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

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

Lineage-through-time (LTT) plots for Anseriformes birds.

<p>The colored lines represent the results of 1000 trees randomly selected from the BEAST analysis. The ref line shows the MCC tree.</p

Phylogram showing the phylogenetic relationship in Anseriformes based on the mito-genomes.

<p>The values on nodes include four parts. The first two values indicate the split time and Bayesian posterior probabilities which were calculated by BEAST 1.7.4. The third values were the Bayesian posterior probabilities calculated by MrBayes 3.2.2, and the last values were the Bayesian posterior probabilities calculated by RAxML version 8. Blue bars at nodes show 95% highest posterior density (HPD) of divergence times.</p