Complete mitochondrial genome of a Light-vented Bulbul subspecies,Pycnonotus sinensis hainanus(Passeriformes: Pycnonotidae)

Demographic history of the fragmented yellowthroated bulbul (Pycnonotus xantholaemus) population in the Deccan Peninsula, India

The yellow-throated bulbul (YTB) is an endemic passerine restricted to scrub forests along hill slopes with exposed rocky outcrops in the Deccan Peninsula, India. It is found in small, discontinuous populations and is vulnerable to extinction due to ongoing habitat loss and subsequent population decline. To assess the genetic connectivity and past demography, we sequenced 1050 nucleotide base pairs of the mitochondrial control region of 60 individuals that represent distinct populations in the geographic range of the species. We recovered 39 haplotypes defined by 81 variable sites. Haplotype diversity was high with low nucleotide diversity, suggesting rapid population growth from a founder population with a small effective population size. The negative values of Tajima’sDand Fu’sFsand small positive value of Ramos-Onsins and Rozas’R2suggest deviation from neutrality and population expansion. The haplotype network and demographic expansion parameters further suggest historical population expansion. Mismatch analysis statistics and Bayesian skyline plots estimate population expansion during the late Pleistocene. Although the species presently occurs in small, disconnected we found no structuring of the population. Dispersal events are the most likely explanation for the absence of genetic structuring in the YTB population. These results represent important data for the design of a conservation plan for this endemic and globally threatened species.

The complete mitochondrial genome of the Heosemys depressa (Testudines, Geoemydidae)

The complete mitochondrial genome of Heosemys depressa was obtained and characterized in this study. The mitochondrial genome is a circular molecule of 16,773bp in length, and harbours 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 non-coding D-loop region (control region). Its gene arrangement type is identical to the type of most vertebrate. Phylogenetic analysis suggests that H. depressa is closely related to H. annandalii than to the other species. Our data provide a useful resource for the phylogenetic studies of genus Heosemys.

The Mitochondrial Genomes of Aquila fasciata and Buteo lagopus (Aves, Accipitriformes): Sequence, Structure and Phylogenetic Analyses

The family Accipitridae is one of the largest groups of non-passerine birds, including 68 genera and 243 species globally distributed. In the present study, we determined the complete mitochondrial sequences of two species of accipitrid, namely Aquila fasciata and Buteo lagopus, and conducted a comparative mitogenome analysis across the family. The mitogenome length of A. fasciata and B. lagopus are 18,513 and 18,559 bp with an A + T content of 54.2% and 55.0%, respectively. For both the two accipitrid birds mtDNAs, obvious positive AT-skew and negative GC-skew biases were detected for all 12 PCGs encoded by the H strand, whereas the reverse was found in MT-ND6 encoded by the L strand. One extra nucleotide'C'is present at the position 174 of MT-ND3 gene of A. fasciata, which is not observed at that of B. lagopus. Six conserved sequence boxes in the Domain II, named boxes F, E, D, C, CSBa, and CSBb, respectively, were recognized in the CRs of A. fasciata and B. lagopus. Rates and patterns of mitochondrial gene evolution within Accipitridae were also estimated. The highest dN/dS was detected for the MT-ATP8 gene (0.32493) among Accipitridae, while the lowest for the MT-CO1 gene (0.01415). Mitophylogenetic analysis supported the robust monophyly of Accipitriformes, and Cathartidae was basal to the balance of the order. Moreover, we performed phylogenetic analyses using two other data sets (two mitochondrial loci, and combined nuclear and mitochondrial loci). Our results indicate that the subfamily Aquilinae and all currently polytypic genera of this subfamily are monophyletic. These two novel mtDNA data will be useful in refining the phylogenetic relationships and evolutionary processes of Accipitriformes.

Complete mitochondrial genome of the Eurasian siskin, Spinus spinus (Passeriformes: Fringillidae)

The Eurasian siskin (Spinus spinus), also called the European siskin, common siskin or just siskin, is found throughout Europe and Asia. In this study, the complete mitochondrial genome of S. spinus was determined to be 16,828 bp. The size of protein-coding genes (PCGs) in the S. spinus mitochondrial genome was 11,400 bp. The longest PCG of S. spinus mtDNA was nad5 (1818 bp), whereas the shortest is atp8 (168 bp). The nad6 gene of S. spinus mitogenome had strong skews of T versus A (-0.54), and G versus C (0.64). According to the distribution of the conserved motifs in other avian CRs, the CR of S. spinus can be divided into three domains: ETAS domain I, central conserved domain II, and CSB domain III.

Characterization of the complete mitochondrial genome of Collared Finchbill, Spizixos semitorques (Passeriformes: Pycnonotidae)

The complete mitochondrial genome of Spizixos semitorques is 17,045 bp long with an A+T content of 55.52%, which composed of 13 typical protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 extensive heteroplasmic control regions (CR1 and CR2). Genome organization of S. semitorques is similar to that of other birds. All of the PCGs started with ATG, except for cox1, which began with GTG. Six types of termination codons were used, canonical TAA and TAG termination codons are found in seven protein-coding genes, while AGA for nad1 and nad5, AGG for cox1, and the remaining genes (nad2, cox3, nad4) have incomplete termination codons (TA- or T- -). All tRNA genes have a typical clover-leaf structure. Furthermore, a minisatellite of 24 nucleotides (5'-CACAAAAATCAAACAAAAATACAA-3') with 2.9 tandem repeats at the end of CR2 were detected.