Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA

Clarification of the genetic structure and population history of a species can shed light on the impacts of landscapes, historical climate change and contemporary human activities and thus enables evidence‐based conservation decisions for endangered organisms. The red panda (Ailurus fulgens) is an endangered species distributing at the edge of the Qinghai‐Tibetan Plateau and is currently subject to habitat loss, fragmentation and population decline, thus representing a good model to test the influences of the above‐mentioned factors on a plateau edge species. We combined nine microsatellite loci and 551 bp of mitochondrial control region (mtDNA CR) to explore the genetic structure and demographic history of this species. A total of 123 individuals were sampled from 23 locations across five populations. High levels of genetic variation were identified for both mtDNA and microsatellites. Phylogeographic analyses indicated little geographic structure, suggesting historically wide gene flow. However, microsatellite‐based Bayesian clustering clearly identified three groups (Qionglai‐Liangshan, Xiaoxiangling and Gaoligong‐Tibet). A significant isolation‐by‐distance pattern was detected only after removing Xiaoxiangling. For mtDNA data, there was no statistical support for a historical population expansion or contraction for the whole sample or any population except Xiaoxiangling where a signal of contraction was detected. However, Bayesian simulations of population history using microsatellite data did pinpoint population declines for Qionglai, Xiaoxiangling and Gaoligong, demonstrating significant influences of human activity on demography. The unique history of the Xiaoxiangling population plays a critical role in shaping the genetic structure of this species, and large‐scale habitat loss and fragmentation is hampering gene flow among populations. The implications of our findings for the biogeography of the Qinghai‐Tibetan Plateau, subspecies classification and conservation of red pandas are discussed.     

Genetic variation in the zoo population of the red panda subspecies Ailurus fulgens fulgens

Genetic variation present in the global and regional zoo populations of the red panda is estimated by computer simulations. In this study it is demonstrated that inbreeding depression could occur on the short term in the regional populations. Migration between regional populations is recommended to ensure the future survival of the red panda in captivity. More genealogical lineages should be represented in the breeding program.     

圈养小熊猫遗传多样性与种群遗传结构分析

小熊猫是亚洲特有的珍稀濒危动物,目前受到栖息地减少、片断化和人类活动干扰等威胁。中国圈养小熊猫已经有60 多年历史,约55 个机构曾经饲养过小熊猫,现今圈养数量有400 多只,评估小熊猫圈养种群的遗传多样性和遗传结构对科学维持圈养种群和保存遗传种质资源意义重大。本研究利用19 个微卫星座位,对中国境内11 个小熊猫圈养种群的116 只个体进行了遗传多样性评估及遗传结构分析。结果显示11 个种群都具有较高的遗传多样性,平均基因丰富度3.505 ± 1.033 (北京)至4.026 ± 1.219 (冕宁),期望杂合度0.631 ± 0.225(黄山)至0.782 ±0.171 (温岭)。其中福州和无锡种群极显著偏离Hardy-Weinberg 平衡。整个圈养群体内各个种群遗传分化系数为0.055,呈显著分化,表明11 个种群遗传分化水平较高。Bayesian 遗传聚类分析将11 个种群聚为三个遗传簇,与野生种群的遗传聚类结果一致。结论:小熊猫圈养种群与野生种群相比,同样具有较高的遗传多样性。因此,圈养小熊猫遗传管理的重点不再是引进野生个体充实圈养种群,应制订科学的繁殖计划,避免近交,从而维持圈养种群的遗传多样性。     

Seasonal energy utilization in bamboo by the red panda (Ailurus fulgens)

Seasonal energy intake and digestion of bamboo by red pandas were measured in energy balance trials at the field station at an altitude of 3,100 m in Yele Natural Reserve, Mianning County of Sichuan Province, Peoples Republic of China. Two‐week trials were conducted at monthly intervals by feeding animals with only natural bamboo browse, Bashania spanostachya, from May to November 1995. Results demonstrated that energy intake, digestible energy, and digestibility differed significantly among seasons and diets. Energy digestibilities were high in summer‐autumn, intermediate in spring, and low in winter. These variations correlated positively with the nutrient contents of bamboo. The daily metabolic energy requirement measured varied from 2,603.3 kJ in the spring to 3,139.8 kJ in the summer‐autumn to 2,740.8 kJ in the winter. The results also showed that shoots were more easily digested than leaves and exhibited the highest digestibility. Restricted by the capacity of digestive tracts, red pandas poorly utilized the energy provided by bamboo as indicated by the lower energy digestibility (averaging 26.47% for leaves and 44.08% for shoots among the seasons). To fulfill their daily energy requirements, red pandas ingested a large amount of energy from bamboo leaves, which varied from 10,145.8 kJ in the spring, 12,045.1 kJ in the summer‐autumn, and 12,276.9 kJ in the winter to maximize the rate of energy intake. Zoo Biol 19:27–33, 2000. © 2000 Wiley‐Liss, Inc.     

An ARMS-based technique for sex determination of red panda (Ailurus fulgens)

Molecular sexing is a key component in the investigation of wild populations. In this study, we developed a fast, accurate and reliable amplification refractory mutation system (ARMS) technique for sex determination of red panda based on the exon 4 of the ZFX/ZFY gene. The amplicons were distinguished simply by agarose gel electrophoresis, exhibiting one fragment in females (X: 300 bp) and two in males (X: 300 bp, Y: 166 bp). Robustness of this ARMS system was confirmed by testing both 43 captive red pandas using DNA samples with known-sex and 10 wild red pandas using faecal DNA samples with unknown sex.     

Isolation and characterization of 12 novel microsatellite loci for the red panda (Ailurus fulgens)

The information on dispersal patterns and mating systems of red pandas is quite important for the understanding of the genetic diversity and divergence of this species. And microsatellite marker is an ideal tool to analyze dispersal patterns and mating systems. Thus, we describe in this paper the isolation and characterization of 12 microsatellite loci in the red panda from genomic DNA-enriched libraries. These loci were highly polymorphic with numbers of alleles per locus in 24 individuals ranging from 2 to 14, observed heterozygosity from 0.143 to 0.864 and expected heterozygosity from 0.297 to 0.872. All loci except for RP6 locus followed Hardy–Weinberg expectations. No significant linkage association was found among all these loci. The 12 novel polymorphic microsatellite loci will be of use in studying dispersal patterns and mating systems of red pandas.     

Isolation and characterization of 16 tetranucleotide microsatellite loci in the red panda (Ailurus fulgens)

A total of 15 polymorphic tetranucleotide microsatellite loci in the red panda, Ailurus fulgens, were characterized in this study. Based on evaluations of 33 red pandas, the number of observed alleles for each locus ranged from seven to 17 and the expected and observed heterozygosities were 0.412–0.897 and 0.121–0.909, respectively. The mean polymorphic information content was 0.721. These markers would greatly strengthen the utilization of microsatellite tools in genetic variation studies in red panda populations.     

Isolation and characterization of microsatellite loci for the red panda,Ailurus fulgens

We report on the isolation and characterization of 10 microsatellites in the red panda Ailurus fulgens from genomic DNA‐enriched libraries. Twenty‐one microsatellites were screened from the libraries, and 10 of the screened microsatellites were polymorphic. The number of observed alleles for each locus in 24 individuals ranged from three to 12, and the expected and observed heterozygosity was 0.60–0.90 and 0.50–1.00, respectively. These markers should prove a useful tool for the study of genetic variation in red panda in the future.     

小熊猫对同性和异性气味的行为反应

食肉目动物的复杂社会行为在种间和种群间变化较大,这种变化是动物对其生态环境的适应表现特征之一。食肉目的动物与嗅觉通讯相关的气味源有肛周腺、肛囊腺、尾下腺、会阴腺、足腺、尿液、唾液和粪便等十几种,产生的气味物质包含有个体、性别和群体的识别信息,在其繁殖调控中发     

Demographic trends in a captive population of red pandas (Ailurus fulgens)

Birth and survivorship data based upon 39 litters born over a ten-year period are examined and discussed. Reproduction in red pandas is characterized by seasonal breeding, small mean litter size, and relatively high survivorship of young, and in general follows a typical “K-selected” life-history strategy. The mean litter size was two, and the sex ratio at birth was approximately 1 male to 1.11 females. Higher male mortality in the early age classes resulted in a sex ratio in favor of females. Mortality was not correlated with age or experience of the mother but was found to be highly positively correlated with an increase in the inbreeding coefficient of the young. There was no significant difference in mortality among the different litter-size classes, and in general mortality decreased with age. Recommendations concerning future management for the study population are given.     

