Genetic variation and phylogenetic relationship between three serow species of the genus Capricornis based on the complete mitochondrial DNA control region sequences

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.     

Reclassification of the serows and gorals: the end of a neverending story?

相似文献   

Cross-species amplification of Bovidae microsatellites and low diversity of the endangered Korean goral

The Korean goral (Nemorhaedus caudatus) is an endangered species of wild goat. The conservation and management of this species could benefit from a better understanding of its genetic diversity and structure. Cross-species amplification of 34 Bovidae microsatellite loci was tested on a panel of 6 Korean gorals and 10 domestic goats. After polymerase chain reaction (PCR) optimization, 29 (85.3%) microsatellite loci amplified successfully for the Korean gorals and 27 (79.4%) for the domestic goats. Of the amplified products, 16 (55.2%) were polymorphic in the Korean goral and 22 (81.5%) in domestic goats. Nei's unbiased mean heterozygosity and mean allele number per locus were, respectively, 0.356 and 2.6 in the Korean goral and 0.636 and 4.8 in domestic goats. Low genetic diversity in the Korean gorals observed in this preliminary microsatellite survey suggests an urgent need for further detailed study of genetic diversity in Korean goral populations and a population management strategy based on these studies. Current results of cross-species amplification of domestic Bovidae microsatellites could be employed for the necessary population genetic studies on the Korean goral and other endangered Caprinae species.     

韩国青羊分布的变化

Amur goral(Nemorhaedus caudatus)is a rare species among Asian mammals. It is listed as Vulnerable in the 1996 IUCN Red List of the Threatened Animals[1], and designated as the natural monument (No. 217) in Republic of Korea[2]. This species is distributed in Northeast and Southwest of China, south of the Russian Far East and the Korean peninsula[3-5].But subspecies are different with inhabitants in China, which occur 5 species of gorals[4].     

Complete mitochondrial genome of the Himalayan serow (Capricornis thar) and its phylogenetic status within the genus Capricornis

The genus Capricornis (Caprinae, Bovidae) includes six species, i.e., Capriconis sumatraensis, Capricornis swinhoei, Capricornis crispus, Capricornis rubidus, Capricornis milneedwardsii and Capricornis thar. Based on morphological, anatomical and physiological evidence, the Himalayan serow (C. thar), which is distributed in the mountain regions of the Tibetan Plateau and adjacent areas, is generally classified as a species of the genus Capricornis. However, considering the lack of molecular phylogenetic evidence, a heated controversy still exists over the taxonomic position of the Himalayan serow. To determine the phylogenetic status of C. thar, we sequenced the complete mitochondrial genome (mtDNA) of one Himalayan serow using the polymerase chain reaction (PCR) technique. Then, we constructed a molecular phylogenetic tree of the genus Capricornis and its related species in the Caprinae subfamily based on maximum likelihood and Bayesian interference methods. The results reflect that the structural characteristics, nucleotide content and codon usage bias of the mitochondrial genome of the Himalayan serow were similar to those of other serows. A phylogenetic analysis using two rRNA genes and 12 encoded protein-coding genes indicated that C. thar is clustered within the C. milneedwardsii clade, which is a sister group of C. sumatraensis. The present study provides useful information about the evolution of the Himalayan serow, which will be essential for conservation genetic studies.     

Organization and variation of the mitochondrial DNA control region in five Caprinae species

The complete mitochondrial DNA (mtDNA) control region was analyzed from five species of the subfamily Caprinae; Naemorhedus caudatus, N. goral, Capra hircus, Capricornis swinhoei, and Capricornis crispus. Among these species, the control region ranged from 1,096 to 1,212 bp in length. Our results were compatible with the scheme of three domains (ETAS, Central, and CSB) within the control region. A + T < G + C was observed in all the domains. In the Korean gorals, of the 31 variable sites in the whole control region resulting in 15 haplotypes, 27 variable sites were in the ETAS domain. We found two to three tandem repeat in all five species examined in this study, three in N. caudatus and N. goral, two in Capra hircus and C. crispus, and one in C. swinhoei, respectively. All of these repeat units include two short sections of mirror symmetry (TACAT and ATGTA). Short mirror symmetries were well-resolved among five different species, although left domain has high substitution rates. By Kimura’s two parameter method, the genetic distances between the genera Naemorhedus and Capricornis were calculated and divergence time between Naemorhedus and Capricornis may be nearly 2Myr.     

Isolation and characterization of 15 microsatellite loci in the Korean goral (Nemorhaedus caudatus)

Microsatellites have been applied in a variety of fields, including conservation genetics. Species‐specific microsatellites are considered as more powerful genetic markers to generate an accurate genetic composition of a species itself. Accordingly, we characterized 15 polymorphic microsatellite loci from Korean goral, Nemorhaedus caudatus, one of the most endangered species in South Korea. The new markers should benefit future studies of the endangered species of other Asian gorals and their relatives for the study of genetic diversity and potential conservation management.     

四川三例疑似偶蹄目动物的分子鉴定

测定了3例来自四川崇州的疑似偶蹄目动物样本细胞色素b基因(Cytb),利用NCBI数据库中的BLAST功能对目标序列进行相似性搜索,发现与所测序列相似性高的分别为偶蹄目鹿科毛冠鹿Elaphodu scephalophus和牛科台湾鬣羚Capricornis swinhoei;联合下载四川有分布偶蹄目动物4科19种以及1条台湾鬣羚Cytb基因序列进行系统发育关系重建分析,结果显示有两例待鉴定样本(4#、5#)以置信度值100与毛冠鹿聚在一起;另一例待鉴定样本(1#)对应序列和鬣羚Capricornis milneedwardii聚在一起后与台湾鬣羚形成姊妹关系,然后以置信度值100和斑羚Naemorhedus griseus又形成姊妹关系。因此,3例疑似偶蹄目动物有2例可能为毛冠鹿,1例可能为鬣羚;在MEGA4.0软件中以Kimura2-parameter模型计算2例疑似为毛冠鹿(4#、5#)的目标序列与GenBank上毛冠鹿及赤麂Mun-tiacus muntjak、小麂Muntiacus reevesi序列间的遗传距离,发现两例疑似为毛冠鹿个体间遗传距离为0,2例疑似为毛冠鹿样本序列和下载的毛冠鹿序列间的遗传距离小(0.017),和赤麂、小麂间遗传距离大(0.119～0.120、0.116～0.119);1例疑似鬣羚(1#)的样本和下载鬣羚序列间遗传距离很小(0.006～0.009),和台湾鬣羚的遗传距离较大(0.043),和斑羚遗传距离更大(0.098)。结合四川有分布偶蹄目状况,认为3例待鉴定样本2例可能为毛冠鹿,1例可能是鬣羚。     

Species and sex identification of the Korean goral (Nemorhaedus caudatus) by molecular analysis of non-invasive samples

Korean long-tailed goral (Nemorhaedus caudatus) is one of the most endangered species in South Korea. However, detailed species distribution and sex ratio data on the elusive goral are still lacking due to difficulty of identification of the species and sex in the field. The primary aim of this study was to develop an economical PCR-RFLP method to identify species using invasive or non-invasive samples from five Korean ungulates: goral (N. caudatus), roe deer (Capreolus pygargus), feral goat (Capra hircus), water deer (Hydropotes inermis) and musk deer (Moschus moschiferus). The secondary aim was to find more efficient molecular sexing techniques that may be applied to invasive or non-invasive samples of ungulate species. We successfully utilized PCR-RFLP of partial mitochondrial cytochrome b gene (376 bp) for species identification, and sex-specific amplification of ZFX/Y and AMELX/Y genes for sexing. Three species (goral, goat and water deer) showed distinctive band patterns by using three restriction enzymes (XbaI, StuI or SspI). Three different sexing primer sets (LGL331/335 for ZFX/Y gene; SE47/48 or SE47/53 for AMELX/Y gene) produced sex-specific band patterns in goral, goat and roe deer. Our results suggest that the molecular analyses of non-invasive samples might provide us with potential tools for the further genetic and ecological study of Korean goral and related species.     

A comparison of food habits of two sympatric ruminants of Mt. Yatsugatake,central Japan: sika deer and Japanese serow

Comparison of food habits of sympatric animals provides understanding of interspecific relations. Previous studies of food habits of the two ruminants of Japan, sika deer (Cervus nippon) and Japanese serows (Capricornis crispus), have shown that sika deer are variable, and they are gazers in northern Japan, but browsers in southern Japan, whereas Japanese serows are browsers. However, these studies described the food habits of each species separately, and no study has compared the food habits of these species living in sympatry. Therefore, we examined these species on Mt. Yatsugatake, central Japan, using microhistological analyses and nutritional analyses of feces. Sasa nipponica, a dwarf bamboo, predominated in the fecal composition of sika deer, whereas both S. nipponica and dicotyledonous plants were found in the feces of Japanese serows. Crude protein levels of serow feces were higher than those of deer. The particle sizes of plant fragments in serow feces were smaller than those in deer feces, suggesting that serow fed more selectively on digestible plants than deer did. These results support the suggestions of previous studies conducted in different habitats and show that sika deer are less selective grazers, and Japanese serows are more selective browsers. Thus, food differences are likely explained by the feeding ecophysiology of the animals and not habitat differences.     

