Phylogenetic Analysis of Brine Shrimp （Artemia） in China Using DNA Barcodinge

DNA barcoding is a powerful approach for characterizing species of organisms, especially those with almost identical morphological features, thereby helping to to establish phylogenetic relationships and reveal evolutionary histories. In this study, we chose a 648-bp segment of the mitochondrial gene, cytochrome c oxidase subunit 1 （COI）, as a standard barcode region to establish phylogenetic relationships among brine shrimp （Artemia） species from major habitats around the world and further focused on the biodiversity of Artemia species in China, especially in the Tibetan Plateau. Samples from five major salt lakes of the Tibetan Plateau located at altitudes over 4,000 m showed clear differences from other Artemia populations in China. We also observed two consistent amino acid changes, 153A/V and 183L/F, in the COI gene between the high and low altitude species in China. Moreover, indels in the COI sequence were identified in cyst and adult samples unique to the Co Qen population from the Tibetan Plateau, demonstrating the need for additional investigations of the mitochondrial genome among Tibetan Artemia populations.     

NEW SPECIES AND NEW CHINESE RECORDS OF CALLIONYMID FISHES FROM THE SOUTH CHINA SEA

In the present paper, 3 new species and one new Chinese record of callionymidfishes, from the South China Sea are described, and the keys to the Chinese species ofCallionymus and Calliurichthys are given for reference (in Chinese). All the specimensare deposited in the Institute of Zoology, Academia Sinica, Peking.     

Phylogeographic studies of plants in China: Advances in the past and directions in the future

<正>Phylogeography has been one major focus of evolutionary biology in recent years,with many important advances in Chinese species.In this issue,we collected 11 phylogeographic studies of plants by Chinese laboratories. We further synthesized the main findings and patterns emerging from these and previous phylogeographic studies in China and asked where phylogeographic research should be directed in the coming years.Numerous examples have shown that phylogeographic patterns in China did not show an expected expansion-contraction pattern at large scale, mirroring the geological records showing that no unified ice sheet had developed in China during the Quaternary Period.Instead,regional expansions and intraspecific divergences are very common in most studied species during the Quaternary oscillations.Different intraspecific lineages or alleles(haplotypes) were detected in multiple localized refugia,from where regional or local expansions are likely to have started.Hybridizations and introgressions are frequent between intraspecific lineages or between different species.We also reviewed computational methods for phylogeographic analyses.Despite the great progress made in recent years,there remains much to discover about the spatial-temporal dimensions and underlying speciation mechanisms of Chinese plants.Phylogeographic studies represent a key knot that connects the genus phylogeny(macroevolution) and speciation and adaptation (microevolution).Therefore,we advocate that:(i) phylogeographic studies of plants in China should be directed to the closely related species or a monophyletic group(for example,a genus or a section) in the coming years;and (ii) population genetic data based on direct sequencing multiple loci,especially those from nuclear genome and statistical tests should be widely adopted and enforced.The recovered intraspecific divergences and phylogeographic patterns of multiple-species may allow us to better understand the high plant diversity in China and set up concrete hypotheses for studying plant speciation and diversification mechanisms in this region.     

Shu-szi Sin:A Chinese pioneer biologist,ancient agronomist,and educator

Shu-szi Sin(辛树帜,1894-1977)(Fig.1),a Chinese pioneer biologist and ancient agronomist,initiated the earliest sci-entific biological investigation of the Dayao mountain in both Guangxi and Guangdong provinces,discovering more than 20 new species that have been acknowledged internation-ally.He was one of the founders and initiators of the China Botanical Society and the China Zoological Society.Mr.Sin was also a great educator.Among one of those who first introduced the scientific method into agricultural history research,Mr.Sin helped to set up the National Northwest Agriculture and Forestry College(now Northwest A&F University)and the Lanzhou University.He devoted himself to the development of higher education in Northwest China.     

LYSTROSAURS OF XINJIANG, CHINA

<正> Since the first report on Chinese lystrosaurs made by Yuan and Young in 1934, abundant material has been collected from the Early Triassic of Jiuchaiyuan Formation of Jimusar (Fuyuan), Junggar basin and Taoshuyuan, Turpan basin. Up to now 7 species of Lystrosaurus——L. broomi, L. hedini, L. weidcnreichi, L. youngi, L. robustus, L. latifrons and L. shichanggouensis, have been erected in China. All the species were described based on almost complete skulls, except L. weidenreichi, which was on some materials of postcranial skeleton. It was thought generally that L. broomi and L. youngi are closely related to the South African L. murrayi and L. curvatus respectively. Furthermore, the two Chinese species were considered as synonymous with their counterparts of South Africa by Colbert in 1974, when he revised this genus. The characters of the Chinese lystrosaurs, however, appeared to give no support to Colbert's suggestion. A comprehensive study of the Chinese lystrosaurs based on the type specimens and the additional materials, and the revised diagnoses. for 4 species are given in the present paper.     

Heat shock response and mammal adaptation to high elevation (hypoxia)

The mammal's high elevation(hypoxia) adaptation was studied by using the immu-nological and the molecular biological methods to understand the significance of Hsp(hypoxia) ad-aptation in the organic high elevation,through the mammal heat shock response.(1) From high ele-vation to low elevation(natural hypoxia) :Western blot and conventional RT-PCR and real-time fluo-rescence quota PCR were adopted.Expression difference of heat shock protein of 70(Hsp70) and natural expression of brain tissue of Hsp70 gene was determined in the cardiac muscle tissue among the different elevation mammals(yak) .(2) From low elevation to high elevation(hypoxia induction) :The mammals(domestic rabbits) from the low elevation were sent directly to the areas with different high elevations like 2300,3300 and 5000 m above sea level to be raised for a period of 3 weeks be-fore being slaughtered and the genetic inductive expression of the brain tissue of Hsp70 was deter-mined with RT-PCR.The result indicated that all of the mammals at different elevations possessed their heat shock response gene.Hsp70 of the high elevation mammal rose abruptly under stress and might be induced to come into being by high elevation(hypoxia) .The speedy synthesis of Hsp70 in the process of heat shock response is suitable to maintain the cells' normal physiological functions under stress.The Hsp70 has its threshold value.The altitude of 5000 m above sea level is the best condition for the heat shock response,and it starts to reduce when the altitude is over 6000 m above sea level.The Hsp70 production quantity and the cell hypoxia bearing capacity have their direct ratio.     

A genetic adaptive pattern＊low hemoglobin concentration in the himalayan highlanders

Mean hemoglobin （Hb） concentration of about 3 500 subjects derived from 17 studies of Himalayan highlanders （Tibetans, Sherpas, and Ladakhis） was compared with lowlanders （Chinese Han, Indian Tamils） lived in the Himalayas, and European climbers during Everest expeditions as well as Andean natives. The results found that Hb concentration in Himalayan highlanders was systemically lower than those reported for Andean natives and lowland immigrants. These comparative data demonstrated that a healthy native population may successfully reside at high altitude without a significant elevation in Hb, and the lower Hb levels of Himalayan highlanders than those of migrated lowlanders and Andean natives are an example of favourable adaptation over the generations. In addition, excessive polycythemia has frequently been used as a marker of chronic mountain sickness （CMS）. Altitude populations who have a higher Hb concentration also have a higher incidence of CMS. The low Hb in Himalayans suggested as showing adaptation over many generations in Tibetan stock. Recent work in Tibet, suggested that Tibetans there may have adapted to high altitude as a result of evolutionary pressure selecting for genes which give an advantage at altitude. All of the population genomic and statistical analysis indicated that EPAS1 and EGLN1 are mostly likely responsible for high altitude adaptation and closely related to low Hb concentration in Tibetans. These data supported the hypothesis that Himalayan highlanders have evolved a genetically different erythropoietic response to chronic hypoxia by virtue of their much longer exposure to high altitude.     

Plant community complexity in the arid valley of Minjiang River, southwestern China

Biocomplexity theory is becoming increasingly important in understanding natural vegetation dynamics and interrelation among all components of the ecosystem. In this study, based on the field investigation of plant species and environmental factors (altitude, microtopography, soil water content, and soil nutrients) in an arid valley of the upper reaches of Minjiang River, Sichuan Province, southwestern China, plant community complexity and its relationship with environmental factors, community diversity, species evenness and richness were studied. Both total and structural complexities of the communities showed a “high- low-high” tendency with the increase in altitude of the area, which meant that the complexity of communities was the highest at the sites of low and high altitude, whereas it was the lowest at the sites of intermediate altitude. It was found that the total community complexity had significant quadratic correlations with soil organic matter (SOM) content, total nitrogen (N), hydrolyzable N, soil water content, and available potassium (K), whereas it had no significant correlations with soil total K, total phosphorus (P), available P, and pH value. The total community complexity positively correlated with community diversity, species evenness and species richness, whereas the structural complexity negatively correlated with the community evenness. Of the two components of the total community complexity, namely, the structural complexity and the structural diversity, the structural complexity was more sensitive than the structural diversity to the changes of species in the community, which was not only related to the community evenness but also to the community richness. The relative contribution of both the structural complexity and the structural diversity to the total complexity would be different for different study areas or ecosystems.     

Plant community complexity in the arid valley of Minjiang River, southwestern China

Biocomplexity theory is becoming increasingly important in understanding natural vegetation dynamics and interrelation among all components of the ecosystem. In this study, based on the field investigation of plant species and environmental factors (altitude, microtopography, soil water content, and soil nutrients) in an arid valley of the upper reaches of Minjiang River, Sichuan Province, southwestern China, plant community complexity and its relationship with environmental factors, community diversity, species evenness and richness were studied. Both total and structural complexities of the communities showed a “high- low-high” tendency with the increase in altitude of the area, which meant that the complexity of communities was the highest at the sites of low and high altitude, whereas it was the lowest at the sites of intermediate altitude. It was found that the total community complexity had significant quadratic correlations with soil organic matter (SOM) content, total nitrogen (N), hydrolyzable N, soil water content, and available potassium (K), whereas it had no significant correlations with soil total K, total phosphorus (P), available P, and pH value. The total community complexity positively correlated with community diversity, species evenness and species richness, whereas the structural complexity negatively correlated with the community evenness. Of the two components of the total community complexity, namely, the structural complexity and the structural diversity, the structural complexity was more sensitive than the structural diversity to the changes of species in the community, which was not only related to the community evenness but also to the community richness. The relative contribution of both the structural complexity and the structural diversity to the total complexity would be different for different study areas or ecosystems.     

中国南方海域鲎的种类和分布

The northern sea area of the South China Sea is situated between 107.5°～122.5°East longitude and 17°～25° North latitude with high temperature and a large quantity of rainfall which belongs to the oceanic climate of the torrid zone and subtropical zone. From September, 1994 to June, 1998,during the research on the species of Horseshoe crab within the scope between the south from North gulf and the north to Xiamen, choosing Xiamen, Shantou, Wuchuan, Donghaidao and Qishui as fixed positions and irregularly going to Xuwen and Suixi in Guangdong province and Fangcheng in Guangxi province, we found that there was only Tachypleus tridentatus in the northern sea area of the South China Sea and the sea area from Wuchuan to Xiamen, and found that there were two species of horseshoe crab which were Tachypleus tridentatus and Carcinoscorpius rotundicauda in the southern area to East Sea Island, referring to East Sea Island, Qishui, Xuwen, Suixi and Fangcheng, most of which were Tachypleus tridentatus, and found a great number of larvae of Tachypleus tridentatus including zooids with different sizes from 7cm bodily length to mature. In Minan we found not only big colonies of adult Carcinoscorpius rotundicauda , but also a great number of larvae of Carcinoscorpius rotundicauda with different body size from 7cm body length to maturity. All these show that the northern sea area of the South China Sea is the area where both Tachypleus tridentatus and Carcinoscorpius rotundicauda distribute and reproduce. On January 1st, 1998 at the town of Qishui in Leizhou, we found an adult male Horseshoe crab and majority of its eggs was immature, while the eggs with above 4mm diameters were only 0.87 percent but the eggs with below 1.0mm diameter was 58 percent(1 160 pills). It shows that Qishui is a place where Tachyplers tridentatus survive in the winter.     

