title: Extremely low genetic diversity indicating the endangered status of Ranodon sibiricus (Amphibia: Caudata) and implications for phylogeography.
abstract: BACKGROUND
  The Siberian salamander (Ranodon sibiricus), distributed in geographically isolated areas of Central Asia, is an ideal alpine species for studies of conservation and phylogeography. However, there are few data regarding the genetic diversity in R. sibiricus populations.
  
  
  RESULTS
  We used two genetic markers (mtDNA and microsatellites) to survey all six populations of R. sibiricus in China. Both of the markers revealed extreme genetic uniformity among these populations. There were only three haplotypes in the mtDNA, and the overall nucleotide diversity in the mtDNA was 0.00064, ranging from 0.00000 to 0.00091 for the six populations. Although we recovered 70 sequences containing microsatellite repeats, there were only two loci that displayed polymorphism. We used the approximate Bayesian computation (ABC) method to study the demographic history of the populations. This analysis suggested that the extant populations diverged from the ancestral population approximately 120 years ago and that the historical population size was much larger than the present population size; i.e., R. sibiricus has experienced dramatic population declines.
  
  
  CONCLUSIONS
  Our findings suggest that the genetic diversity in the R. sibiricus populations is the lowest among all investigated amphibians. We conclude that the isolation of R. sibiricus populations occurred recently and was a result of recent human activity and/or climatic changes. The Pleistocene glaciation oscillations may have facilitated intraspecies genetic homogeneity rather than enhanced divergence. A low genomic evolutionary rate and elevated inbreeding frequency may have also contributed to the low genetic variation observed in this species. Our findings indicate the urgency of implementing a protection plan for this endangered species.
authors.affiliation: State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Shao-Yu
authors.initials: SY
authors.lastname: Chen
authors.forename: Yi-Jun
authors.initials: YJ
authors.lastname: Zhang
authors.forename: Xiu-Ling
authors.initials: XL
authors.lastname: Wang
authors.forename: Jian-Yun
authors.initials: JY
authors.lastname: Sun
authors.forename: Yan
authors.initials: Y
authors.lastname: Xue
authors.forename: Peng
authors.initials: P
authors.lastname: Zhang
authors.forename: Hui
authors.initials: H
authors.lastname: Zhou
authors.forename: Liang-Hu
authors.initials: LH
authors.lastname: Qu
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D002681:China; D004272:DNA, Mitochondrial / Q000235:genetics; D056727:Endangered Species; D014644:Genetic Variation; D005828:Genetics, Population; D006239:Haplotypes / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D058974:Phylogeography; D017422:Sequence Analysis, DNA; D014562:Caudata / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial