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There have been many reports on the genetic mechanism in rhesus macaques (RMs) for environmental adaptation to high altitudes, but the synergistic involvement of gut microbiota in this adaptation remains unclear. Here we performed fecal metagenomic and metabolomic studies on samples from high- and low-altitude populations to assess the synergistic role of gut microbiota in the adaptation of RMs to high-altitude environments. Microbiota taxonomic annotation yielded 7471 microbiota species. There were 37 bacterial species whose abundance was significantly enriched in the high-altitude populations, 16 of which were previously reported to be related to the host’s dietary digestion and energy metabolism. Further functional gene enrichment found a stronger potential for gut microbiota to synthesize energy substrate acetyl-CoA using CO2 and energy substrate pyruvate using oxaloacetate, as well as a stronger potential to transform acetyl-CoA to energy substrate acetate in high-altitude populations. Interestingly, there were no apparent differences between low-altitude and high-altitude populations in terms of genes enriched in the main pathways by which the microbiota consumed the three energy substrates, and none of the three energy substrates were detected in the fecal metabolites. These results strongly suggest that gut microbiota plays an important energy compensatory role that helps RMs to adapt to high-altitude environments. Further functional enrichment after metabolite source analysis indicated the abundance of metabolites related to the degradation of exogenous toxins was also significantly higher in high-altitude populations, which suggested a contributory role of gut microbiota to the degradation of exogenous toxins in wild RMs adapted to high-altitude environments.

Background Blastocystis is a common intestinal protist with a wide range of hosts. Thus far, 38 subtypes have been identified. In recent years, wild animals have been confronted with habitat fragmentation as well as an increasing risk of zoonotic disease transmission due to human disturbance. Only limited data are available on Blastocystis infection and subtype distribution in wild rhesus macaques in China. The aim of the present study was to investigate the prevalence and genetic diversity of Blastocystis in nine wild rhesus macaque populations in China. Methods A total of 276 faecal samples were collected from five high-altitude populations (high-altitude group [HAG]; 2800–4100 m a.s.l.) and four low-altitude populations (low-altitude group [LAG]; 5–1000 m a.s.l) of rhesus macaques. PCR-based analysis, using a new primer pair for the amplification of a 1690-bp sequence of the small subunit ribosomal RNA (SSU rRNA) gene, was used for prevalence and genetic diversity analysis. Result Analysis of faecal samples revealed that Blastocystis infection was common in rhesus macaques, with an infection positivity rate of 80.1% (n = 221/276 samples). There was no significant difference (P = 0.121) in positivity rate between the LAG (84.3%) and HAG (76.8%). Overall, 33 haplotypes were obtained and classified into four subtypes (STs), of which three were potentially zoonotic subtypes (ST1, 29.7%; ST2, 16.7%; ST3, 31.9%) and one that was first identified in this study and named ST39 (12.0%). The STs were distributed differently among the rhesus macaque populations, except for ST3, which was found in all populations. Phylogenetic analyses revealed two major divergent clades of ST3 for the HAG and LAG. Genetic diversity analysis showed a high genetic diversity of ST3 (haplotype diversity: 0.846; nucleotide diversity: 0.014) in the rhesus macaques, but a high genetic differentiation (FST > 0.25) and a low gene flow (Nm = 0.09) between the HAG and LAG. Conclusion Our study, which is the first investigation on Blastocystis infection in multiple wild rhesus macaque populations in China, indicates a potential risk of zoonotic transmission of Blastocystis in the study areas. Blastocystis ST3 showed high genetic diversity in wild rhesus macaques and significant genetic differentiation between the HAG and LAG. Our results provide fundamental information on the genetic diversity and prevalence of Blastocystis in wild rhesus macaque populations. Graphical Abstract