Russian ethnic history inferred from mitochondrial DNA diversity

With the aim of gaining insight into the genetic history of the Russians, we have studied mitochondrial DNA diversity among a number of modern Russian populations. Polymorphisms in mtDNA markers (HVS-I and restriction sites of the coding region) of populations from 14 regions within present-day European Russia were investigated. Based on analysis of the mitochondrial gene pool geographic structure, we have identified three different elements in it and a vast "intermediate" zone between them. The analysis of the genetic distances from these elements to the European ethnic groups revealed the main causes of the Russian mitochondrial gene pool differentiation. The investigation of this pattern in historic perspective showed that the structure of the mitochondrial gene pool of the present-day Russians largely conforms to the tribal structure of the medieval Slavs who laid the foundation of modern Russians. Our results indicate that the formation of the genetic diversity currently observed among Russians can be traced to the second half of the first millennium A.D., the time of the colonization of the East European Plain by the Slavic tribes. Patterns of diversity are explained by both the impact of the native population of the East European Plain and by genetic differences among the early Slavs.     

Mitochondrial phylogeography and subspecific variation in the red panda (Ailurus fulgens): implications for conservation

The red panda (Ailurus fulgens) is an endangered species and its present distribution is restricted to isolated mountain ranges in western China (Sichuan, Yunnan, and Tibet provinces) and the Himalayan Mountains chain of Nepal, India, Bhutan, and Burma. To examine the evolutionary history across its current range, and to assess the genetic divergence among current subspecies and population structure among different geographic locations, we sequenced mitochondrial DNA from the control region (CR) and cytochrome (cyt) b gene for 41 individuals in Sichuan, Yunnan, Tibet of China, and Burma. 25 CR haplotypes (10 for cyt b) were identified from 11 geographic locations. Only three haplotypes were shared among sample localities, including one among current subspecies. Nine haplotypes were shared with the study of Su et al. [Mol. Biol. Evol. 18 (2001) 1070]. CR haplotype diversity was high (0.95+/-0.02) and nucleotide diversity among all haplotypes was relatively low (0.018+/-0.009). Phylogenetic confirmed trees show a shallow pattern with very little structure or statistical robustness. The application of two coalescent-based tests for population growth allowed us to interpret this phylogeny as the result of a recent population expansion. Analysis of molecular variance and nested clade analysis failed to detect significant geographic structure in both data sets. The lack of significant differentiation between subspecies does not indicate the presence of evolutionary significant units. We suggest that the present population structure has resulted from habitat fragmentation and expansion from glacial refugia. Due to its habitat requirements it is likely that the red panda has undergone bottlenecks and population expansions several times in the recent past. The present population may exhibit a pattern reminiscent of a relatively recent population expansion.     

Ecology of the red panda Ailurus fulgens in the Wolong Reserve, China

Red panda behaviour was studied in the Wolong Reserve, Sichuan, China to understand better the ecology of this herbivorous member of the Carnivora. Leaves of montane bamboo were the most common food in all months (93.7% of 791 droppings), supplemented in spring with bamboo shoots, and in late summer with arboreal fruits. Home-range estimates by radiotelemetry for one adult female (94 ha) and one adult male (111 ha) most closely approximated allometrically-predicted range size for omnivores. Pandas were active45–49% of the time, with highest levels in April, and, for the female in summer when lactating. Activity was higher in daylight than at night, especially in summer, coincident with arboreal foraging. The hypothesis that pandas rest in direct sunlight in winter to minimize heat loss while reducing peripheral circulation, was inferentially supported by their spending significantly more time resting on clear compared to overcast winter days. The red panda's anatomy, diet and low metabolic rate suggest an arboreal folivorous lineage incorporating terrestrial foraging to capitalize on a super-abundant food resource–bamboo. Energy content of the annual recruitment of bamboo leaves within home ranges was substantially greater than annual energy requirements predicted allometrically. Gross food availability was not limiting to the radio-collared pandas, but may have been so in unoccupied habitats with a lower bamboo density following the bamboo die-back. Maternity den trees are probably a limiting resource in clearcut and deciduous forest habitats.     

Identification and characterization of ten polymorphic microsatellite loci in the red panda Ailurus fulgens

Ten polymorphic microsatellite loci were characterized from two genomic DNA-enriched libraries of the red panda (Ailurus fulgens). The number of observed alleles among 35 samples of red pandas ranged from five to 12. Observed and expected heterozygosities were 0.286–0.971 and 0.443–0.894, and the mean polymorphic information content was 0.712. All loci followed Hardy–Weinberg expectations except Aifu-14 and Aifu-16, which may due to the presence of inbreeding or null alleles. Three pairs of loci exhibited significant linkage disequilibrium after Bonferroni correction for multiple comparisons. These microsatellites would be useful to strengthen population management, genetic diversity exploration, and demographic history speculation of this species.     

Pregnancy detection from fecal progestin concentrations in the red panda (Ailures fulgens fulgens)

The reproductive physiology of red pandas (Ailures fulgens fulgens) has not been well documented. This critically endangered species is not self‐sustaining in captivity despite several breeding populations, with low reproductive success and high infant mortality being leading causes of the decline. Hormone profiles were monitored in three groups of females (mated with birth, mated no birth, and not paired) to document pregnancy and parturition. Fecal samples were analyzed for progestins using a radio‐immuno assay. Females that gave birth had significantly higher progestins during the study period compared to females that mated and did not give birth and females that were not paired with a male. Two critical time frames were detected, Weeks 7–11 and Weeks 13–20, in which pregnant females could be differentiated from the others with a 95% confidence interval (CI). Detecting pregnancy in captive red pandas may assist animal care staff in management of the females and increase the survival rate of offspring. Zoo Biol 0:1–11, 2005. © 2005 Wiley‐Liss, Inc.     

Genetic diversity and population structure of Sepiella japonica (Mollusca: Cephalopoda: Decapoda) inferred by mitochondrial DNA (COI) variations

In order to describe the genetic diversity of five geographical populations of cuttlefish (Sepiella japonica) along with Chinese coast and determined their phylogenetic relationship, partial mitochondrial COI gene (681bp in length) was amplified from 96 individuals collected from these populations and sequenced. The 5 populations of cuttlefish inhabit Yellow Sea, East China Sea and South China Sea. Out of 22 polymorphic nucleotides identified, 8 were represented by a single sequence, 12 were parsimony informative, which defined 22 haplotypes. Haplotype and nucleotide diversity were low among populations. Of 22 haplotypes, 15 appeared only in a single population, 6 appeared in 2 or 3 populations and 1 was shared by all populations. The COI gene was monomorphic in Qingdao population. The haplotypes identified clustered into 2 clades, each covered individuals from 5 populations each. Pairwise F_ST were not proportional to the geographical distances. Among the 5 populations, relatively high level of genetic diversity was found in Ningde population which was recommended to be the best choice of germplasm resources for artificial releasing project.     

Genetic diversity of Besermyans inferred from mitochondrial DNA polymorphism

The first data are presented on mtDNA diversity in Besermyans, the Finno-Ugric ethnic group related to Udmurts. An analysis of mtDNA polymorphism showed that Besermyans stood out from the other populations of Volga-Ural region due to the presence of a large proportion of the Mongoloid component. The sample of Besermyans contained East Eurasian haplotypes not detected in ethnic populations of the Volga region and Cisurals, while they were detected in South Siberia, mostly among Turkic-speaking populations. An analysis of the genetic distances between Besermyans and the neighboring ethnic groups showed that Besermyans were distant from other populations of Volga-Ural region and close to Turkic-speaking populations of South Siberia. Thus, the data obtained favor the suggestion on the mixed Udmurto-Turkic origin of Besermyans.     

紫色色杆菌感染小熊猫引起肺炎的临床调查

本文报道了福州大熊猫研究中心小熊猫感染紫色色杆菌引起肺炎的群发病例。7 只小熊猫中,出现以呼吸衰竭为主要临床症状的3 只小熊猫在发病3 d内全部死亡,病死率100% 。死亡的小熊猫解剖病变为气管内有白色泡沫样分泌物,肺有化脓性坏死并严重淤血;胸腔,心包积液且胸水浑浊;肝脏呈弥漫性空泡变性,淤血和散在局灶性坏死。通过流行病学调查,病理解剖观察,细菌分离培养和鉴定及动物回归试验,诊断为紫色色杆菌无色变种感染。根据GenBank 数据库提供的紫色色杆菌16S RNA 基因序列,设计一对引物(5’GAG CAAACA GGA TTA GAT ACC 3’;5’TTA CGG TTA CCT TGT TAC GAC 3’),获得目的基因片段739 bp,将核苷酸序列测定的结果与GenBank 数据库提供的7 株紫色色杆菌进行同源性比较。分离的菌株(FJ08A) 与CV09 株、ESBV4400株同源性均为98.8% ,与AY117554 株、EAV2 株、AJ871127 株、LMG3953 株、JS1 株同源性分别为98. 2% 、98.0% 、94.9%、93.1% 、92.8% 。依据调查结果和药物敏感试验,对其余4 只未发病的小熊猫采取肌
肉注射头孢哌酮钠和口服复方新诺明进行预防性治疗,效果良好,未有新病发生。结果表明:(1)紫色色杆菌是革兰氏阴性菌,致病性强,致死率高,腹腔注射分离的紫色色杆菌菌液导致接种小白鼠在2 ～3 d 内全部死亡。小熊猫感染后,发病迅速,致死率高,应引起重视;(2)紫色色杆菌是一种条件致病菌,外伤感染是主要致病因素。