Phylogeographic patterns and conservation implications of the endangered Chinese giant salamander.

Understanding genetic diversity patterns of endangered species is an important premise for biodiversity conservation. The critically endangered salamander Andrias davidianus, endemic to central and southern mainland in China, has suffered from sharp range and population size declines over the past three decades. However, the levels and patterns of genetic diversity of A. davidianus populations in wild remain poorly understood. Herein, we explore the levels and phylogeographic patterns of genetic diversity of wild-caught A. davidianus using larvae and adult collection with the aid of sequence variation in (a) the mitochondrial DNA (mtDNA) fragments (n = 320 individuals; 33 localities), (b) 19 whole mtDNA genomes, and (c) nuclear recombinase activating gene 2 (RAG2; n = 88 individuals; 19 localities). Phylogenetic analyses based on mtDNA datasets uncovered seven divergent mitochondrial clades (A-G), which likely originated in association with the uplifting of mountains during the Late Miocene, specific habitat requirements, barriers including mountains and drainages and lower dispersal ability. The distributions of clades were geographic partitioned and confined in neighboring regions. Furthermore, we discovered some mountains, rivers, and provinces harbored more than one clades. RAG2 analyses revealed no obvious geographic patterns among the five alleles detected. Our study depicts a relatively intact distribution map of A. davidianus clades in natural species range and provides important knowledge that can be used to improve monitoring programs and develop a conservation strategy for this critically endangered organism.

Complete mitochodrial genome of the redlip loach Leptobotia rubrilaris (Teleostei, Cypriniformes: Cobitidae).

In this study, the complete mitochondrial genome sequence of the Leptobotia rubrilaris has been obtained. The genome includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region with the total length of 16,585 bp. The gene arrangement and composition were identical to other vertebrate. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The complete mitochondrial genome sequence of L. rubrilaris would contribute to better understand population genetics and protect its genetic diversity.

The mitochondrial genome of Mystacoleucus marginatus (Cypriniformes, Cyprinidae).

The mitochondrial genome of Mystacoleucus marginatus (Cypriniformes, Cyprinidae) has been sequenced. The total sequence is 16,611 bp in size with 56.67% AT content. It contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 1 putative control region. The gene content and organization are similar to that of most other vertebrates. Most genes are encoded on the heavy strand except ND6 and eight tRNA genes on light strand. This molecular information will contribute to better understand its evolution and population genetics.

The mitogenome of Leptobotia microphthalma (Teleostei, Cypriniformes: Cobitidae).

The Leptobotia microphthalma belongs to family Cobitidae, which is endemic to the upper reaches of the Yangtze River in China. In this studying, the complete mitochondrial genome sequence of L. microphthalma has been obtained with PCR, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region with the total length of 16,512 bp. The gene arrangement and composition are similar to that of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The complete mitochondrial genome sequence of L. microphthalma would contribute to better understand population genetics and protect its genetic diversity.

[Age structure and genetic diversity of Homatula pycnolepis in the Nujiang River basin].

This study examined the age structure of the Loach, Homatula pycnolepis through the otolith growth rings in 204 individual specimens collected from the Xiaomengtong River of the Nujiang River (Salween River) basin in April, 2008. There were only two different age classes, 1 and 2 years of age-no 3 year olds were detected. The age structure of H. pycnolepis was simple. The complete mitochondrial DNA cytochrome b gene sequences (1140) of 80 individuals from 4 populations collected in the Nujiang River drainage were sequenced and a total of 44 variable sites were found among 4 different haplotypes. The global haplotype diversity (Hd) and nucleotide diversity (Pi) were calculated at 0.7595, 0.0151 respectively, and 0, 0 in each population, indicating a consistent lack of genetic diversity in each small population. There was obvious geographic structure in both the Nujiang River basin (NJB) group, and the Nanding River (NDR) group. The genetic distance between NJB and NDR was calculated at 0.0356, suggesting that genetic divergence resulted from long-term isolation of individual population. Such a simple age structure and a lack of genetic diversity in H. pycnolepis may potentially be due to small populations and locale fishing pressures. Accordingly, the results of this study prompt us to recommend that the NJB, NDR and Lancang River populations should be protected as three different evolutionary significant units or separated management units.

The mitogenome of Liobagrus marginatoides (Teleostei, Siluriformes:Amblycipitidae).

