Hidden hotspots of amphibian biodiversity in China.

Identifying and protecting hotspots of endemism and species richness is crucial for mitigating the global biodiversity crisis. However, our understanding of spatial diversity patterns is far from complete, which severely limits our ability to conserve biodiversity hotspots. Here, we report a comprehensive analysis of amphibian species diversity in China, one of the most species-rich countries on Earth. Our study combines 20 y of field surveys with new molecular analyses of 521 described species and also identifies 100 potential cryptic species. We identify 10 hotspots of amphibian diversity in China, each with exceptional species richness and endemism and with exceptional phylogenetic diversity and phylogenetic endemism (based on a new time-calibrated, species-level phylogeny for Chinese amphibians). These 10 hotspots encompass 59.6% of China's described amphibian species, 49.0% of cryptic species, and 55.6% of species endemic to China. Only four of these 10 hotspots correspond to previously recognized biodiversity hotspots. The six new hotspots include the Nanling Mountains and other mountain ranges in South China. Among the 186 species in the six new hotspots, only 9.7% are well covered by protected areas and most (88.2%) are exposed to high human impacts. Five of the six new hotspots are under very high human pressure and are in urgent need of protection. We also find that patterns of richness in cryptic species are significantly related to those in described species but are not identical.

DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs.

DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.

The complete mitochondrial genome of the common lizard Zootoca vivipara (Squamata: Lacertidae).

The mitochondrial genome of Zootoca vivipara (Squamata: Lacertidae) is a circular molecule of 17,046 bp in size and consists of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and a control region. The A + T content of the overall base composition of H-strand is 63.43% (T: 30.95%, C: 24.03%, A: 32.48%, G: 12.54%). Protein-coding genes begin with ATG as start codon except COII with GTG. ND1, ATP8, ATP6, ND4L, ND5 and Cyt b genes are terminated with TAA as stop codon, ND2 ends with TAG, COI and ND6 end with AGG, and the other four protein-coding genes end with an incomplete stop codon (a single stop nucleotide T).

The complete mitochondrial genome of the Amur rat-snake Elaphe schrenckii (Squamata: Colubridae).

In this study, the whole mitochondrial genome of Elaphe schrenckii (Squamata: Colubridae) is first sequenced. It is a circular molecule of 17,165 bp in size and consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 2 control regions (CRI and CRII). Except for eight tRNAs and ND6 gene, all other mitochondrial genes were encoded on the heavy strand (H strand). The gene order and orientation of E. schrenckii mitogenome are basically identical to that of other alethinophidian snakes. Mitochondrial genome analyses based on MP, ML and NJ yielded identical phylogenetic trees, indicating a close phylogenetic affinity of 12 species of Colubridae snakes. This study will facilitate the further research of the population genetics of this species and systematic analyses of the genus Elaphe.

Sequencing and analysis of the complete mitochondrial genome of Elaphe anomala (Squamata Colubridae).

In this study, the complete mitogenome sequence of Elaphe anomala (Squamata: Colubridae) is first determined using long PCR. It is a circular molecule of 17,164 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 2 control regions (CRI and CRII). The gene order and nucleotide composition of E. anomala are very similar with E. schrenckii. Mitochondrial genomes analyses based on the NJ method yield phylogenetic tree of 17 species snakes of Colubridae. Species E. anomala, E. schrenckii, E. bimaculata and E. davidi seemed to have formed a monophyletic group with the high bootstrap value (100%) except E. poryphyracea. Oligodon ningshaanensis and Thermophis zhaoermii are special species. The molecular data presented here provide a useful tool for setting the stage for further studies.

The complete mitochondrial genome of Takydromus amurensis (Squamata: Lacertidae).

The complete mitogenome sequence of Takydromus amurensis (Squamata: Lacertidae) is determined using long PCR for the first time in this study. It is a circular molecule of 17 333 bp in length (GenBank accession number: KU641018). Similar to the most other lizards, the complete mtDNA sequence of T. amurensis contained two rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, 13 protein-coding genes (PCGs) and a control region (D-loop). The nucleotide composition was 31.23% A, 26.06% C, 13.91% G and 28.8% T. Mitochondrial genomes analyses based on NJ method yield phylogenetic trees, including 14 reported lizards belonging to three families (Lacertidae, Gekkonidae and Agamidae). These molecular data presented here provide a useful tool for systematic analyses of genus Takydromus.

The complete mitochondrial DNA sequence and the phylogenetic position of Rhabdophis tigrinus (Reptilia: Squamata).

The complete mitochondrial genome of Rhabdophis tigrinus (Reptilia: Squamata) is presented for the first time in this study. It is a circular molecule of 17 415 bp in length (GenBank accession no. KU641019), consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes (12S and 16S rRNA) and two control regions (D-loop), with the typical gene order and direction of transcription in Serpentes. The overall base composition is 33.65% A, 26.70% C, 13.16% G and 26.49% T. Mitochondrial genomes analyses based on NJ method yield phylogenetic trees, including 14 reported snakes belonging to four families (Colubridae, Elapidae, Viperidae and Typhlopidae). These molecular data presented here provide a useful tool for systematic analyses of genus Rhabdophis and family Colubridae.

Different mechanisms lead to convergence of reproductive strategies in two lacertid lizards (Takydromus wolteri and Eremias argus).

Life history traits may vary within and among species. Rarely, however, are both variations examined concurrently to identify the life history adaptation. We found that female body size, offspring number and size, and incubation period showed convergent evolution in two lacertid lizards (Takydromus wolteri and Eremias argus) that occur sympatrically in high-latitude and low-latitude localities. Females from the high-latitude population were larger and produced larger clutches than those from the low-latitude population. In both species, the incubation period was shorter for the high-latitude population than for the low-latitude population. However, the physiological mechanism underlying the shorter incubation period differed between the species. These results suggest that: (1) sympatric lizards may adopt similar reproductive strategies in response to their common environments, and (2) embryonic development of the two species follows different pathways for adaptation to low temperatures. This study highlights the importance of understanding the adaptive evolution of life history in response to environmental changes at the embryonic life stages.