the Naumann’s and dusky thrush complexes and the red-throated and black-throated thrush complexes based on haplotype sequences of the partial ND2 and COI genes (Fig. 1). The BI and ML trees of the dataset had similar topologies, and only the nodes of two thrush complexes were significantly supported by the posterior probability (PP> 95%) and the bootstrap value (BS> 75). The rest of the nodes within the Naumann’s and dusky thrush complexes or the red-throated and black-throated thrush complexes were weakly supported in both trees. Moreover, the haplotypes of the Naumann’s and dusky thrushes and the red-throated and black-throated thrushes were mixed, and no monophyletic subclade was observed for any thrush. We found that when combined with the identification of morphological characteristics, the haplotypes of most individuals were correctly assigned to their corresponding species or Turdus complex. There were a few haplotypes from intermediate specimens mixed between the twoTurdus complexes. Three haplotypes from Naumann’s thrush and one haplotype from the dusky thrush were distributed in the clade of red-throated and black-throated thrush complexes. In contrast, three haplotypes from the black-throated thrush and four haplotypes from the red-throated thrush were located in the clade of Naumann’s and dusky thrush complexes.
Based on the microsatellite dataset, a NJ tree was constructed based on SADs between individuals from the Naumann’s and dusky thrush complexes and the red-throated and black-throated thrush complexes (Fig. 2). Although the test performance was worse when SADs were used (data not shown), and the bootstrap support values were relatively low, all individuals were divided into two groups, corresponding to two thrush complexes. Notably, each group was mixed with several individuals from other groups.