Liobagrus marginatoides is endemic to southwest China (Ding, 1994), according to morphological taxonomy, and it is very similar to Liobagrus nigricauda, but its population is much smaller. In this study, the complete mitochondrial genome sequence of L. Marginatoides has been obtained with polymerase chain reaction (PCR), which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region with the total length of 16,498 bp. The gene arrangement and composition are similar to that of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. Just like most other vertebrates, the against bias of G has a universality in different statistics results. The complete mitochondrial genome sequence of L. Marginatoides would contribute to better understand population genetics and protect its genetic diversity.

The mitogenome of Liobagrus nigricauda (Teleostei, Siluriformes: Amblycipitidae).

Liobagrus nigricauda is endemic to the Yangtze River system (Ding 1994, The fishes of Sichuan province. pp. 470-78) and listed as an endangered species (IUCN 2012, Red list of threatened species. http://www.iucnredlist.org ). In this study, the complete mitochondrial genome sequence of L. nigricauda has been obtained with polymerase chain reaction (PCR), which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a noncoding control region with the total length of 16,512 bp. The gene arrangement and composition are similar to that of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. Just like most other vertebrates, the bias against G has a universality in different statistics results. The mitogenome sequence of L. nigricauda would contribute to better understand population genetics and to protect its genetic diversity.

The complete mitochondrial genome of Liobagrus kingi (Teleostei, Siluriformes: Amblycipitidae).

Liobagrus kingi is endemic to southwest China and listed as endangered species (IUCN 2012). Genetic diversity is necessary for conservation issue. In studying this, the complete mitochondrial genome sequence of L. kingi has been obtained with PCR, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region with the total length of 16,483 bp. The gene arrangement and composition are similar to that of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. Just like most other vertebrates, the against bias of G has a universality in different statistical results. The complete mitochondrial genome sequence of L. kingi would contribute to better understand population genetics and protect its genetic diversity.

[Genetic structure and variation of Glyptothorax laosensis of the Lancang River based on cytochrome b].

The hillstream catfish, Glyptothorax laosensis, is endemic to basin of Lancang River (also known as Mekong River). Genetic variation was detected within and among 8 populations of G. laosensis in Lancang River based on mitochondrial cytochrome b sequences. A total 16 nucleotides sites were detected in 1 138 bp fragment, which defined 15 haplotypes from 129 sequences. The variation level was very low, with mean h=0.299 and π=0.00032, respectively, and no variation was detected in some populations. Hierarchical analysis of molecular variance (AMOVA) showed no significant genetic structuring among populations. The unimodel mismatch distribution of pairwise haplotype difference and the negatively selective neutrality test (Tajima's D=2.3696, P<0.02; Fu's Fs=20.975, P<0.05) suggested that a recent population expansion had occurred.

[Genetic diversity and differentiation between populations of Glyptothorax zanaensis in the middle and lower reaches of the Nujiang River].

The development of hydroelectricity in the Nujiang River would have adverse impacts on the populations of Glyptothorax zanaensis. In order to assess the genetic diversity and differentiation of this species, we sequenced the cytochrome b gene of the mitochondria in 102 individuals of the fish collected from 6 sampling sites (Gongshan, Gudeng and Lushui in the Nujiang Prefectural District and Daojie, Mengnuo and Mucheng in the Baoshan Municipal District). A total of 87 variation sites were detected in the fragment of 1 137 bp in length, with which the 102 samples were defined as 36 haplotypes. The haplotype diversity (h) and the nucleotide diversity (pi) of total samples were 0.851+/-0.028 and 0.01356+/-0.0008, respectively. Therefore, the genetic diversity of G. zanaensis was relatively low. However, the genetic diversity of the Nujiang population was significantly higher than that of the Baoshan population. The pairwise Fst value between the populations (0.475-0.846) was higher than that within the population (0.002-0.108), which implied that the Fst value was positively related to geographic distance. Analysis of molecular variance (AMOVA) showed that the genetic differentiation between the populations and within the populations were 53.65% and 46.35%, respectively. The fixation index (Fst value) was 0.5365, indicating that there existed significant differentiation between the Nujiang population and the Baoshan population. The phylogentic tree and networks of the haplotypes of G. zanaensis showed that there were two separate lineages: the Nujiang lineage and the Baoshan lineage. Each lineage represents at least one separated management unit, or belongs to an evolutionary significant unit. It was suggested that in the construction of hydroelectric projects the measures for protecting G. zanaensis should be adopted in fully considering the populations of G. zanaensis and the status quo of their population structure to avoid the occurrence of gene exchange among populations.