Long read genome assemblies complemented by single cell RNA-sequencing reveal genetic and cellular mechanisms underlying the adaptive evolution of yak.

Wild yak (Bos mutus) and domestic yak (Bos grunniens) are adapted to high altitude environment and have ecological, economic, and cultural significances on the Qinghai-Tibetan Plateau (QTP). Currently, the genetic and cellular bases underlying adaptations of yak to extreme conditions remains elusive. In the present study, we assembled two chromosome-level genomes, one each for wild yak and domestic yak, and screened structural variants (SVs) through the long-read data of yak and taurine cattle. The results revealed that 6733 genes contained high-FST SVs. 127 genes carrying special type of SVs were differentially expressed in lungs of the taurine cattle and yak. We then constructed the first single-cell gene expression atlas of yak and taurine cattle lung tissues and identified a yak-specific endothelial cell subtype. By integrating SVs and single-cell transcriptome data, we revealed that the endothelial cells expressed the highest proportion of marker genes carrying high-FST SVs in taurine cattle lungs. Furthermore, we identified pathways which were related to the medial thickness and formation of elastic fibers in yak lungs. These findings provide new insights into the high-altitude adaptation of yak and have important implications for understanding the physiological and pathological responses of large mammals and humans to hypoxia.

The CXCL12-CXCR4 signaling promotes oocyte maturation by regulating cumulus expansion in sheep.

Gonadotropins and growth factors synergistically regulate folliculogenesis and oocyte development. C-X-C motif chemokine 12 (CXCL12) and its receptor CXCR4 are expressed in ovaries of sheep, cattle and other species, however, roles of this multifunctional signal axis in oocyte maturation are not defined. Using sheep as a model, we examined the expression patterns and functions of the CXCL12-CXCR4 axis during oocyte maturation. CXCL12 and CXCR4 mRNA and protein were present in oocytes and granulosa cells. Relative abundance of CXCR4 transcript was controlled by epidermal growth factor (EGF). Transient inhibition of CXCR4 suppressed oocyte nuclear maturation while supplementing recombination CXCL12 significantly increased percent of oocyte undergone metaphase I phase. Inhibition of CXCR4 function decreased cumulus expansion growth rate. Furthermore, granulosa cell migration was impaired and expression of hyaluronan synthase 2 (HAS2) and hyaluronan binding protein tumor necrosis factor-alpha-induced protein 6 (TNFAIP6) were downregulated by CXCR4 inhibition. These findings revealed a novel role of the CXCL12-CXCR4 signaling in oocyte development in sheep.

[Effect of Naoshuantong capsule on change of SSQOL index in patients with ischemic stroke in six mouths follow-up].

To evaluate the effect of Naoshuantong capsule on the life quality of patients with ischemic stroke in six months of follow-up studies, and observe the adverse events. The results would provide reference for the secondary prevention on the recovery stage of ischemic stroke. 696 patients from 12 Class III Grade I hospitals nationwide were divided into 2 groups by central randomization system. The study group, 344 cases, were treated with Naoshuantong capsule plus Aspirin, and the control group, 352 cases, were treated with Aspirin. The patients were treated for 6 months. At the end of treatment, SS-QOL used for evaluating the quality of life was observed. The safety index was defined by adverse observation event. The incidence of adverse events and laboratory tests results were observed before and after treatment at the same time. The results indicated that compared to the control group, the treatment group had significant statistical difference in the impact of effort, self-care ability and the the work or labor ability of patients (P < 0.05). No serious adverse events were observed. Naoshuantong capsule showed some superiority to Asprin on improving the quality of life on patients with ischemic stroke, and it could be used in secondary prevention on the recovery stage of ischemic stroke. Naoshuantong capsule is safe and effective in the treatment of convalescence ischemic stroke.

[Adaptation of vigilance behavior in ex situ conservation of Tibetan antelope].