Background The expression and biological functions of circular RNAs (circRNAs) in reproductive organs have been extensively reported. However, it is still unclear whether circRNAs are involved in sex change. To this end, RNA sequencing (RNA-seq) was performed in gonads at 5 sexual stages (ovary, early intersexual stage gonad, middle intersexual stage gonad, late intersexual stage gonad, and testis) of ricefield eel, and the expression profiles and potential functions of circRNAs were studied. Results Seven hundred twenty-one circRNAs were identified, and the expression levels of 10 circRNAs were verified by quantitative real-time PCR (qRT–PCR) and found to be in accordance with the RNA-seq data, suggesting that the RNA-seq data were reliable. Then, the sequence length, category, sequence composition and the relationship between the parent genes of the circRNAs were explored. A total of 147 circRNAs were differentially expressed in the sex change process, and GO and KEGG analyses revealed that some differentially expressed (such as novel_circ_0000659, novel_circ_0004005 and novel_circ_0005865) circRNAs were closely involved in sex change. Furthermore, expression pattern analysis demonstrated that both circSnd1 and foxl2 were downregulated in the process of sex change, which was contrary to mal-miR-135b. Finally, dual-luciferase reporter assay and RNA immunoprecipitation showed that circSnd1 and foxl2 can combine with mal-miR-135b and mal-miR-135c. These data revealed that circSnd1 regulates foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. Conclusion Our results are the first to demonstrate that circRNAs have potential effects on sex change in ricefield eel; and circSnd1 could regulate foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. These data will be useful for enhancing our understanding of sequential hermaphroditism and sex change in ricefield eel or other teleosts.

Background An increasing number of long noncoding RNAs (lncRNAs) have been found to play important roles in sex differentiation and gonad development by regulating gene expression at the epigenetic, transcriptional and posttranscriptional levels. The ricefield eel, Monopterus albus, is a protogynous hermaphroditic fish that undergoes a sequential sex change from female to male. However, the roles of lncRNA in the sex change is unclear. Results Herein, we performed RNA sequencing to analyse lncRNA expression patterns in five different stages of M. albus development to investigate the roles of lncRNAs in the sex change process. A total of 12,746 lncRNAs (1503 known lncRNAs and 11,243 new lncRNAs) and 2901 differentially expressed lncRNAs (DE-lncRNAs) were identified in the gonads. The target genes of the DE-lncRNAs included foxo1, foxm1, smad3, foxr1, camk4, ar and tgfb3, which were mainly enriched in signalling pathways related to gonadal development, such as the insulin signalling pathway, MAPK signalling pathway, and calcium signalling pathway. We selected 5 highly expressed DE-lncRNAs (LOC109952131, LOC109953466, LOC109954337, LOC109954360 and LOC109958454) for full length amplification and expression pattern verification. They were all expressed at higher levels in ovaries and intersex gonads than in testes, and exhibited specific time-dependent expression in ovarian tissue incubated with follicle-stimulating hormone (FSH) and human chorionic gonadotropin (hCG). The results of quantitative real-time PCR (qRT-PCR) analysis and a dual-luciferase assay showed that znf207, as the gene targeted by LOC109958454, was expressed in multiple tissues and gonadal developmental stages of M. albus, and its expression was also inhibited by the hormones FSH and hCG. Conclusions These results provide new insights into the role of lncRNAs in gonad development, especially regarding natural sex changes in fish, which will be useful for enhancing our understanding of sequential hermaphroditism and sex changes in the ricefield eel (M. albus) and other teleosts.

In this paper, a wide neighborhood arc-search interior-point algorithm for convex quadratic programming with box constrains and linear constraints (BLCQP) is presented. The algorithm searches the optimizers along the ellipses that approximate the entire central path. Assuming a strictly feasible initial point is available, we show that the algorithm has $$O(n^{\frac{3}{4}}\log \frac{{({x^0} - l)^T}{s^0} + {(w - {x^0})^T}{t^0}}{\varepsilon })$$ iteration complexity bound, which is the best known complexity result for such methods. The numerical results show that our algorithm is effective and promising.

