The large and complex gut microbiota in animals has profound effects on feed utilization and metabolism. Currently, gastrointestinal diseases due to dysregulated gut microbiota are considered important factors that limit growth of the captive forest musk deer population. Compared with captive forest musk deer, wild forest musk deer have a wider feeding range with no dietary limitations, and their gut microbiota are in a relatively natural state. However, no reports have compared the gut microbiota between wild and captive forest musk deer. To gain insight into the composition of gut microbiota in forest musk deer under different food-source conditions, we employed high-throughput 16S rRNA sequencing technology to investigate differences in the gut microbiota occurring between captive and wild forest musk deer. Both captive and wild forest musk deer showed similar microbiota at the phylum level, which consisted mainly of Firmicutes and Bacteroidetes, although significant differences were found in their relative abundances between both groups. α-Diversity results showed that no significant differences occurred in the microbiota between both groups, while β-diversity results showed that significant differences did occur in their microbiota compositions. In summary, our results provide important information for improving feed preparation for captive forest musk deer and implementing projects where captive forest musk deer are released into the wild.

BackgroundHirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. Analysis of codon usage patterns would contribute to our understanding of the evolutionary mechanisms and genetic architecture of H. manillensis, which in turn would provide insight into the characteristics of other leeches. We analysed codon usage and related indices using 18,000 coding sequences (CDSs) retrieved from H. manillensis RNA-Seq data.ResultsWe identified four highly preferred codons in H. manillensis that have G/C-endings. Points generated in an effective number of codons (ENC) plot distributed below the standard curve and the slope of a neutrality plot was less than 1. Highly expressed CDSs had lower ENC content and higher GC content than weakly expressed CDSs. Principal component analysis conducted on relative synonymous codon usage (RSCU) values divided CDSs according to GC content and divided codons according to ending bases. Moreover, by determining codon usage, we found that the majority of blood-diet related genes have undergone less adaptive evolution in H. manillensis, except for those with homologous sequences in the host species.ConclusionsCodon usage in H. manillensis had an overall preference toward C-endings and indicated that codon usage patterns are mediated by differential expression, GC content, and biological function. Although mutation pressure effects were also notable, the majority of genetic evolution in H. manillensis was driven by natural selection.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4937-x) contains supplementary material, which is available to authorized users.

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Diarrhea constitutes one of the most common diseases affecting the survival of captive musk deer and is usually caused by an imbalance in intestinal microbiota. Currently, research regarding the structure and function of intestinal microbiota in diarrheic musk deer is lacking. Therefore, in the present study, high-throughput 16S-rRNA gene sequencing was used to analyze the intestinal microbiota in feces of healthy captive musk deer (HMD) (n = 8) and musk deer with mild (MMD) (n = 8), and severe (n = 5) (SMD) diarrhea to compare the difference in intestinal microbiota of musk deer under various physiological conditions. The results showed that the diversity of HMD fecal microbiota was significantly higher than that of the two diarrhea samples. β Diversity results indicated that there were extremely significant differences in bacterial communities between the HMD sample and the MMD and SMD samples. However, no significant difference was found between the two diarrhea samples. LefSe analysis showed that the degree of intestinal physiological dysfunction in musk deer was correlated with the types of major pathogens. The main pathogen in the MMD group is Escherichia–Shigella, whereas Fusobacterium is the main pathogen in the SMD group. PICRUSt functional profile prediction indicated that the intestinal microbiota disorder could also lead to changes in the abundance of genes in metabolic pathways of the immune system. Altogether, this study provides a theoretical basis for the exploration of treatments for diarrhea in captive musk deer, which is of considerable significance to the implementation of the musk deer release into the wild program.

The superfamily Dytiscoidea contains six families with an aquatic lifestyle, with most of its extant diversity in two families: the burrowing water beetles (Noteridae) and the diving beetles (Dytiscidae). The other families have few species (up to six) and generally highly disjunct extant distributions. Aspidytidae currently contains one genus with two species, one in China and one in South Africa. Here we provide the first molecular data for the Chinese species, allowing us to explore the phylogenetic relationships and position of both species of this small family for the first time. Based on a matrix of 11 genes we inferred a phylogenetic hypothesis for Dytiscoidea including all extant families. Unexpectedly, Aspidytidae were consistently recovered as paraphyletic relative to Amphizoidae, despite being well characterized by apparently synapomorphic adult features. A re-examination of larval characters in the two aspidytid species revealed that the larva of the Chinese species is strikingly similar to that of Amphizoidae. Both share a series of plesiomorphic features but also some potential synapomorphies, including a dense vestiture of short setae on the head capsule, anteriorly shifted posterior tentorial grooves and widely separated labial palps. Arguably these features may belong to the groundplan of the clade Aspidytidae + Amphizoidae, with far-reaching secondary modifications (including reversals) in the South African Aspidytes niobe. At present we retain the family Aspidytidae, however, due to the strong adult morphological synapomorphies of the two extant species, and the fact that the molecular paraphyly of the family may result from the highly divergent nature of the two extant species. This long evolutionary separation and strong divergence, in terms of gene sequences and Zoological Journal of the Linnean Society, 2016, 176, 537-546. With 11 figures. larval features, is undeniable, substantial levels of saturation in third codon positions of protein-coding genes being present between the two taxa. We address this issue taxonomically by introducing the new genus Sinaspidytes gen. nov. for the Chinese Aspidytes wrasei. The continued contentious relationships amongst Dytiscidae, Hygrobiidae, Aspidytidae and Amphizoidae highlight the need for more data to address dytiscoid phylogenetics, possibly involving a genomic approach.

This study used 16S rRNA high-throughput sequencing technology to examine the differences in gut microbiota between the Père David's deer populations in the Beijing and Shishou areas of China in order to understand the effects of ex situ conservation on the intestinal microflora in the Père David's deer.Results: On the phylum level, the main bacteria found in the Père David's deer populations from both areas were similar: Firmicutes and Bacteroidetes. However, the relative abundances of the two groups were significantly different. Alpha diversity results indicated that there was a difference in the evenness of the microflora between the two groups, and the beta diversity results further indicated that there was a significant difference in the microflora structure between the two groups.Conclusions: During the ex situ conservation process of the Père David's deer, their food sources may change, resulting in differences in the gut microbiota. The intestinal microflora in the Père David's deer from the same area are clustered. Therefore, the impact of changes in food on the gut microbiota of the Père David's deer should be taken into consideration during ex situ conservation.

A quantitative analysis of wing variation in grasshoppers can help us to understand how environmental heterogeneity affects the phenotypic patterns of insects. In this study, geometric morphometric methods were used to measure the differences in wing shape and size of Trilophidia annulata among 39 geographical populations in China, and a regression analysis was applied to identify the major environmental factors contributing to the observed morphological variations. The results showed that the size of the forewing and hindwing were significantly different among populations; the shape of the forewing among populations can be divided into geographical groups, however hindwing shape are geographical overlapped, and populations cannot be divided into geographical groups. Environmental PCA and thin-plate spline analysis suggested that smaller individuals with shorter and blunter-tip forewings were mainly distributed in the lower latitudes and mountainous areas, where they have higher temperatures and more precipitation. Correspondingly, the larger-bodied grasshoppers, those that have longer forewings with a longer radial sector, are distributed in contrary circumstances. We conclude that the size variations in body, forewing and hindwing of T. annulata apparently follow the Bergmann clines. The importance of climatic variables in influencing morphological variation among populations, forewing shape of T. annulata varies along an environmental gradient.Environmental heterogeneity and ecological gradients can generate phenotypic variation in many organisms [1][2][3] . Understanding how environmental heterogeneity affects phenotypic patterns in organisms is a major focus in evolutionary ecology [4][5][6][7] . Under certain environment, phenotype changes can increase fitness in organisms [8][9][10][11] . Phenotypic clinal patterns associated with environmental gradients are often described as ecogeographical rules known as Bergmann's rule or converse-Bergmann' s rule [12][13][14][15] . Bergmann's rule was initially used to explain the relationship between changes in the body size of endotherms and changes in latitude and altitude; it described a positive relationship between body size and latitude, in which smaller individuals are typically found at lower latitudes where climates are generally warmer. A number of studies have shown that the body size of insects along environmental gradients fit Bergmann clines or converse-Bergmann clines, but other studies have suggested that Bergmann's rule might not work in insects 16,17 . These ecogeographical rules have been extensively examined and convincingly demonstrated in insects 18 . However, morphological variations within insect species might reflect different patterns of dispersal and habitat availability coupled with different life-history types (e.g., hemimetabolism or holometamorphosis). The adaptive significance of these clines in insects has been fiercely debated 19,20 . Shelomi claimed that researches on these ecogeographical rules in insects should focus on widesprea...

The genus Lespedeza (tribe: Desmodieae) consists of about 40 species that have high medicinal and economic value. However, in this genus, using morphological characters, the species identification is quite complicated, which can be solved by the analysis of the complete chloroplast genomes. As primary organelle genomes, the complete genome sequences of chloroplasts (cp) provide unique molecular information to study the divergence of species, RNA editing, and phylogeny. Therefore, to the best of our knowledge, for the first time, we sequenced the complete cp genomes of two representative Lespedeza species: Lespedeza davurica and Lespedeza cuneata. The cp genomes of both the species were found to be 149,010 bp in length, exhibiting the typical angiosperm chloroplast structure containing four regions. The Lespedeza cp genomes showed similar conserved gene contents, order, and orientations with a total GC content of 35.0%. A total of 128 genes, including 83 protein-coding genes, 37 tRNAs, and eight rRNAs, were identified from each genome. Unique molecular features of the two Lespedeza cp genome sequences were obtained by performing the analysis of repeats, sequence divergence, codon usage, and predicting the RNA editing sites in addition to phylogenetic analysis with other key genera in tribe Desmodieae. Using the two datasets, the phylogenetic relationship of Lespedeza species among Deasmodieae was discovered, suggesting that whole cp genomes provided useful information for phylogenetic studies of these species.