黑麂MHC - DQA2 基因多态性

利用牛特异性扩增DQA2 第2 外显子的嵌套引物,对黑麂基因组DNA 进行PCR 扩增和克隆测序,基于该
序列设计出黑麂DQA2 基因第2 外显子特异性引物。利用该引物,通过PCR - SSCP 以及克隆测序技术,从40 个
黑麂样品中获得4 个不同的DQA2 等位基因。没有一个个体同时具有2 个以上的等位基因,所有序列均不含插入
或缺失突变,不含终止密码子,因此,本研究所扩增的DQA2 基因可能是表达的单基因座位。抗原结合区(Peptide
binding region,PBR)非同义替换率(dn)显著大于同义替换率(ds) (P <0.05),暗示该座位曾经历过明
显的正选择作用;进一步利用CODEML 程序中的相关模型以及贝叶斯法检测出4 个受选择作用的氨基酸位点
(α11、α58、α62、α66),这4 个位点均位于PBR 区。基于NJ 法构建的部分偶蹄类DQA 外显子2 系统发生关系
显示,黑麂4 个DQA2 等位基因与牛、羊以及梅花鹿的DQA2 等位基因构成独立的进化枝,在该进化枝内,黑麂
DQA2 等位基因优先与牛DQA2 等位基因聚类,暗示黑麂DQA2 基因在进化过程中存在跨物种进化现象。上述结
果表明平衡选择是维持黑麂DQA2 基因多态性的主要机制。然而,本研究从40 个样品中仅检测出2 个杂合子,
黑麂DQA2 等位基因之间的频率存在显著差异,推测可能是所检测的样品来源于不同种群,由于华伦德效应
(The Whalund effect)导致杂合度降低,也不排除本文所设计的引物在PCR 扩增过程中存在无效等位基因。     

黑麂粪便DNA提取及其PCR检测

采集了黑麂(Muntiacus crinifrons)的新鲜粪便以及在野外自然条件下保存较长时间的粪便样品,晾干后带回实验室,提取其DNA;同时提取黑麂肌肉、皮张样品的DNA,用以对比粪便样品的提取效果。电泳检测结果显示,此方法使用实验室中常用的分子生物学试剂,可以从黑麂粪便样品中抽提到高质量的粪便DNA并克服分子粪便学研究中常见的PCR反应抑制物的影响。为其它濒危鹿科动物的非损伤性取样提供了的新途径,为其遗传结构、遗传多样性现状等研究提供了更加广阔的取材空间。     

Phylogenomics of several deer species revealed by comparative chromosome painting with Chinese muntjac paints

A set of Chinese muntjac (Muntiacus reevesi) chromosome-specific paints has been hybridized onto the metaphases of sika deer (Cervus nippon, CNI, 2n = 66), red deer (Cervus elaphus, CEL, 2n = 62) and tufted deer (Elaphodus cephalophus, ECE, 2n = 47). Thirty-three homologous autosomal segments were detected in genomes of sika deer and red deer, while 31 autosomal homologous segments were delineated in genome of tufted deer. The Chinese muntjac chromosome X probe painted to the whole X chromosome, and the chromosome Y probe gave signals on the Y chromosome as well as distal region of the X chromosome of each species. Our results confirmed that exclusive Robertsonian translocations have contributed to the karyotypic evolution of sika deer and red deer. In addition to Robertsonian translocation, tandem fusions have played a more important role in the karyotypic evolution of tufted deer. Different types of chromosomal rearrangements have led to great differences in the genome organization between cervinae and muntiacinae species. Our analysis testified that six chromosomal fissions in the proposed 2n = 58 ancestral pecoran karyotype led to the formation of 2n = 70 ancestral cervid karyotype and the deer karyotypes is more derived compare with those of bovid species. Combining previous cytogenetic and molecular systematic studies, we analyzed the genome phylogeny for 11 cervid species.     

