Dataset Information

Molecular phylogeography and population genetic structure of an endangered species Pachyhynobius shangchengensis (hynobiid Salamander) in a fragmented habitat of southeastern China.

ABSTRACT: The salamander Pachyhynobius shangchengensis (Hynobiidae) is a vulnerable species restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes in the Mount Dabieshan region in southeastern China. However, molecular phylogeography and population genetic structure of P. shangchengensis remain poorly investigated. In this study, we explored the genetic structure and phylogeography of P. shangchengensis based on partial sequences of the mitochondrial DNA (mtDNA) cytochrome b and cytochrome c oxidase subunit I genes. Fifty-one haplotypes and four clades were found among 93 samples. Phylogenetic analyses revealed four deeply divergent and reciprocally monophyletic mtDNA lineages that approximately correspond to four geographic regions separated by complicated topography and long distances. The distinct geographic distributions of all lineages and the estimated divergence time suggest spatial and temporal separation coinciding with climatic changes during the Pleistocene. Analysis of molecular variance indicated that most of the observed genetic variation occurred among the four groups, implying long-term interruption of gene flow, and the possible separation of P. shangchengensis into four management units for conservation.

SUBMITTER: Zhao Y

PROVIDER: S-EPMC3799735 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Molecular phylogeography and population genetic structure of an endangered species Pachyhynobius shangchengensis (hynobiid Salamander) in a fragmented habitat of southeastern China.

Zhao Yanyu Y Zhang Yanhua Y Li Xiaochen X

PloS one 20131018 10

The salamander Pachyhynobius shangchengensis (Hynobiidae) is a vulnerable species restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes in the Mount Dabieshan region in southeastern China. However, molecular phylogeography and population genetic structure of P. shangchengensis remain poorly investigated. In this study, we explored the genetic structure and phylogeography of P. shangchengensis based on partial sequences of the mitochondrial DNA ( ...[more]

PMID: 24205092

Similar Datasets

Project description:High elevation montane areas are called "sky islands" when they occur as a series of high mountains separated by lowland valleys. Different climatic conditions at high elevations makes sky islands a specialized type of habitat, rendering them naturally fragmented compared to more continuous habitat at lower elevations. Species in sky islands face unsuitable climate in the intervening valleys when moving from one montane area to another. The high elevation shola-grassland mosaic in the Western Ghats of southern India form one such sky island complex. The fragmented patches make this area ideal to study the effect of the spatial orientation of suitable habitat patches on population genetic structure of species found in these areas. Past studies have suggested that sky islands tend to have genetically structured populations, possibly due to reduced gene flow between montane areas. To test this hypothesis, we adopted the comparative approach. Using Amplified Fragment Length Polymorphisms, we compared population genetic structures of two closely related, similar sized butterfly species: Heteropsis oculus, a high elevation shola-grassland specialist restricted to the southern Western Ghats, and Mycalesis patnia, found more continuously distributed in lower elevations. In all analyses, as per expectation the sky island specialist H. oculus exhibited a greater degree of population genetic structure than M. patnia, implying a difference in geneflow. This difference in geneflow in turn appears to be due to the natural fragmentation of the sky island complexes. Detailed analysis of a subset of H. oculus samples from one sky island complex (the Anamalais) showed a surprising genetic break. A possible reason for this break could be unsuitable conditions of higher temperature and lower rainfall in the intervening valley region. Thus, sky island species are not only restricted by lack of habitat continuity between montane areas, but also by the nature of the intervening habitat.