Tibetan antelope (Pantholops hodgsoni) are an endemic and endangered species of the Tibetan Plateau. Ex situ conservation may represent an important way to protect Tibetan antelope; however, this process may influence aspects of their behavior. To investigate the ability of these antelopes to adapt to new environments, a study on the vigilance behavior of captive antelope in different seasons was conducted. Using instantaneous scan sampling, focal animal sampling, and all-occurrence recording methods, the vigilance rate and vigilance time of captive male and female Tibetan antelope during cold and warm seasons were recorded and analyzed. Very significant sex differences in vigilance behavior were observed during the warm season, but were not observed in the cold season. Interestingly, vigilance behavior showed seasonal variation as there were significant differences in vigilance time and vigilance rate between cold and warm seasons in both males and females. Specifically, males and females showed more vigilance during the cold than warm season. No interaction between season and sex was found in the vigilance behavior of antelope. Comparing vigilance behavioral characteristic with the Kekexili Tibetan antelope indicated that captive antelope could adapt to a new environment.

Functional evolution of leptin of Ochotona curzoniae in adaptive thermogenesis driven by cold environmental stress.

BACKGROUND: Environmental stress can accelerate the directional selection and evolutionary rate of specific stress-response proteins to bring about new or altered functions, enhancing an organism's fitness to challenging environments. Plateau pika (Ochotona curzoniae), an endemic and keystone species on Qinghai-Tibetan Plateau, is a high hypoxia and low temperature tolerant mammal with high resting metabolic rate and non-shivering thermogenesis to cope in this harsh plateau environment. Leptin is a key hormone related to how these animals regulate energy homeostasis. Previous molecular evolutionary analysis helped to generate the hypothesis that adaptive evolution of plateau pika leptin may be driven by cold stress. METHODOLOGY/PRINCIPAL FINDINGS: To test the hypothesis, recombinant pika leptin was first purified. The thermogenic characteristics of C57BL/6J mice injected with pika leptin under warm (23±1°C) and cold (5±1°C) acclimation is investigated. Expression levels of genes regulating adaptive thermogenesis in brown adipose tissue and the hypothalamus are compared between pika leptin and human leptin treatment, suggesting that pika leptin has adaptively and functionally evolved. Our results show that pika leptin regulates energy homeostasis via reduced food intake and increased energy expenditure under both warm and cold conditions. Compared with human leptin, pika leptin demonstrates a superior induced capacity for adaptive thermogenesis, which is reflected in a more enhanced ß-oxidation, mitochondrial biogenesis and heat production. Moreover, leptin treatment combined with cold stimulation has a significant synergistic effect on adaptive thermogenesis, more so than is observed with a single cold exposure or single leptin treatment. CONCLUSIONS/SIGNIFICANCE: These findings support the hypothesis that cold stress has driven the functional evolution of plateau pika leptin as an ecological adaptation to the Qinghai-Tibetan Plateau.

[Impacts of uncertainty in data processing on estimation of CO2 flux components].

Based on the eddy covariance observations at 4 sites (2 forested sites and 2 grassland sites) in Chinese Terrestrial Ecosystem Flux Research Network (ChinaFLUX), this paper analyzed the effects of three data processing methods, i.e., spike detection, threshold (u*c) determination of nocturnal friction velocity (u*), and gap-filling model selection, on the estimation of CO2 flux components. All the three methods had significant impacts on the estimation of annual net ecosystem exchange (NEE), and the determination of (u*c) was an important factor affecting the annual NEE estimation. The estimation deviation of the annual NEE caused by spike detection, determination of (u*c), and gap-filling model selection was 0.62-21.31 g C x m(-2) x a(-1) (0.84%-65.31%), 4.06-30.28 g C x m(-2) x a(-1) (3.76%-21.58%), and 0.69-27.73 g C x m(-2) x a(-1) (0.23%-55.62%), respectively. Comparing with that of forested ecosystem, the NEE estimation of grassland ecosystem was more sensitive to the parameter setting of data processing method, and the relative estimation deviation of annual gross ecosystem exchange and ecosystem respiration induced by the uncertainty in data processing was 3.88%-11.41% and 6.45%-24.91%, respectively.

The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake.

Although new empirical evidence shows that sympatric speciation has occurred in some species, there are few indisputable model organisms for this process of speciation. The two subspecies (Gymnocypris eckloni eckloni and G. e. scoliostomus) of the schizothoracine Gymnocypris fish species complex from a small glacier lake in the Tibetan Plateau, Lake Sunmcuo, fit several of the key characteristics of the sympatric speciation model. We used combined mitochondrial control region sequences and the cytochrome b gene (1894 bp) to address the phylogenetics and population genetics of 232 specimens of G. e. eckloni and G. e. scoliostomus, as well as all of its closely related sister species. We found that: (i) a total of four old lineages were uncovered in the widespread G. e. eckloni, of which only one was shown to be shared with all G. e. scoliostomus individuals and (ii) the new subspecies (G. e. scoliostomus) evolved in Lake Sunmcuo from the ancestral G. e. eckloni population within approximately 0.057 Ma. These two taxa of the species complex are morphologically distinct, and reproductive isolation is further suggested. Ecological disruptive selection based on morphological traits (e.g. mouth cleft characters) and food utilization may be a mechanism of incipient speciation of two sympatric populations within Lake Sunmcuo. This study provides the first genetic evidence for sympatric speciation in the schizothoracine fish.

The protein level of hypoxia-inducible factor-1alpha is increased in the plateau pika (Ochotona curzoniae) inhabiting high altitudes.

The plateau pika (Ochotona curzoniae) is a high hypoxia-tolerant species living only at 3,000-5,000 m above sea-level on the Qinghai-Tibetan plateau. Hypoxia-inducible factor-1 (HIF-1) is a key transcription factor that regulates a variety of cellular and systemic adaptations to hypoxia. To investigate how the plateau pika adapts to a high-altitude hypoxic environment at the molecular level, we examined the expression pattern of the HIF-1alpha protein in the pika by Western blot and immunohistochemical analysis. We found that HIF-1alpha protein is expressed at a significantly high level in the pika, which is higher in most tissues (particularly in the lung, liver, spleen and kidney) of the plateau pika than that of mice living at sea-level. Importantly, we found that the protein levels of HIF-1alpha in the lung, liver, spleen and kidney of the pika were increased with increased habitat altitudes. We observed that the plateau pika HIF-1alpha localized to the nucleus of cells by an immunostaining analysis, and enhanced HRE-driven gene expression by luciferase reporter assays. Our study suggests that the HIF-1alpha protein levels are related to the adaptation of the plateau pika to the high-altitude hypoxic environment.

Effect of graded levels of rapeseed oil in isonitrogenous diets on the development of the gastrointestinal tract, and utilisation of protein, fat and energy in broiler chickens.

The effect of feeding 0, 4, 8 and 16% rapeseed oil from 12-42 days of age was studied in broiler chickens on performance, digestibility of nutrients, and development of gastrointestinal tract, protein and energy metabolism. Thirty six female chickens (Ross 208) with initial body weight average 246 g were allocated to the four groups and kept pair-wise in metabolism cages. The chickens were fed similar amounts of metabolisable energy (ME) per day and similar amounts of essential amino acids relative to ME by adjusting with crystalline amino acids. The chickens were subjected to four balance periods each of five days with two 24 h measurements of gas exchange in two open-air-circuit respiration chambers inserted on the second and third day of each period. The addition of rapeseed oil increased the amount of gutfill indicating a reduced rate of passage and causing a hypertrophy of the gastrointestinal tract. There was a positive effect on feed utilisation as well as on digestibility especially of dietary fat together with higher utilisation of protein with addition of rapeseed oil. The partial fat digestibility of rapeseed oil estimated by regression was 91.1% and the partial metabolisability (ME/GE) of the rapeseed oil was estimated to 85% yielding an apparent metabolisable energy value of 34.30 MJ/kg.

Natural selection and adaptive evolution of leptin in the ochotona family driven by the cold environmental stress.

