How much genetic variation is stored in the endangered and fragmented shrub Tetraena mongolica Maxim?

Tetraena mongolica Maxim (Zygophyllaceae) is an endangered species endemic to western Inner Mongolia and China, and is currently threatened by habitat loss and human over-exploitation. We explored the genetic background, its genetic diversity, population structure, and demographic history, based on 12 polymorphic nuclear microsatellite loci. Our results indicated high genetic diversity in extant populations, but no distinguishable gene cluster corresponding with a specific biogeography. Population demography analysis using a MSVAR indicated a strong, recent population decline approximately 5,455 years ago. These results suggest that the Yellow River and Zhuozi Mountain range may not prevent pollination between populations. Finally, we surmised that the population demography of T. mongolica was likely to have been affected by early mankind activities

Spatial dynamics of Chinese Muntjac related to past and future climate fluctuations

Climate fluctuations in the past and in the future are likely to result in population expansions, shifts, or the contraction of the ecological niche of many species, and potentially leading to the changes in their geographical distributions. Prediction of suitable habitats has been developed as a useful tool for the assessment of habitat suitability and resource conservation to protect wildlife. Here, we model the ancestral demographic history of the extant modern Chinese Muntjac Muntiacus reevesi populations using approximate Bayesian computation (ABC) and used the maximum entropy model to simulate the past and predict the future spatial dynamics of the species under climate oscillations. Our results indicated that the suitable habitats for the M. reevesi shifted to the Southeast and contracted during the Last Glacial Maximum, whereas they covered a broader and more northern position in the Middle Holocene. The ABC analyses revealed that the modern M. reevesi populations diverged in the Middle Holocene coinciding with the significant contraction of the highly suitable habitat areas. Furthermore, our predictions suggest that the potentially suitable environment distribution for the species will expand under all future climate scenarios. These results indicated that the M. reevesi diverged in the recent time after the glacial period and simultaneously as its habitat’s expanded in the Middle Holocene. Furthermore, the past and future climate fluctuation triggered the change of Chinese muntjac spatial distribution, which has great influence on the Chinese muntjac’s population demographic history

Hidden species diversity in Pachyhynobius: a multiple approaches species delimitation with mitogenomes

The lack of distinct morphological features of cryptic species is a hard problem for taxonomy, especially when the taxa are closely related with considerable amounts of ancestral polymorphism. Lately, intensive coalescent-based analyses involving multiple loci have become the preferred method to assess the extent of genetic distinctiveness in otherwise phenotypically similar populations. Previously, phylogenetic studies on Pachyhynobius shangchengensis uncovered five extremely deeply divergent clades, which suggested that this species may be a cryptic species complex. In this study, we used the complete mitochondrial genome data and samples from the entire range of stout salamander (Pachyhynobius), as well as publicly available mitochondrial genomes to assess species boundaries within this genus using a suite of diverse methodologies (e.g. general mixed Yule coalescent model, Automatic Barcode Gap Discovery). The phylogenetic relationships recovered two major groups within P. shangchengensis, with one group formed by four of the six extant populations and corresponding to the central and eastern range of the Dabie mountains, while the other group encompassed two other lineages in the north west of the Dabie mountain range. The species delimitation comparison within Pachyhynobius supported the presence of recognized species within the genus, and consensus was observed across methods for the existence of up to five cryptic species within what has been traditionally considered to be P. shangchengensis. While this implies the existence of four taxa in addition to the described P. shangchengensis species, morphological data and life history information are further required to contribute to the species definition. The observed pattern of genetic variation is likely the outcome of a discontinuous habitat combined with niche conservatism, which produced the sky-island effect observed in Pachyhynobius, and which led to formation of a hidden species diversity in this genus

Yangtze River, an insignificant genetic boundary in tufted deer (Elaphodus cephalophus): the evidence from a first population genetics study

Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer (Elaphodus cephalophus) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River. Results indicated that there are high genetic diversity levels in the two populations, but no distinguishable haplotype group or potential genetic cluster was detected which corresponded to specific geographical population. At the same time, high gene flow was observed between Wulingshan and Dabashan populations. The tufted deer populations experienced population decrease from 0.3 to 0.09 Ma BP, then followed by a distinct population increase. A strong signal of recent population decline (T = 4,396 years) was detected in the Wulingshan population by a Markov-Switching Vector Autoregressions(MSVAR) process population demography analysis. The results indicated that the Yangtze River may not act as an effective barrier to gene flow in the tufted deer. Finally, we surmised that the population demography of the tufted deer was likely affected by Pleistocene climate fluctuations and ancient human activities

Species Delimitation in the Genus Moschus (Ruminantia: Moschidae) and Its High-Plateau Origin.