水鹿的舔盐活动模式呈现性别和季节差异

舔盐是部分植食性动物通过舔舐盐土或盐井补充体内盐分和矿物质的特殊行为,舔盐行为节律特征分析是有蹄类动物活动模式研究的重要组成内容,深入分析野生动物的特殊行为及活动模式,有利于了解其资源利用特征及生存规律。本研究利用远程视频监控系统对卧龙自然保护区天然盐井（臭水沟）进行24h监测,分析了水鹿的舔盐活动模式。结果表明：（1）在天然盐井区域的出现率,雌性水鹿高于雄性,成体高于亚成体（幼体）;（2）水鹿的舔盐频率在秋季最高,冬季最低,且水鹿的舔盐活动主要在夜晚进行,秋季到达盐井的时间（18:00）早于春夏季节（20:00）;（3）雌性水鹿在秋季具有明显的舔盐频率高峰,而雄性水鹿春、夏、秋季的舔盐频率都较高;（4）成体水鹿的舔盐高峰出现在秋季,而亚成体（幼体）的舔盐频率从春季到冬季呈现逐步递减的趋势,且舔 盐高峰时间先于成体水鹿。盐井是水鹿活动频繁的区域,在对具有舔盐习性的物种开展保护的同时应考虑对盐井等必需生境的保护。     

Evidence of higher levels of testosterone during the velvet period in muntjac than in other cervids

Previous studies have shown that despite having a clear seasonal fluctuation in fecal testosterone concentration, the significantly lower testosterone levels found in velvet stags of the nonseasonal breeder muntjac (Muntiacus sp.) apparently did not stop their spermatogenesis as in other deer species. In the present study, in vitro cultivated Leydig cells isolated from adult stags of three native deer species of Taiwan were treated with androstenedione, with or without adding human chorionic gonadotropin. Results showed that, unlike the two seasonal breeders, sika deer (Cervus nippon) and sambar deer (Rusa unicolor), Leydig cells of velvet muntjac had no dramatic reduction in or even maintained the full capability of their testosterone productivity compared with the hard-antlered stage. The decrease in fecal testosterone level observed earlier in muntjac during the velvet period was probably due to a reduction of number of Leydig cells. These results support the hypothesis that testosterone production in muntjac during its velvet period might never be low enough to trigger the quiescent phase of the reproduction cycle.     

Distribution and range expansion of deer in Ireland

• 1 Throughout Europe, the range of many deer species is expanding. We provide current distribution maps for red deer Cervus elaphus, sika Cervus nippon, fallow deer Dama dama and muntjac deer Muntiacus sp. in Ireland, and estimates of range expansion rates for red deer, sika and fallow deer.
• 2 There was a considerable expansion in the ranges of red deer, sika and fallow deer between 1978 and 2008. The compound annual rate of expansion was 7% for red deer, 5% for sika and 3% for fallow deer. The total range increase was 565% for red deer, 353% for sika and 174% for fallow deer. The potential implications of these expansions are discussed.
• 3 There are unknown numbers of red‐sika hybrid deer in some parts of Ireland. Range expansion is likely to lead to further hybridizations with implications for the genetic integrity of deer stocks.
• 4 Sightings of free‐roaming muntjac deer were first recorded in 2007. The distribution of confirmed sightings of single and multiple animals in the eastern region of Ireland suggests multiple releases.
• 5 Deer are already impacting on both the economic and biodiversity values of habitats in Ireland, where, at present, no sustainable deer management policy exists.

     

水鹿的群体结构和活动节律分析

水鹿是我国二级重点保护野生动物。2016年5月到2017年5月,利用红外相机技术在四川鞍子河自然保护区的非盐井生境和盐井生境(盐场)对水鹿的群体结构、日活动节律及舔盐活动节律进行了研究。基于设置的108个红外相机,共收集到水鹿在非盐井区域的独立照片620张,盐井区域的独立照片401张。水鹿日活动节律在不同季节具有较大差异：春季日活动高峰出现在17:00~20:00;夏季无明显日活动高峰;秋季日活动高峰出现在17:00~19:00;冬季日活动高峰分别出现在08:00~10:00、17:00~19:00、23:00~02:00。舔盐活动高峰出现在22:00~04:00,雌雄个体舔盐活动节律大致相同(重叠指数Δ=0.738)。水鹿有单独舔盐和集群舔盐两种方式,其中单独舔盐出现频率较高(占总访问频次的57.6%);舔盐的群体一般大小为2~7只,但以2只的群体居多(占总访问频次的21.5%)。在非盐井区域和盐井区域独立照片中水鹿的雌雄出现比例分别为2.05:1和2.66:1,表明雌鹿可能更需要补充盐分。本研究结果为保护区内水鹿的保护管理提供了基础的科学依据。     