Establishment of vascular endothelial cell lines from the aortas of wild Japanese serows (Capricornis crispus)

Endothelial cell lines were established from the aortas of wild Japanese serows (Capricornis crispus) by transfection of a simian virus 40 (SV40) large T antigen gene. The cloned cell lines, designed SeET (Japanese serow endothelial-SV40T) cells, express SV40T antigen and retain cobblestone-like morphology. Although von Willbrand Factor (vWF) is expressed in the cells, the expression rate and the quantity are lower than in serow primary endothelial cells. The SeET cells exhibit positive uptake of acetylated low density lipoprotein and dose-dependent cell proliferation upon exposure to vascular endothelial growth factor. These results suggest that these SeET cells have preserved endothelial phenotypes and able to function with decreased expression of vWF. The SeET cell line will be a valuable tool for in vitro studies on the physiological properties of endothelial cells and for the propagation of viruses and parasites of Japanese serows.     

同域分布中华鬣羚与中华斑羚时空生态位特征

为了解同域分布有蹄类在环境复杂的山地森林生境中以何种方式维持种间关系以实现稳定共存,基于物种分布模型与日活动模式分析了四川省岷山、邛崃、大相岭、小相岭和凉山五大山系同域分布中华鬣羚(Capricornis milneedwardsii)与中华斑羚(Naemorhedus griseus)的时空生态位特征。结果显示:(1)在四川省五大山系,中华鬣羚的适宜栖息地面积为28006.07 km²,占研究区总面积的26.18%,其中高适宜栖息地面积为10015.90 km²,中华斑羚的适宜栖息地面积为21073.32 km²,占研究区总面积的19.71%,其中高适宜栖息地面积为8396.22 km²;(2)中华鬣羚与中华斑羚在生境因子选择上相似性高、栖息地重叠面积大,其空间生态位重叠度指数D=0.776,I=0.949,其适宜栖息地的主要重叠区域位于岷山和邛崃山系;(3)中华鬣羚与中华斑羚的日活动节律重叠指数为0.812;(4)中华鬣羚与中华斑羚属于同域分布的资源利用型竞争物种,中华鬣羚的存在会显著影响中华斑羚的日活动节律(P=0.016);二者同域分布时都会增加其昼间活动强度,并增加活动高峰期的强度及持续时间。本研究初步分析了中华鬣羚与中华斑羚的时空生态位特征,揭示了二者在空间、时间生态位上种群共存及种间竞争的耦合关系。研究有利于深入理解同域分布动物时空生态位特征、近缘物种的共存机制及种间竞争关系,为有蹄类等珍稀野生动物种群及栖息地的保护提供科学参考。     

Morphometric analyses of non-invasive fecal samples of the Korean long-tailed goral (Naemorhedus caudatus) for species and age identification

The Korean long-tailed goral (Naemorhedus caudatus) is at risk of population decline due to habitat loss and fragmentation. Therefore, it is essential to ascertain its presence and/or the identity of individuals of the goral using non-invasive fecal samples for its conservation and management. In this study, we examined the morphology of fecal samples to provide the baseline data that can be used to distinguish species and age of goral individuals. We detected a significant difference in the length-to-width ratios of feces among the five ungulate species found in Korea. Also, we detected a significant difference in the length-to-width ratios of feces of gorals depending on the age groups. To assess the accuracy of species and age identification based on the fecal morphology, we conducted a series of blind comparison between the mean length-to-width ratios of the fecal pellets and the reference mean ratio values of the fecal pellets. Using 20 fecal pellets, our results showed 73%–86% probability of correct identification of the three species (gorals, goats, and roe deer), and 83%–90% probability of correct identification of >5 year-old goral individuals. The use of fecal morphometric analyses will be useful for the studies of Korean ungulate species, particularly the endangered gorals.     

Population dynamics of japanese serow in relation to social organization and habitat conditions. I. Stability of Japanese serow density in stable habitat conditions

The density of a Japanese serow (Capricornis crispus) population, which has been in stable habitat conditions and free from hunting and predation, was investigated by direct observation of serows at Kusoudomari (336 ha), Wakinosawa village, Aomori Prefecture, Japan, during 1977–89. The vegetation, composed of mature mixed forest ofThujopsis with deciduous trees (43.2%), secondary forest of deciduous trees (23.4%) and a plantation of coniferous trees (30.0%) showed little change during the study period. The serows were counted 17 times each winter for 14 consecutive years. The serow population maintained a stable density with a mean of 12.5 individuals km⁻² (SD=1.4) ranging from 8.6 to 14.6 km⁻². The ratio of the proportion of kids (<1 year old) to serows more than 1 year old decreased, but density did not decrease during the study period. Though extremely severe winters with heavy snowfall in 1984–86 caused a decline in serow density, the density recovered within a few years. It was considered that the stability of the serow density resulted mainly from the stable food supply and the lack of human disturbance, such as forest cutting in the habitat. Stable population density for a long period is probably related to the social organization of the serow.     

Direct evidence for Toxoplasma gondii infection in a wild serow (Capricornis crispus) from mainland Japan

Toxoplasma gondii infection was studied in 41 Japanese serows ( Capricornis crispus ), a goat-antelope in mainland Japan. Blood and muscle specimens were collected from 41 subjects between 2006 and 2010. Presence of antibodies to T. gondii in the sera was examined by using the latex agglutination test (cutoff titer 1:32); 10 of 41 (24.4%) were seropositive. Toxoplasma gondii DNA was detected in muscle tissue of 1 seropositive serow using a semi-nested PCR assay for the B1 gene. A partial nucleotide sequence (220 bp) corresponding to the B1 gene of T. gondii was obtained by direct sequencing; the sequence was 99.1% identical to that of the RH strain. This study is the first report to show direct evidence for the T. gondii infection in Japanese serows.     

Molecular phylogeny and geography of Korean medaka fish (Oryzias latipes)

The phylogeny and geography of the medaka (Oryzias latipes) populations of Korea were investigated by analyzing sequence data for the mitochondrial control region. From the 41 haplotypes including 25 Korean haplotypes detected in 64 Korean specimens and data for the Japanese and Chinese populations, phylogenetic and nested clade analyses were executed to examine the phylogeny of haplogroups and the relation of the genetic architecture of the haplotypes to the historical geography of the Korean medaka fish. The analyses suggest that there are two very distinct lineages of Korean medaka, and that these result from reproductive isolation mechanisms due to geographic barriers. The southeastern lineage has experienced recent range expansion to the western region. The northwestern lineage, sister to Chinese populations, showed evidence of internal range expansion with shared haplotypes.     

Considering threats to population viability of the endangered Korean long-tailed goral (Naemorhedus caudatus) using VORTEX

Population viability analysis (PVA) has frequently been used in conservation biology to predict extinction rates for threatened or endangered species. In this study, we used VORTEX to model Korean long-tailed goral (Naemorhedus caudatus) using previously collected ecological data. We focused on modelling population extinction, mean population size and heterozygosity. The minimum viable population size was found to be at least 50 gorals for 100 years, regardless of carrying capacity. However, populations with fewer than 50 gorals could not remain successful in the model. Inbreeding depression, catastrophes and supplementation also affected patterns of population extinction, mean population size and heterozygosity. Supplementation with new individuals had the strongest effect on extinction, mean population size and heterozygosity, followed by initial population size, inbreeding, catastrophes and carrying capacity. These results suggest that a supplementation by extra goral individuals from goral proliferation facilities would be the most helpful means for the restoration programme. More Korean goral-specific information regarding demographic and habitat parameters is needed for further PVA of the species.     

秦岭地区中段死亡斑羚空间分布规律初探

In recent years, Chinese goral (Nemorhaedus griseus) carcasses were frequently found in the mid-Qinling Mountains. In order to assess the spatial distribution pattern of goral carcasses, data of the individuals from Shaanxi's Fourth Giant Panda Survey was used in this study to analyse how the gorals/goral carcasses sites were related to altitude, slope, aspect, river, and road through quantitative analyses. The results showed:(1) the correlation between the sites of goral carcasses and topographic factors was relatively significant. Goral carcasses tend to be found at relatively low altitude (1 200-2 400 m) and mild slope (6°-25°). The chi-square test also showed that the aspect of the goral carcasses sites was significantly different from the goral sites. Most of the goral carcasses were found at south-facing/half southfacing slopes. (2) The correlation between the sites of goral carcasses and the distance to river was significant. The kernel density analysis and Z-test further showed that there were significant differences between the gorals/goral carcasses sites and the distance to river. Most of the goral carcasses sites were close to river (< 100 m). (3) The correlation between the sites of goral carcasses and the distance to road was not significant. Kernel density analysis and Z-test showed that there was no significant difference between the sites of gorals/goral carcasses and the distance to road. This study proposed several suggestions about how to strengthen the protection of gorals in the future.