Boyang An

Species are the basic units in evolution and biodiversity and thus a reasonable species classification is essential to assess and protect biodiversity. The classifications of the Naumann’s and dusky thrush complexes and the red-throated and black-throated thrush complexes are not well defined in Turdidae (Aves, Passeriformes). Herein, we use qualitative and quantitative morphological characters and molecular data to review the taxonomy of these thrush complexes. These four thrushes can be distinguished with qualitative features of feather color and striping. These birds cannot be divided by quantitative features, which only work on two groups of thrush complexes. Phylogenetic analysis based on mitochondrial genes indicate that all haplotypes might be divided into two monophyletic clades corresponding to two groups of thrush complexes. According to coalescence-based species delimitation and the gen-morph species concept, these two groups of thrush complexes should be separated as two distinctive species (T. naumanni and T. ruficollis) and including two subspecies per species. This species classification is also supported by gene flow analysis. There is a significant mixing between these two thrush species in the neighbor-joining (NJ) tree and the cluster analysis using a few microsatellite loci. This leads to a pattern of nuclear-mitochondrial discordance between the two birds that can be explained by several potential mechanisms. This study provides the first comprehensive classification of the two thrush complexes on a population level using morphological and molecular characteristics, which will be useful in expanding our understanding of species division among thrush complexes.

The classification of some Turdus species, such as the Naumann’s and dusky thrush complexes and the red-throated and black-throated thrush complexes, is controversial. Herein, we used molecular data (mitochondrial genes and microsatellite loci) and morphological characters to review the taxonomy of these thrush complexes and analyze the genetic differentiation between them. Our phylogenetic analysis based on mitochondrial genes indicated that all haplotypes could be divided into two reciprocally monophyletic sister clades corresponding to these two thrush complexes. The same results were revealed by coalescence-based species delimitation. Therefore, these two thrush complexes should be divided into two separate species (T. naumanni and T. ruficollis) and include two subspecies per species according to combined characters from morphological analyses and multilocus approaches. The above classifications were also supported by an analysis of genetic differentiation between T. naumanni and T. ruficollis and within each species. Moreover, there was significant mixing between these two thrush species in the neighbor-joining (NJ) tree and the cluster analysis of microsatellite loci. This led to a pattern of nuclear-mitochondrial discordance between the two species. This could be the result of extensive nuclear introgression between these two sister species. We also provide a potential explanation for the mechanism of gene introgression and nuclear-mitochondrial discordance between the two bird species.

Increasing evidence has shown that many long non-coding RNAs (lncRNAs) are involved in gene regulation in a variety of ways such as transcriptional, post-transcriptional and epigenetic regulation. Promoter-associated non-coding RNAs (pancRNAs), which are categorized into the most abundant single-copy lncRNA biotype, play vital regulatory roles in finely tuning cellular specification at the epigenomic level. In short, pancRNAs can directly or indirectly regulate downstream genes to participate in the development of organisms in a cell-specific manner. In this review, we will introduce the evolutionarily acquired characteristics of pancRNAs as determined by comparative epigenomics and elaborate on the research progress on pancRNA-involving processes in mammalian embryonic development, including neural differentiation.

In vertebrate animals, the molecules encoded by major histocompatibility complex (MHC) genes play an essential role in the adaptive immunity. MHC class I deals with intracellular pathogens (virus) in birds. MHC class I diversity depends on the consequence of local and global environment selective pressure and gene flow. Here, we evaluated the MHC class I gene in four species of the Turdidae family from a broad geographical area of northeast China. We isolated 77 MHC class I sequences, including 47 putatively functional sequences and 30 pseudosequences from 80 individuals. Using the method based on analysis of cloned amplicons (n = 25) for each species, we found two and seven MHC I sequences per individual indicating more than one MHC I locus identified in all sampled species. Results revealed an overall elevated genetic diversity at MHC class I, evidence of different selection patterns among the domains of PBR and non‐PBR. Alleles are found to be divergent with overall polymorphic sites per species ranging between 58 and 70 (out of 291 sites). Moreover, transspecies alleles were evident due to convergent evolution or recent speciation for the genus. Phylogenetic relationships among MHC I show an intermingling of alleles clustering among the Turdidae family rather than between other passerines. Pronounced MHC I gene diversity is essential for the existence of species. Our study signifies a valuable tool for the characterization of evolutionary relevant difference across a population of birds with high conservational concerns.