BACKGROUND: Environmental stress can accelerate the evolutionary rate of specific stress-response proteins and create new functions specialized for different environments, enhancing an organism's fitness to stressful environments. Pikas (order Lagomorpha), endemic, non-hibernating mammals in the modern Holarctic Region, live in cold regions at either high altitudes or high latitudes and have a maximum distribution of species diversification confined to the Qinghai-Tibet Plateau. Variations in energy metabolism are remarkable for them living in cold environments. Leptin, an adipocyte-derived hormone, plays important roles in energy homeostasis. METHODOLOGY/PRINCIPAL FINDINGS: To examine the extent of leptin variations within the Ochotona family, we cloned the entire coding sequence of pika leptin from 6 species in two regions (Qinghai-Tibet Plateau and Inner Mongolia steppe in China) and the leptin sequences of plateau pikas (O. curzonia) from different altitudes on Qinghai-Tibet Plateau. We carried out both DNA and amino acid sequence analyses in molecular evolution and compared modeled spatial structures. Our results show that positive selection (PS) acts on pika leptin, while nine PS sites located within the functionally significant segment 85-119 of leptin and one unique motif appeared only in pika lineages-the ATP synthase alpha and beta subunit signature site. To reveal the environmental factors affecting sequence evolution of pika leptin, relative rate test was performed in pikas from different altitudes. Stepwise multiple regression shows that temperature is significantly and negatively correlated with the rates of non-synonymous substitution (Ka) and amino acid substitution (Aa), whereas altitude does not significantly affect synonymous substitution (Ks), Ka and Aa. CONCLUSIONS/SIGNIFICANCE: Our findings support the viewpoint that adaptive evolution may occur in pika leptin, which may play important roles in pikas' ecological adaptation to extreme environmental stress. We speculate that cold, and probably not hypoxia, may be the primary environmental factor for driving adaptive evolution of pika leptin.

Experimental warming, not grazing, decreases rangeland quality on the Tibetan Plateau.

We investigated experimental warming and simulated grazing (clipping) effects on rangeland quality, as indicated by vegetation production and nutritive quality, in winter-grazed meadows and summer-grazed shrublands on the Tibetan Plateau, a rangeland system experiencing climatic and pastoral land use changes. Warming decreased total aboveground net primary productivity (ANPP) by 40 g x m(-2) x yr(-1) at the meadow habitats and decreased palatable ANPP (total ANPP minus non-palatable forb ANPP) by 10 g x m(-2) x yr(-1) at both habitats. The decreased production of the medicinal forb Gentiana straminea and the increased production of the non-palatable forb Stellera chamaejasme with warming also reduced rangeland quality. At the shrubland habitats, warming resulted in less digestible shrubs, whose foliage contains 25% digestible dry matter (DDM), replacing more digestible graminoids, whose foliage contains 60% DDM. This shift from graminoids to shrubs not only results in lower-quality forage, but could also have important consequences for future domestic herd composition. Although warming extended the growing season in non-clipped plots, the reduced rangeland quality due to decreased vegetative production and nutritive quality will likely overwhelm the improved rangeland quality associated with an extended growing season. Grazing maintained or improved rangeland quality by increasing total ANPP by 20-40 g x m(-2) x yr(-1) with no effect on palatable ANPP. Grazing effects on forage nutritive quality, as measured by foliar nitrogen and carbon content and by shifts in plant group ANPP, resulted in improved forage quality. Grazing extended the growing season at both habitats, and it advanced the growing season at the meadows. Synergistic interactions between warming and grazing were present, such that grazing mediated the warming-induced declines in vegetation production and nutritive quality. Moreover, combined treatment effects were nonadditive, suggesting that we cannot predict the combined effect of global changes and human activities from single-factor studies. Our findings suggest that the rangelands on the Tibetan Plateau, and the pastoralists who depend on them, may be vulnerable to future climate changes. Grazing can mitigate the negative warming effects on rangeland quality. For example, grazing management may be an important tool to keep warming-induced shrub expansion in check. Moreover, flexible and opportunistic grazing management will be required in a warmer future.