Project description:Identification of early warning signals previous to the occurrence of population decline or extinction is a major challenge for the conservation of animal species. Prevalence of morphological abnormalities in a population can be one of these signals. We registered morphological abnormalities in the salamander Ambystoma ordinarium. We also evaluated the relation between habitat quality and the prevalence of abnormalities in this species. We used scores from rapid bioassessment protocols (RBPs) to assess the habitat quality of streams inhabited by A. ordinarium. A preliminary survey indicated that of 29 streams where this species has been historically registered, 13 might have few or no A. ordinarium. The association between habitat quality and the incidence of morphological abnormalities was evaluated in these 16 streams. Of 502 sampled individuals, 224 (44.62%) had at least one body abnormality. Of the 224 individuals with body abnormalities, 84 (37.5%) presented more than one abnormality. Of a total of 5,522 evaluated morphological characters, 344 (6.74%) were abnormal. Partial loss of gills and missing digits were the most frequent abnormalities. Results of a binomial logistic regression indicated that the probability of a character of an individual to be abnormal was significantly associated with habitat quality; as the levels of the quality of the habitat increased, the prevalence of morphological abnormalities decreased. These results suggest that RBPs are a quick and useful method for assessing the habitat quality of streams inhabited by A. ordinarium. Given that RBPs provide rapid and cost-effective assessments of the ecological health of aquatic ecosystems, it will be important to test if the RBPs protocols can be used to rapidly assess habitat quality for other species of stream amphibians. The negative association between habitat quality and the prevalence of morpohological abnormalities that we found indicates that habitat condition plays an important role in the high number of abnormalities registered in A. ordinarium. Therefore, our results suggest that one of the several negative effects of habitat degradation on amphibians is an increase in the frequency of morphological abnormalities with marked consequences for the survival and general fitness of aquatic amphibians.

Project description:BackgroundPandi's mushroom-tongue salamander (Bolitoglossa pandi) is one of the threatened amphibians in South America, as well as a flagship species for the Colombian conservation agenda. This species is endemic to the Andean cloud forests of the western slope of the Cordillera Oriental of Colombia, occurring only in the department of Cundinamarca within a narrow elevational range. At night, B. pandi can be seen perching on the upper side of leaves at heights ranging from ground level to 2.5 m. During the day, it can be found under leaf litter or cover objects. Few studies have provided relevant information that can help the Colombian government to formulate lines of action for the conservation of this species; consequently, its threat assessments so far have been based on very limited information.MethodsWe conducted surveys for salamanders in four municipalities of Cundinamarca, Colombia, using two approaches: visual encounter surveys (Guaduas and Villeta) and the basic sampling protocol for single-species occupancy modeling (Supatá and Venecia). Multivariate analyses were employed to explore the correlation between habitat structure and natural history traits, abundance, and detection/non-detection of B. pandi. We evaluated the B. pandi activity pattern through kernel density curves for each sampling occasion and explored the variability of salamander abundance during their activity period by performing a nested ANOVA.ResultsWe report the discovery of two new populations of B. pandi, which represent the most northwestern records known. A significant correlation between body length, body mass, and habitat structure was observed. Multivariate analyses indicated that leaf litter depth, mean temperature, percent vegetation cover, and altitude were the habitat variables that together explained 60.3% of the B. pandi abundance variability, as well as the main determinants of its optimal habitat. Bolitoglossa pandi exhibits an activity pattern characterized by two main activity peaks, in which niche time-partitioning was observed. Across the surveyed area, we found a healthy, stable, highly dense population of B. pandi (>1,300 individuals), with seasonal variability between development stages.DiscussionGiven the high habitat specificity of B. pandi, the species is highly vulnerable to local changes. Thus, we recommend that B. pandi be retained as Endangered (EN) on the IUCN Red List, based on the IUCN Criterion B, given its restricted extent of occurrence (ca. 2,500 km2) and the ongoing threats from agriculture, cattle ranching, logging, and urban development, which continue to reduce its suitable habitat.

Dataset Information

Molecular phylogeography and population genetic structure of an endangered species Pachyhynobius shangchengensis (hynobiid Salamander) in a fragmented habitat of southeastern China.

Publications

Molecular phylogeography and population genetic structure of an endangered species Pachyhynobius shangchengensis (hynobiid Salamander) in a fragmented habitat of southeastern China.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure