Summary statistics observed in major lineages of <i>O</i>. <i>schmackeri</i> species complex.

<p>* SSD sum of squared deviation, <i>tau</i> expansion parameter</p><p>** <i>P</i><0.01</p><p>Summary statistics observed in major lineages of <i>O</i>. <i>schmackeri</i> species complex.</p

Analysis of molecular variance (AMOVA) among ND2+tRNA sequences of O. schmackeri species complex.

<p>Analysis of molecular variance (AMOVA) among ND2+tRNA sequences of O. schmackeri species complex.</p

The Bayesian phylogenetic tree of <i>O</i>. <i>schmackeri</i> species complex based on the ND2+tRNA sequences.

<p>Numbers above branches represent Bayesian posterior probability (PP). The estimated divergence times with a 95% HPD between the major clades are given in rectangular boxes.</p

Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (<i>Odorrana schmackeri</i>, Ranidae)

<div><p>Paleogeological events and Pleistocene climatic fluctuations have had profound influences on the genetic patterns and phylogeographic structure of species in southern China. In this study, we investigated the population genetic structure and Phylogeography of the <i>Odorrana schmackeri</i> species complex, mountain stream-dwelling odorous frogs, endemic to southern China. We obtained mitochondrial sequences (1,151bp) of the complete ND2 gene and two flanking tRNAs of 511 individuals from 25 sites for phylogeographic analyses. Phylogenetic reconstruction revealed seven divergent evolutionary lineages, with mean pairwise (K2P) sequence distances from 7.8% to 21.1%, except for a closer ND2 distance (3.4%). The complex geological history of southern China drove matrilineal divergence in the <i>O</i>. <i>schmackeri</i> species complex into highly structured geographical units. The first divergence between lineage A+B and other lineages (C-G) had likely been influenced by the uplift of coastal mountains of Southeast China during the Mio-Pliocene period. The subsequent divergences between the lineages C-G may have followed the formation of the Three Gorges and the intensification of the East Asian summer monsoon during the late Pliocene and early Pleistocene. Demographic analyses indicated that major lineages A and C have been experienced recent population expansion (c. 0.045–0.245 Ma) from multiple refugia prior to the Last Glacial Maximum (LGM). Molecular analysis suggest that these seven lineages may represent seven different species, three described species and four cryptic species and should at least be separated into seven management units corresponding to these seven geographic lineages for conservation.</p></div

Haplotype networks and nested clade design for <i>O</i>. <i>schmackeri</i> species complex.

<p>Colours represent different lineages. The haplotype codes correspond to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138757#pone.0138757.s002" target="_blank">S2 Table</a>. Unsampled haplotypes were represented by small closed circles.</p

Mismatch distributions for six major lineages of <i>O</i>. <i>schmackeri</i> species complex.

<p>The dotted and thin lines represent the observed and expected mismatch distributions of a stationary population, respectively.</p

The geographic distribution of <i>O</i>. <i>schmackeri</i> species complex sampled in this study.

<p>Localities are detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138757#pone.0138757.s001" target="_blank">S1 Table</a>. Populations are presented as pie-diagrams with slice-size proportional to the frequency of the major lineages. Colors of pie-diagrams correspond to the lineages in Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138757#pone.0138757.g002" target="_blank">2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138757#pone.0138757.g003" target="_blank">3</a>.</p

Mean genetic distances among different lineages of <i>O</i>. <i>schmackeri</i> species complex based on the Kimura 2-parameter model (lower-left), standard error (upper-right) estimated by bootstrap method (replication = 1000).

<p>Mean genetic distances among different lineages of <i>O</i>. <i>schmackeri</i> species complex based on the Kimura 2-parameter model (lower-left), standard error (upper-right) estimated by bootstrap method (replication = 1000).</p

Additional file 1: of Poor awareness of syphilis prevention and treatment knowledge among six different populations in south China

Dataset of the syphilis awareness survey among six different populations in Shenzhen, China. (XLS 934 kb

A Comprehensive Analysis of the Phylogeny, Genomic Organization and Expression of Immunoglobulin Light Chain Genes in <i>Alligator sinensis</i>, an Endangered Reptile Species

<div><p>Crocodilians are evolutionarily distinct reptiles that are distantly related to lizards and are thought to be the closest relatives of birds. Compared with birds and mammals, few studies have investigated the Ig light chain of crocodilians. Here, employing an <i>Alligator sinensis</i> genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization of the <i>Alligator sinensis</i> IgL gene loci. The <i>Alligator sinensis</i> has two IgL isotypes, λ and κ, the same as <i>Anolis carolinensis</i>. The Igλ locus contains 6 C_λ genes, each preceded by a J_λ gene, and 86 potentially functional V_λ genes upstream of (J_λ-C_λ)_n. The Igκ locus contains a single C_κ gene, 6 J_κs and 62 functional V_κs. All V_L genes are classified into a total of 31 families: 19 V_λ families and 12 V_κ families. Based on an analysis of the chromosomal location of the light chain genes among mammals, birds, lizards and frogs, the data further confirm that there are two IgL isotypes in the <i>Alligator sinensis</i>: Igλ and Igκ. By analyzing the cloned Igλ/κ cDNA, we identified a biased usage pattern of V families in the expressed V_λ and V_κ. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed λ and κ sequences. Phylogenetic analysis of the V genes revealed V families shared by mammals, birds, reptiles and <i>Xenopus</i>, suggesting that these conserved V families are orthologous and have been retained during the evolution of IgL. Our data suggest that the <i>Alligator sinensis</i> IgL gene repertoire is highly diverse and complex and provide insight into immunoglobulin gene evolution in vertebrates.</p></div