As indicated in the recent studies about primal-dual interior-point methods (IPMs) based on kernel functions, a kernel function not only serves to determine the search direction and measure the distance of the current iteration point to the $$\mu $$ -center, but also affects the iteration complexity and the practical computational efficiency of the algorithm. In this paper, we propose a new IPM for semidefinite optimization (SDO) based on a parameterized kernel function which is a generalization of the one presented by Bai et al. (Optim Methods Softw 17(6):985–1008, 2002). By using the good properties of the parameterized kernel function, we deduce that the iteration bound for large-update method is $$O(\sqrt{n}\log {n}\log {\frac{n}{\epsilon }})$$ for $$q=O(n)$$ , which is the best known complexity results for such methods. In our knowledge, this result is the first instance of primal-dual interior point method for SDO which involving the kernel function. Some numerical results have been provided.

Gastrointestinal microbiome plays an important role in animal metabolism, immune system and pathology associated with health and disease. Many wild slow lorises were confiscated from illegal trade into captivities and experienced a range of changes in living environment and diet. Microbiome analysis contributes to improving captive management by identifying the alteration in their gastrointestinal microbial communities and aiding in determining the factors affecting the health of captive slow lorises. The fecal samples of eighteen Bengal slow lorises (Nycticebus bengalensis) were used to compare gut microbiota from four rescue centers located in Dehong, Gejiu, Nanning and Puer cities of China. The results showed a significant site-dependent difference in microbial community diversity. Similar to other Lorisinae species, the Phyla including Bacteroidetes, Firmicutes and Proteobacteria dominated their gut microbiome composition. The Gejiu group exhibited a higher overall diversity and the unique OTUs, which is resulted from long-term isolated husbandry and heavy human disturbances. The scarcity of gums in the captive diet was likely to cause a lower abundance of Prevotella associated with soluble fiber degradation. The variation of intestinal microbiota in different environments highlights the necessity to improve feed preparation and husbandry management for the captive Bengal slow lorises.

In this paper, we propose a new full-Newton step interior-point method (IPM) for $$P_{*}(\kappa )$$ linear complementarity problem (LCP). The search direction is obtained by applying algebraic equivalent transformation on the centering equation of the central path which is introduced by Darvay et al. for linear optimization (Optim Lett 12(5):1099–1116, 2018). They point out that the search direction can also be obtained by using a positive-asymptotic kernel function. This kernel function has not been used in the complexity analysis of IPMs for $$P_{*}(\kappa )$$ -LCP before. Assuming a strictly feasible starting point is available, we show that the algorithm has the iteration complexity bound $$O((1+4\kappa )\sqrt{n}\log {\frac{n}{\epsilon }})$$ , which is the best known complexity result for such methods. Some numerical results have been provided.

The gut microbiome of captive primates can provide a window into their health and disease status. The diversity and composition of gut microbiota are influenced by not only host phylogeny, but also host diet. Old World monkeys (Cercopithecidae) are divided into two subfamilies: Cercopithecinae and Colobinae. The diet and physiological digestive features differ between these two subfamilies. Accordingly, highthroughput sequencing was used to examine gut microbiota differences between these two subfamilies, using data from 29 Cercopithecinae individuals and 19 Colobinae individuals raised in captivity. Through a comparative analysis of operational taxonomic units (OTUs), significant differences in the diversity and composition of gut microbiota were observed between Cercopithecinae and Colobinae. In particular, the gut microbiota of captive Old World monkeys clustered strongly by the two subfamilies. The Colobinae microbial diversity was higher than that of Cercopithecinae. Additionally, Firmicutes, Lactobacillaceae, Veillonellaceae, and Prevotella abundance were higher in Cercopithecinae, while Bacteroidetes, Ruminococcaceae, Christensenellaceae, Bacteroidaceae, and Acidaminococcaceae abundance were higher in Colobinae. PICRUSt analysis revealed that the predicted metagenomes of metabolic pathways associated with proteins, carbohydrates, and amino acids were significantly higher in Colobinae. In the context of host phylogeny, these differences between Cercopithecinae and Colobinae could reflect adaptations associated with their respective diets. This well-organized dataset is a valuable resource for future related research on primates and gut microbiota. Moreover, this study may provide useful insight into animal management practices and primate conservation.

