High-throughput sequencing yields a complete mitochondrial genome of Emberiza godlewskii (aves, emberidae).

Emberiza godlewskii (Taczanowski, 1874) is a passerine bird of eastern Asia which belongs to the genus Emberiza in the bunting family Emberizidae. Obtaining the complete mitochondrial genome sequence of E. godlewskii is helpful to understand the species delimitation for further study of E. cia/godlewskii complex. The circular genome (16,839 bp in length) contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. The base composition shows that purine percentage (52.87%) is slightly higher than pyrimidine (47.13%). The phylogenetic analysis based on the published data of the mitochondrial genome showed that E. godlewskii is closely related to E. cioides. This new mitochondrial genome data will provide more essential molecular data for further study related to E. cia/godlewskii complex.

A new bunting species in South China revealed by an integrative taxonomic investigation of the Emberiza godlewskii complex (Aves, Emberidae).

Species boundaries of birds across the Euro-Asian continent, especially the widely distributed passerines with multiple subspecies, are not completely resolved. The Rock Bunting complex, Emberiza cia and E. godlewskii, is subject to ongoing debate due to geographic variation in its morphology, and deep genetic splits. In this study, the phylogenetic relationships of the E. cia/godlewskii complex were evaluated based on multilocus coalescence methods combined with analyses of plumage color and morphological variation. Although the northern and southern populations of E. godlewski formed reciprocally monophyletic groups, the northern E. godlewskii clade is the sister group to E. cia, rendering E. godlewskii as currently defined paraphyletic. The significant differences in morphometry and plumage color reflectance are complementary and support the phenotypic validity of northern and southern E. godlewskii. Thus, we recommend the following taxonomic revisions: the northern and southern E. godlewskii subspecies should be recognized as different full species, such as E. godlewskii and E. yunnanensis, respectively. This resolves the issue that E. godlewskii, as currently defined, is paraphyletic. Our research provides direct evidence of cryptic species in old world buntings and highlights the underestimation of species diversity in birds in East Asia.

Effects of environmental metal pollution on reproduction of a free-living resident songbird, the tree sparrow (Passer montanus).

Anthropogenic metal pollution is known to adversely affect bird reproduction; however, few systematic studies are available on the effects of metal pollution on breeding performance and parental investment in a common resident songbird, the tree sparrow (Passer montanus). We conducted this study in two sites, a long-term heavy metal polluted site (Baiyin [BY]) and a relatively unpolluted site at approximately 110 km distance (Liujiaxia [LJX]), to assess the potential effects of environmental metal contamination on breeding parameters (clutch size, hatching success, fledging success, and growth of nestlings) and parental investment. The results showed smaller clutch size, lower fledging success, and differences in incubation behaviors of tree sparrows in BY than in LJX. Although there was no difference in parental body condition (residual body mass) between the two study sites, the parents responded differently with respect to reproduction due to varying metal levels in their habitats and bodies. Higher Cd levels in the primary feathers of females in BY were associated with lower clutch sizes. Parental investment including incubation duration and feeding rates showed no significant difference between the two sites during the incubation and nestling periods, but the frequencies of incubation visits were higher in BY. Parental behavior during the incubation period was also negatively affected by the parental Pb and Cd levels. Although the nestling growth patterns were relatively similar between the two sites, the nestlings were smaller, had lower body weight, and fledged later and fledging rate was also lower in BY than in LJX. Metal concentrations were higher in nestling organs and feces in BY. Taken together, metal pollution might adversely affect nestling growth condition. Our results suggest a negative response in the reproduction of tree sparrows to long-term environmental metal pollution.

Metal Exposure Risk Assessment for Tree Sparrows at Different Life Stages via Diet from a Polluted Area in Northwestern China.

To estimate the risk of metal (Cu, Zn, Pb, and Cd) exposure of tree sparrows through food at different life stages (including nestling, juvenile, adult in summer, and adult in winter), metal daily intake (MDI), metal daily intake per unit of body weight (MDIBW ), and exposure risks (hazard quotient and hazard index) of tree sparrows at different life stages from a polluted area, Baiyin, and a control area, Liujiaxia, were assessed. Metal daily intakes and MDIBW s of tree sparrows from Baiyin were higher than those from Liujiaxia, which can be attributed to higher metal concentrations of food sources in Baiyin than those in Liujiaxia. Metal daily intakes and MDIBW s of nestlings were higher than those of adults and juveniles. This difference is observed probably because nonphytophagous invertebrates, the predominant food fed to nestlings, possessed the highest metal concentrations. In addition, adults in summer had higher MDIs and MDIBW s than juveniles and adults in winter. This finding is probably observed because juveniles and adults in winter consumed a higher proportion of maize, which had the lowest metal concentrations. In addition, the biomagnification of 4 metals through the food chain increased the health risks of tree sparrows. Exposure risks of tree sparrows to metals were comparable to those of waterfowl and raptors, even when soil metals were below threshold. Environ Toxicol Chem 2019;38:2785-2796. © 2019 SETAC.

Deep south-north genetic divergence in Godlewski's bunting (Emberiza godlewskii) related to uplift of the Qinghai-Tibet Plateau and habitat preferences.

BACKGROUND: Geological events and climatic changes played important roles in shaping population differentiation and distribution within species. In China, populations in many species have contracted and expanded responding to environmental changes with the uplift of the Qinghai-Tibet Plateau (QTP) and glacial cycles during Pleistocene. In this study, we analysed the population structure of Godlewski's Bunting, Emberiza godlewskii, to determine the effects of major historical events, geographic barriers and past climatic changes on phylogenetic divergence and historical demographic dynamics of this species. RESULTS: A phylogeny based on concatenated mitochondrial and nuclear DNA datasets show two (northern and southern) clades approximately diverged 3.26 million years ago (Ma). The West Qinling Mountains serve as a dividing line between the two lineages. Both lineages experienced a recent demographic expansion during interglacial periods (marine isotope stages (MISs) 2-6). Bayesian skyline plots and the results of ecological niche modelling suggested a more intensive expansion of the northern lineage during the late Pleistocene, whereas the southern lineage was comparatively mild in population growth. CONCLUSIONS: Our results provide insights into the distribution patterns of avian taxa and the possible mechanisms for a south and north divergence model in China. The deep divergence may have been shaped by the uplift of the QTP. Habitat preferences might have facilitated the lineage divergence for E. godlewskii. Moreover, the West Qinling Mountains act as a dividing line between the two lineages, indicating a novel phylogeographic pattern of organisms in China. The difference in population expansion mode between two lineages resulted from different effects caused by the climate of the LGM and the subsequent habitat changes accompanying the arrival of a colder climate in northern and southern regions of China.

Habitat Selection and Genetic Structure of the Endangered Frog Species Odorrana wuchuanensis (Anura: Ranidae).

Understanding the habitat selection and population genetic structure of an endangered species can play important roles in its protection. The Wuchuan odorous frog (Odorrana wuchuanensis) is endemic to the karst regions of southwest China. This frog is currently listed as "Critically Endangered" by the IUCN, but little is known about its habitat selection and population genetics. In this study, we conducted analyses of habitat selection with occurrence/absence sites and environmental data, and assessed the genetic structure between north and south populations in Guizhou provinces in China using three mitochondrial markers. The results revealed that the probability of this frog occupying cave habitats increased with higher average humidity in July and higher lowest temperature in January, but was negatively related to precipitation in January. Analyses of F statistics combined with analyses of median-joining haplotype networks and the phylogenetic tree showed low genetic differentiation between the two populations of O. wuchuanensis. Considering the small population size and geographic isolation because of the complex karst terrains, we suggest careful management practices are needed to protect this species.

Sequence and analysis of the complete mitochondrial genome of the Saxaul Sparrow, Passer ammodendri (Passeriformes, Passeridae).

The complete mitochondrial genome of the Saxaul Sparrow (Passer ammodendri) was 16 782 bp in length. The Genbank accession number was KT895996. And the content of A, T, C, and G were 30.08% (5048 bp), 22.91% (3845 bp), 32.08% (5384 bp), and 14.93% (2505 bp), respectively. It contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, 1 control region and was similar to most of the other Passeridae birds in gene arrangement and composition. All protein-coding genes used the typical initiation codon ATG, except GTG for COI and ATA for ND3 which was the same to the Tree Sparrow (Passer montanus) but different from the House Sparrow (Passer domestic). Most of the stop codons were consistent with the Tree Sparrow and the House Sparrow except for ND1, ND3, and ND6 genes, which were terminated with AGG, TAA, and TAG codons, respectively. Besides, the phylogenetic relationship of Passeriformes based on complete mitochondrial genomes showed that the genetic distance among Passeridae, Emberizidae, and Fringillidae was closer than the others.

Sequencing and analysis of the complete mitochondrial genome of Brown Shrike, Lanius cristatus (Passeriformes, Laniidae).

The complete mitochondrial genome of the Brown Shrike (Lanius cristatus) was 16 821 bp in length. The accession number was KT004451 and the contents of A, T, C, and G were 31.10%(5237 bp), 25.60%(4309 bp), 28.60%(4814 bp), and 14.60%(2461 bp), respectively. Gene organization and length was similar to other species of birds. It comprises of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. All protein-coding genes use the typical initiation codon ATG, except for COX1 which was initiated with GTG. All the complete stop codon was coincident with the Black-headed Gull (Chroicocephalus ridibundus) and the Grey-backed Shrike (Lanius tephronotus), except for ND2, which was terminated with TAG. In addition, the phylogenetic relationships of Passeriformes based on complete mitochondrial genomes showed that the genetic distance of Laniidae and Corvidae was closer than others.