The authenticity of controversial species is a significant challenge for systematic biologists. Moschidae is a small family of musk deer in the Artiodactyla, composing only one genus, Moschus. Historically, the number of species in the Moschidae family has been debated. Presently, most musk deer species were restricted in the Tibetan Plateau and surrounding/adjacent areas, which implied that the evolution of Moschus might have been punctuated by the uplift of the Tibetan Plateau. In this study, we aimed to determine the evolutionary history and delimit the species in Moschus by exploring the complete mitochondrial genome (mtDNA) and other mitochondrial gene. Our study demonstrated that six species, M. leucogaster, M. fuscus, M. moschiferus, M. berezovskii, M. chrysogaster and M. anhuiensis, were authentic species in the genus Moschus. Phylogenetic analysis and molecular dating showed that the ancestor of the present Moschidae originates from Tibetan Plateau which suggested that the evolution of Moschus was prompted by the most intense orogenic movement of the Tibetan Plateau during the Pliocene age, and alternating glacial-interglacial geological eras

The genetic distance among four species of <i>Moschus</i> based on each gene in mitochondrial genome.

<p>Ma, Mb, Mm, Mc represents <i>M</i>. <i>anhuiensis</i>, <i>M</i>. <i>berezovskii</i>, <i>M</i>. <i>moschiferus</i> and <i>M</i>. <i>chrysogaster</i>, respectively.</p

Sliding window analyses showing the nucleotide diversity based on alignment of complete mtDNAs of four species in <i>Moschus</i> (<i>M</i>. <i>chrysogaster</i>, <i>M</i>. <i>moschiferus</i>, <i>M</i>. <i>berezovskii</i> and <i>M</i>. <i>anhuiensis</i>).

<p>The black line shows the value of nucleotide diversity (<i>π</i>) in a sliding window analysis of window size 300 bp with step size 10, the value is inserted at its mid-point. Gene boundaries are indicated with an indication of the total number of variable positions per gene; ATP8 with ATP6, ND4L with ND4, and ND5with ND6 are overlapping.</p

Geographic distribution of <i>Moschus</i> species and consensus mitochondrial gene tree.

<p>Tree is equivalent to that of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134183#pone.0134183.g003" target="_blank">Fig 3</a>. All the information about geographic distribution of <i>Moschus</i> species were came from IUCN (<a href="http://www.iucnredlist.org/" target="_blank">http://www.iucnredlist.org/</a>), except a new distribution area of <i>M</i>. <i>berezovskii</i>, which was marked by a star [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134183#pone.0134183.ref039" target="_blank">39</a>].</p

Predicted initiation and termination codons for 13 mitochondrial protein-coding genes in 11 species in Artiodactyla.

<p>Notes: A: <i>M</i>. <i>berezovskii</i> (NC 012694, JQ409122), B: <i>M</i>. <i>moschiferus</i> (NC 013753, JN632662), C: <i>M</i>. <i>anhuiensis</i> (NC 020017, KP684124), D: <i>M</i>. <i>chrysogaster</i> (KC 425457, KP684123), E: <i>Tragulus kanchil</i> (NC 020753), F: <i>Rangifer tarandus</i> (NC 007703), G: <i>Muntiacus reeves</i> (NC 004069), H: <i>Bos taurus taurus</i> (EU 177832), I: <i>Nanger granti</i> (NC 020725), J: <i>Ovis aries</i> (NC 001941), K: <i>Axis porcinus</i> (NC 020681).</p><p>Predicted initiation and termination codons for 13 mitochondrial protein-coding genes in 11 species in Artiodactyla.</p

Phylogram showing the phylogenetic relationship in Moschidae.

<p>The values on nodes include three parts. The first two values indicate the split time and Bayesian posterior probabilities which were calculated by BEAST 1.7.4. The last values were the Bayesian posterior probabilities calculated by MrBayes 3.1.2.</p