We propose a wide neighborhood primal-dual interior-point algorithm with arc-search for semidefinite programming. In every iteration, the algorithm constructs an ellipse and searches an $$\varepsilon $$ -approximate solution of the problem along the ellipsoidal approximation of the central path. Assuming a strictly feasible starting point is available, we show that the algorithm has the iteration complexity bound $$O\left( n^{\frac{3}{4}}\log \frac{{X^{0}}\bullet {S}^{0}}{\varepsilon }\right) $$ for the Nesterov–Todd direction, which is similar to that of the corresponding algorithm for linear programming. The numerical results show that our algorithm is efficient and promising.

The hypothalamic-pituitary-ovarian (HPO) axis regulates the breeding process cycle of laying hens. However, the key regulatory genes of the HPO axis and pathways that drive chicken egg laying performance remain elusive. A total of 856 Chinese Luhua chicken was raised and the highest two hundred and the lowest two hundred chicken egg production were considered as high egg production (HEP) and low egg production (LEP) according to the total egg number at 300 days of age, respectively. RNA-seq sequencing (RNA-Seq) was conducted to explore the chicken transcriptome from the hypothalamus, pituitary gland and ovary tissue of 6 Chinese Luhua chicken with 3 high and low-rate egg production. In total, 76.09 Gb RNA-seq sequences were generated from 15 libraries with an average of 5.07 Gb for each library. Further analysis showed that 414, 356 and 10 differentially expressed genes (DEGs) were identified in pituitary gland, ovary and hypothalamus between HEP and LEP chickens, respectively. In pituitary gland, DEGs were involve in regulation of cellular glucose homeostasis, Ras protein signal transduction, negative regulation of hormone secretion. In Ovary DEGs were mainly involved in embryonic organ development, regulation of canonical Wnt signaling, response to peptide hormone. Our study identified DEGs that regulate mTOR signaling pathway, Jak-STAT signaling pathway, Tryptophan metabolism and PI3K-Akt signaling pathways at HPO-axis in laying hens. These important data contribute to improve our understanding of reproductive biology of chicken and isolating effective molecular markers that can be used for genetic selection in Chinese domestic Luhua chicken.

The goral (Naemorhedus caudatus), a species of the Caprinae, is classified as globally vulnerable on the IUCN Red List of Threatened Species because of its sharply declining population size, which is attributable to habitat destruction. In this study, we determined and described the complete mitochondrial genome of N. c. griseus, a goral subspecies from the western Sichuan of China; the mitochondrial genome of this goral is 16,557 bp in length (GenBank accession No: MG865962) and contains 13 protein-coding genes (PCGs), two rRNA genes, 23 tRNA genes, and one control region (D-loop). Ten PCGs start with ATG, but ND2, ND3, and ND5 use ATA as the start codon. The overall base composition of the mitochondrial DNA is 34.6% A, 28.6% T, 22.4% C, and 14.4% G. The G+C content is 36.8%. Phylogenetic analysis revealed that N. c. griseus clustered into a clade with other Naemorhedus species with high bootstrap support. This work provides additional molecular information for studying the conservation genetics and evolutionary relationships of this endangered species.

Knowledge about the impact of different geographical environments on rhesus macaque gut microbiota is limited. In this study, we compared the characteristics of gut microbiota in six different Chinese rhesus macaque populations, including Hainan, Nanning, Guizhou, Xichang, Jianchuan and Tibet. Through the composition analysis of operational taxonomic units (OTUs), we found that there were significant differences in the abundance of core overlapping OTUs in the six Chinese groups. Specifically, the Tibet population exhibited the highest gut microbial diversity and the most unique OTUs. Statistically significant differences in the composition of gut microbiota among the six groups at phylum and family level were evident. Specifically, Tibet had higher abundances of Firmicutes and lower abundances of Bacteroidetes than the other geographical groups, and the higher abundance of Firmicutes in the Tibetan group was mainly caused by a significant increase in the family Ruminococcaceae and Christensenellaceae. Phylogenetic investigation of communities by reconstruction of unobserved state analysis showed that the enrichment ratio for environmental information processing and organismal systems was the highest in the Tibet population. Additionally, our results suggested that in the adaptation process of rhesus macaques to different geographical environments, the abundance of the core common flora of the intestinal microbes had undergone varying degree of change and produced new and unique flora, both of which helped to reshape the gut microbiota of rhesus macaques. In particular, this change was more obvious for animals in the high-altitude environments.

The white-lipped deer (Cervus albirostris) is a rare and endangered species endemic to the Qinghai–Tibet Plateau in China. In this study, we determined the complete mitochondrial genome sequence of the white-lipped deer. The total length of the mitogenome is 16473 bp. It has the typical structure of a vertebrate mitochondrial genome including 13 protein-coding genes(PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region (D-loop). tRNASer lacks the stem of the dihydrouridine (DHU) arm and fails to form a typical cloverleaf secondary structure. A phylogenetic tree based on the 13 PCG sequences of nine species closely related to white-lipped deer shows the classification status of the species within the family Cervidae. These results provide new molecular biology information to further understand the diversity of the white-lipped deer, which will help to protect this population.

In this paper, we propose an arc-search interior-point algorithm for convex quadratic programming with a wide neighborhood of the central path, which searches the optimizers along the ellipses that approximate the entire central path. The favorable polynomial complexity bound of the algorithm is obtained, namely O(nlog((x0)Ts0/e)) which is as good as the linear programming analogue. Finally, the numerical experiments show that the proposed algorithm is efficient.

Due to the synergistic effects of hunting and habitat loss, populations of the western black-crested gibbon are currently restricted to isolated forest fragments. The home range use of this species in fragmented forests is presumptively related to spatial, food and vegetation attributes, as in other primates. We examined the distributions of different food resources, the structure of the vegetation (tree density, DBH, and height), and the microhabitat use of one gibbon group in an isolated and disturbed forest at Bajiaohe in southern Yunnan, China. The results indicated that the gibbons used the edge habitat frequently, which was subject to more anthropogenic disturbance than the interior forest, and they appeared to adapt to discontinuous canopy cover by using bamboo and tsaoko plants for travel. The group also modified its diet in response to fluctuations in food availability and the local flora. However, the gibbons intensively used areas with high tree fruit availability across the two study periods. It is suggested that the microhabitat use by the group was mostly affected by the distribution of particular food resources and canopy gaps caused by selective logging. Protecting the current distribution area and planting native important food species to boost habitat quality and connectivity should be considered as part of conservation plans of the western black crested gibbon living in limited areas.

The Sichuan deer (Cervus elaphus macneilli) is a rare animal native to western Sichuan and southeastern Tibet, China. In this study, the entire Sichuan deer mitochondrial genome was sequenced; it was 16350 bp long (GenBank accession No: KX449334) and contained 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region (D-loop). Ten PCGs started with ATG, but ND2, ND3, and ND5 used ATA as the start codon. PCG homology between C.e.macneilli and four other red deer subspecies ranged from 93.9 to 96%, which indicates a clear difference among subspecies. Phylogenetic analysis revealed that the Sichuan deer clustered into a clade with other red deer subspecies with high bootstrap support. This work provides additional molecular information for studying red deer conservation genetics and evolutionary relationships.

Forest musk deer (FMD) is an endangered species, and its population size has dropped dramatically. In this study, we determined the complete mitochondrial genome of a FMD. The genome was 16,353 bp long, and contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and one control region. Most PCGs were distributed on the heavy strand except ND6 and eight tRNA genes, which were encoded on the light strand. The nucleotide composition was asymmetric, with an overall A+T content of 62.1%. Comparison with one previously described mitochondrial genome revealed 94.4% sequence homology and 1128 nucleotide mutation sites, which represents a substantial difference. A phylogenetic tree based on Cytb genes of eight closely related musk deer species showed that our sample clustered with two FMD subspecies from Yunnan, China. These results provide novel molecular information that can potentially be used for genetic diversity conservation of this species.

The Vietnam Warty Newt (Paramesotriton deloustali) is threatened by habitat loss and illegal capture for traditional medicines use and domestic pet trade. In this study, we described the complete mitochondrial genome (mitogenome) of P. deloustali. The entire mitogenome sequence of P. deloustali is 16,391 bp long, containing 13 protein coding genes, two ribosomal RNA, 22 transfer RNA genes, one control region and an additional 261 bp non-coding sequence between tRNAThr and tRNAPro genes. Our new data of the complete mitogenome of P. deloustali will offer solid genetic information for further conservation genetics research of this threatened species.