Sequencing and analysis of the complete mitochondrial genome of Rufous-tailed Shrike, Lanius isabellinus (Passeriformes, Laniidae).

The complete mitochondrial genome of the Rufous-tailed Shrike (Lanius isabellinus) was 16 819 bp in length. The GenBank accession number is KP995437 and the contents of A, T, C, and G are 31.1% (5234 bp), 25.5% (4293 bp), 28.7% (4826 bp), and 14.7% (2466 bp), respectively. Gene organization and length are similar to other species of birds. It comprises 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. All protein-coding genes use the typical initiation codon ATG, except for COX1 that uses GTG. All the complete stop codons were co-incident with the Black-headed Gull (Chroicocephalus ridibundus) and the Grey-backed Shrike (Lanius tephronotus), except for ND2 that was terminated with TAG. In addition, the phylogenetic relationships of Passeriformes based on complete mitochondrial genome showed that genetic distance of Laniidae and Corvidae was closer than other species.

Sequence and analysis of the complete mitochondrial genome of the Wuchuan Odorous Frog Odorrana wuchuanensis (Anura: Ranidae).

The complete mitochondrial genome of the Wuchuan Odorous Frog was 18,256 bp in length including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region and was similar to that of typical vertebrates. The base composition was 27.89% A, 29.00% C, 15.34% G, and 27.78% T. All genes were encoded on the H-strand except ND6 and eight tRNA genes (tRNAPro, tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, and tRNAGlu), which were encoded on the L-strand. The phylogenetic relationship of Anura based on complete mitochondrial genomes showed that O. wuchuanesis is closest to O. margaretae with strong support and the genetic distance between Ranidae, Dicroglossidae, and Rhacophoridae was closer than others.

The phylogenetic position and speciation dynamics of the genus Perdix (Phasianidae, Galliformes).

The nuclear gene (c-mos) and mitochondrial genes (CYT B and ND2) sequences, representing 44 phasianid species and 26 genera (mainly distributed in China), were used to study the phylogeny of the genus Perdix, which comprises three partridge species. Maximum parsimony and Bayesian methods were employed, and the analysis of mitochondrial sequence data and the combined dataset showed that Perdix is specifically related either to typical pheasants or to Ithaginis. Phylogenetic trees also indicated that: (1) Perdix is monophyletic; (2) the Tibetan partridge (Perdix hodgsoniae) has been consistently placed as basal to all other Perdix, and the Daurian partridge (Perdix dauuricae) is placed sister to gray partridge (Perdix perdix); (3) the Daurian partridge subspecies przewalskii and Tibetan partridge subspecies hodgsoniae are basal to other subspecies in their species clade, respectively. Speciation in Perdix was likely promoted by the late Pliocene/early Pleistocene intensive uplift of the Tibetan Plateau and by Pleistocene glaciations.

Phylogeography of the ring-necked pheasant (Phasianus colchicus) in China.

The ring-necked pheasants (Phasianus colchicus) are widely distributed in China. We used mitochondrial DNA control-region data to investigate the origin and past demographic changes in 139 ring-necked pheasants (P. colchicus) sampled from the species' distribution range. A total of 1078 nucleotides from the control region of mitochondrial DNA were sequenced, and 88 polymorphic positions defined 102 haplotypes. High level of genetic diversity was detected in all populations studied which could be associated with the wide ecological distributions and niche variation. Phylogenetic analyses of all haplotypes identified five major clades. The haplotypes of Gray-rumped Pheasants existed in the three clades: A (western clade), B (eastern clade) and C (Sichuan Basin clade). Two haplotypes of Kirghiz Pheasants were in the clade B, and the rest haplotype of Kirghiz Pheasants formed the clade D. Only one haplotype from White-winged Pheasants made up clade E. The results of AMOVA showed a low gene flow (Nm=0.44) and significant genetic differentiation (Fst=0.31, P<0.001) among all populations. Based on the divergence time, we speculate that the divergence of the ring-necked pheasant occurring in the late Pleistocene may have resulted from three events: (1) the uplift of Qinghai-Tibet Plateau, (2) the existence of Qinling Mountains and Liupan Mountains, (3) the isolation of Sichuan Basin. Demographic population expansion was strongly confirmed by the non-significant mismatch distribution analysis. The described subspecies of the ring-necked pheasant could not be supported by the phylogeographical structuring.