New insights into the karyotypic relationships of Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis)

To investigate the karyotypic relationships between Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis), a complete set of Chinese muntjac chromosome-specific painting probes has been assigned to G-banded chromosomes of these three species. Sixteen autosomal probes (i.e. 6-10, 12-22) of the Chinese muntjac each delineated one pair of conserved segments in the forest musk deer and gayal, respectively. The remaining six autosomal probes (1-5, and 11) each delineated two to five pairs of conserved segments. In total, the 22 autosomal painting probes of Chinese muntjac delineated 33 and 34 conserved chromosomal segments in the genomes of forest musk deer and gayal, respectively. The combined analysis of comparative chromosome painting and G-band comparison reveals that most interspecific homologous segments show a high degree of conservation in G-banding patterns. Eleven chromosome fissions and five chromosome fusions differentiate the karyotypes of Chinese muntjac and forest musk deer; twelve chromosome fissions and six fusions are required to convert the Chinese muntjac karyotype to that of gayal; one chromosome fission and one fusion separate the forest musk deer and gayal. The musk deer has retained a highly conserved karyotype that closely resembles the proposed ancestral pecoran karyotype but shares none of the rearrangements characteristic for the Cervidae and Bovidae. Our results substantiate that chromosomes 1-5 and 11 of Chinese muntjac originated through exclusive centromere-to-telomere fusions of ancestral acrocentric chromosomes.     

钱江源国家公园体制试点区功能分区对黑麂保护的有效性评估

功能分区是统一协调国家公园不同保护管理目标的主要措施, 对于国家公园的有效管理有重要意义。钱江源国家公园是我国首批国家公园体制试点区之一, 被分为核心保护区、生态保育区、游憩展示区和传统利用区4个部分, 对应不同的保护管理措施。本研究分析了钱江源国家公园体制试点区现有功能分区与其首要保护对象黑麂(Muntiacus crinifrons)的适宜栖息地之间的空间关系。在红外相机调查获取的94个黑麂分布点的基础上, 结合海拔、地形、植被特征、人为活动干扰等15个环境特征变量, 采用MaxEnt模型预测国家公园内黑麂适宜栖息地的空间分布。结果表明, 黑麂倾向于出现在森林较为原始和道路密度较低的区域, 其适宜栖息地面积42.5 km ², 占国家公园总面积的16.9%。其中, 69.3%的黑麂适宜栖息地位于核心保护区, 30.4%位于生态保育区, 表明国家公园现有功能分区能很好地满足黑麂栖息地保护的需求。此结果也证明黑麂可以作为其分布范围内保存较好的亚热带森林生态系统的指示性物种。通过生境恢复、廊道建设和跨省共建促进黑麂栖息地的完整性保护, 是加强该区域黑麂栖息地保护的关键措施。     

Cervid satellite DNA and karyotypic evolution of Indian muntjac

Five satellite DNA families (designated as satellite I?CV) have been identified in the Cervidae so far. Among those, satellite I, II and IV are centromere specific. Satellite I and II are shared by large number of deer species, where satellite IV is highly conserved among several deer species examined. Satellite III was initially thought to be roe deer specific but later identified in Chinese water deer as well. SatelliteV is Y-chromosome specific for several Asian deer species examined but also found in the pericentric region of Indian muntjac chromosome 3 and in X chromosome of Chinese water deer. The observation of interstitial hybridization sites on Indian muntjac chromosomes with satellite DNA I probe generated from Chinese muntjac provides the first molecular evidence supporting the tandem fusion theory that 2n=6??/7??of Indian muntjac karyotype could derive from an ancestral Chinese muntjac-like species with 2n=46. Interspecies chromosome painting study and the maximum number of interstitial hybridization detected with satellite I and satellite II DNA probes lend support to the hypothesis that the Indian muntjac karyotype could evolve directly from an ancestral Chinese water deer-like species with 2n=70. Such hypothesis is further substantiated by the finding of satellite V signals presented in specific chromosome regions between the Chinese water deer and the Indian muntjac chromosomes.