Tylototriton ziegleri is distributed in northern Vietnam and is a new member of the genus Tylototriton. The conservation status of this species has not yet been assessed by the IUCN, but several other species of Tylototriton have been listed as near threatened or vulnerable due to habitat destruction and illegal hunting. We determined the complete sequence and structural characteristics of the mitochondrial genome of T. ziegleri. The entire mitogenome is 16,266 bp in length, and contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, a control region, and a non-coding region. The length, gene arrangement, and composition are similar to mitogenomes of other species of Tylototriton. A phylogenetic tree based on the mitogenome sequences of several Asian species within Salamandridae confirmed the genus Tylototriton as monophyletic, with T. ziegleri being the sister species of T. asperrimus and both constituting the sister group of T. wenxianensis. This work provides basic molecular data which are critical for further genetic research and conservation of the genus Tylototriton.

Trachypithecus poliocephalus : (Primates: Cercopithecidae), classified as critically endangered (IUCN) and in China was listed National First Class Protected Animal. In this study, the complete mitochondrial genome sequence of T. poliocephalus has been reported for the first time in China. The complete mitochondrial genome of T. poliocephalus was sequenced and it contained 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and one control region (D-loop).

In this study, the complete mitochondrial genome sequence of Prionodon pardicolor pardicolor has been reported for the first time in China. The total length of the mitogenome was 16,689 bp. It contained the typical structure, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (D-loop). tRNASer lost the stem of DHC loop and failed to form a typical cloverleaf secondary structure. Mitochondrial control region of P. p. pardicolor was 1242 bp long, laying between the tRNAPro and tRNAPhe genes. Based on the 13 PCG sequences, homology and single-nucleotide mutation loci were performed between P. p. pardicolor and P. pardicolor. As a result, the homology between two species was 99.6% on average, and Nucleotide mutation loci was 41. Also, in view of their mitochondrial control region comparison, P. p. pardicolor drop 28 bp nucleotides.

In Zhang’s recent works, a second-order Mehrotra-type predictor-corrector algorithm for linear optimization was extended to semidefinite optimization and derived that the algorithm for semidefinite optimization had O(n 3/2log(X 0)T•S 0/e) iteration complexity based on the NT direction as Newton search direction. In this paper, we extend the second-order Mehrotra-type predictor-corrector algorithm for linear optimization to semidefinite optimization and discuss the polynomial convergence of the algorithm by modifying the corrector direction and new iterates. It is proved that the iteration complexity is reduced to O(nlogX 0•S 0/e), which coincides with the currently best iteration bound of Mehrotra-type predictor-corrector algorithm for semidefinite optimization.

In this paper, we present a new large-update interior-point algorithm for \(P_*(\kappa )\)-linear complementarity problem. The new algorithm is based on a trigonometric kernel function which differs from the existing kernel functions in which it has a double barrier term. By a simple analysis, we show that the new algorithm enjoys \({ O}((1+2\kappa )n^\frac{2}{3}\log \frac{n}{\varepsilon })\) iteration complexity. This complexity estimate improves a result from El Ghami et al. (Optim Theory Decis Mak Oper Res Appl 31: 331–349, 2013) and matches the currently best known complexity result for \(P_*(\kappa )\)-linear complementarity problem based on trigonometric kernel functions.

Tylototriton shanorum, an endemic species of Myanmar, is threatened by illegal capture and environmental destruction. Here, the complete mitochondrial genome (mitogenome) of T. shanorum is described. The entire mitogenome sequence of T. shanorum is 17,096 bp long, containing 13 protein coding genes, two ribosomal RNA, 22 transfer RNA genes, one control region. In addition, two additional 3′ Cytb like sequences and two complete tRNAThr genes, one pseudo tRNAThr, and three noncoding sequences (NC1, NC1′ and NC2) were situated between Cytb and tRNAPro genes. The new complete mitogenome sequence of T. shanorum will be useful for conservation genetics, evolutionary biology, phylogeography, as well as phylogenetic relationships studies of this threatened species.

The Oriental Fire-bellied Newt (Cynops orientalis David) has been listed as Near Threatened species (NT) recently due to habitat destruction and degradation and illegal trade in the domestic and international pet markets. We sequenced and characterized the complete mitochondrial genome (mitogenome) of C. orientalis in this paper. The complete mitogenome sequence of C. orientalis is 16,294 bp in length, containing 37 genes (13 protein coding genes, two ribosomal RNA, 22 transfer RNA genes and one control region). The new sequenced complete mitogenome of C. orientalis will provide useful information for application in conservation genetics and evolution for this near threatened species.

The critically endangered western black-crested gibbon (Nomascus concolor) is distributed in isolated habitat fragments in northern Vietnam, northwestern Laos, and southwestern China. To assess the behavioral adaptation of this species to forest fragments and its response to seasonal variation in food availability and climate, we present activity patterns of a group inhabiting an isolated forest based on two year-long studies in southern Yunnan, China. Annually, the gibbons spent nearly half of their active time resting, followed by moving and feeding. In both study periods, the time allocated to activities varied significantly between months, and was affected by food availability and climate factors. The group delayed retirement when tree fruit was abundant, and they decreased time spent moving and playing during periods of low fruit availability. In the cold months, the gibbons decreased time spent moving, and they decreased active time and resting time when rainfall was high. The results suggest that the group may seek to maximize net energy intake like energy maximizers when high quality food is most available, and adopt an energy-conserving strategy during periods of lower food availability and temperature. The gibbons showed similar diurnal variation in activity patterns to a group inhabiting a continuous forest at Dazhaizi, Mt. Wuliang, central Yunnan. However, they had a longer active period, and devoted more time to resting but less time to feeding. The individuals also spent lower percentages of time engaged in social behavior than those at Dazhaizi. These differences may be due to their smaller home range and unusual group composition caused by habitat fragmentation.

In this paper, we present a large-update primal-dual interior-point method for symmetric cone optimization (SCO) based on a new kernel function, which determines both search directions and the proximity measure between the iterate and the center path. The kernel function is neither a self-regular function nor the usual logarithmic kernel function. Besides, by using Euclidean Jordan algebraic techniques, we achieve the favorable iteration complexity $O(\sqrt r (\log r)^2 \log (r/\varepsilon ))$ , which is as good as the convex quadratic semi-definite optimization analogue.

Nycticebus pygmaeus has been listed as vulnerable by IUCN due to habitat destruction and hunting for traditional medicine and trade. Identifying the species and sources in markets is important for resource conservation and trade controls. In this study, we sequenced and characterized the complete mitochondrial genome of N. pygmaeus. The entire mtDNA of N. pygmaeus, 16,856 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and one control region, was similar to those of other Nycticebus in gene arrangement and composition. This work contributes to providing basic molecular data which is critical for further genetic research and conservation of this vulnerable species.

This paper proposes a new infeasible interior-point algorithm with full-Newton steps for P *(κ) linear complementarity problem (LCP), which is an extension of the work by Roos (SIAM J. Optim., 2006, 16(4): 1110–1136). The main iteration consists of a feasibility step and several centrality steps. The authors introduce a specific kernel function instead of the classic logarithmical barrier function to induce the feasibility step, so the analysis of the feasibility step is different from that of Roos’s. This kernel function has a finite value on the boundary. The result of iteration complexity coincides with the currently known best one for infeasible interior-point methods for P *(κ) LCP. Some numerical results are reported as well.

We report the sequencing at 131× coverage, de novo assembly and analyses of the genome of a female Tibetan wild boar. We also resequenced the whole genomes of 30 Tibetan wild boars from six major distributed locations and 18 geographically related pigs in China. We characterized genetic diversity, population structure and patterns of evolution. We searched for genomic regions under selection, which includes genes that are involved in hypoxia, olfaction, energy metabolism and drug response. Comparing the genome of Tibetan wild boar with those of neighboring Chinese domestic pigs further showed the impact of thousands of years of artificial selection and different signatures of selection in wild boar and domestic pig. We also report genetic adaptations in Tibetan wild boar that are associated with high altitudes and characterize the genetic basis of increased salivation in domestic pig.

The molecular evidence of phylogenetic status regarding the Formosan serow (Capricornis swinhoei) is not robust and little is known about the genetic diversity of the Sumatran serow (Capricornis sumatraensis), which partly is due to the hardness in sample collection. Here we determined the sequences of the complete mitochondrial DNA control region (1,014 bp) of 19 Sumatran-serow individuals. Nine new haplotypes were defined based on 78 variable sites. Combined analysis with other 32 haplotypes downloaded from the public database, including 1 Sumatran-serow, 11 Formosan-serow and 20 Japanese-serow (Capricornis crispus) haplotypes, a relatively high level of nucleotide diversity was first observed in Sumatran serow (π = 0.0249). By comparative analysis with structural consensus sequences from other mammals, we have identified central, left and right domains and depicted the putative functional structure, including extend termination associated sequences and conserve sequence blocks, in mtDNA control region. The alignment of mtDNA control region revealed that both Sumatran and Japanese serow have two tandem repeats (TRs), but three TRs in Formosan serow. Phylogenetic analyses revealed that the Formosan serow is distinct species with the Japanese serow, but a sister group with the Sumatran serow. The divergence time estimated among three serow species revealed that Pleistocene climate changes and the uplift of Qinghai-Tibetan plateau might play an important role in the genetic differentiation of the serows. These results mainly provide the convinced evidence on the genetic relationship between three serow species.

Tibetan macaque (Macaca thibetana), an endangered species endemic to China, is categorized as a Category II species under the Chinese Wild Animal Protection Law and listed in Appendix II of the Convention on International Trade in Endangered Species. To further assess genetic diversity and population structure within this species, we sequenced 477 bp of mitochondrial DNA control region in 30 Tibetan macaques from the Guizhou (GZ) and Yunnan (YN) of China and conducted population genetic analysis, along with 15 previously described haplotype sequences representing 55 individuals from Sichuan (SC) and Anhui (AH). 87 polymorphic sites were detected in the alignment of 45 sequences and defined 22 haplotypes, of which 9 were newly identified. Haplotype diversity (h), nucleotide diversity (π) and average number of nucleotide differences (K) is 0.911 ± 0.015, 0.06090 ± 0.00126 and 28.32, respectively, indicating higher genetic diversity in the whole Tibetan macaque population. Analysis of molecular variance (AMOVA) partitioned the total variation into 83.63 % among populations and 16.37 % within populations, revealing that variations occured among populations mainly. Further analysis demonstrated that significant genetic differentiation (Fst = 0.83628, P < 0.01) and poor gene flow (Nm < 1) had occurred among these four populations. On the phylogenetic tree and haplotype network plot, 22 haplotypes cluster together according to their geographical origins, exhibiting an obvious phylogeographic pattern. We speculate that the significant genetic differentiation among these macaque populations might result from long-term geographic barrier and human activity. In particular, Yangtze River probably play a vital role in population differentiation of Tibetan macaques.

Mehrotra-type predictor-corrector algorithm is one of the most effective primal-dual interiorpoint methods. This paper presents an extension of the recent variant of second order Mehrotra-type predictor-corrector algorithm that was proposed by Salahi, et al. (2006) for linear optimization. Based on the NT direction as Newton search direction, it is shown that the iteration-complexity bound of the algorithm for semidefinite optimization is {ie1108-1}, which is similar to that of the corresponding algorithm for linear optimization.

In this paper, we design a primal-dual interior-point algorithm for linear optimization. Search directions and proximity function are proposed based on a new kernel function which includes neither growth term nor barrier term. Iteration bounds both for large- and small-update methods are derived, namely, O(nlog(n/ɛ)) and \(O(\sqrt n \log (n/\varepsilon ))\). This new kernel function has simple algebraic expression and the proximity function has not been used before. Analogous to the classical logarithmic kernel function, our complexity analysis is easier than the other primal-dual interior-point methods based on logarithmic barrier functions and recent kernel functions.