圈养繁殖在大熊猫保护生物学中的作用

栖息地的日益恶化、片段化和种群孤岛化已成为保护大熊猫的严重障碍。尽管就地保护濒危物种是最有希望的措施,但对于大熊猫而言,研究表明圈养繁殖也是保护这一极危物和中的有效手段之一,对保护遗传多样性起以了重要作用,是延缓绝灭速率的保证。本文阐述了大圈养繁殖的必要性及其在保护生物学中的作用。     

Spatial genetic structure and dispersal of giant pandas on a mountain-range scale

Understanding the spatial genetic structure of populations can provide insight into the ecological or evolutionary processes of the species, and enable wise conservation decisions. We examined the spatial genetic structure of a giant panda (Ailuropoda melanoleuca) population in a heterogeneous mountainous landscape using noninvasive genetic sampling and 12 microsatellite loci. Nonrandom genetic structure was detected through spatial autocorrelation analysis, demonstrating a significantly positive autocorrelation over closer distances. Additional spatial analyses showed significantly positive genetic correlation among spatially-proximate males, and no correlation among females and among male–female pairs. These findings suggest a female-biased dispersal pattern and cryptic family grouping among giant pandas on a large mountain-range scale. The spatial extent of genetic structure occurred within 12.5 km, measured by a least-cost path distance model integrating information of habitat quality and habitat preferences of this species. Using the bearing analysis of PASSAGE, we found that directional genetic autocorrelations were in agreement with habitat structure, and habitat heterogeneity may affect the direction of giant panda dispersal. The characterization of spatial genetic structure can provide potentially valuable information for the conservation and management of giant pandas and their habitat.     

中国兽类遗传与进化研究进展与展望

中国兽类物种丰富,且具有150个特有种。本文综述了60年来中国兽类遗传与进化的研究进展,内容涵盖系统发育关系重建、遗传多样性评估、种群遗传结构、适应性进化以及趋同进化的分子机制。本文重点概述了食肉目（大、小熊猫）、有蹄类、翼手目、灵长目、小型兽类以及海兽类等重要类群的研究进展,为中国兽类的物种保护提供了重要资料。另外,本文还对中国兽类遗传与进化研究未来的研究方向提出几点建议,包括运用各种组学技术、筛选新型遗传标记和候选基因（调控序列）、结合表观遗传学并借助进化发育生物学研究方法,以期全面深入地理解中国兽类分类地位、起源以及特异表型产生和独特适应的发育遗传学机制等,进而实现“天人合一”保护生物学的新理念和新愿景。     

野生大熊猫现状、面临的挑战及展望

截至2003年底,我国野生大熊猫种群数量达1596只,分布在陕西、四川和甘肃3省的45个县境内,总栖息地面积达2304991hm^2。与第2次大熊猫调查相比,野生大熊猫生存状况已得到改善,分布范围扩大、栖息地面积增加、种群数量进一步增长。本文在第3次大熊猫调查的基础上,就野生大熊猫种群及栖息地现状进行了分析,指出未来保护大熊猫所面临的3个方面的挑战,即来自物种自身生物学特性的挑战、栖息地破碎化及隔离小种群未来命运的挑战以及大熊猫保护与社区经济发展需求相冲突的挑战。作者还就我国大熊猫保护前景进行了展望,即自然保护区数量将进一步增加,栖息地状况将进一步改善;种群数量在总体保持稳定的基础上将逐步增长,但局部小种群灭绝风险将加剧;圈养种群将形成能自我维持的种群,圈养个体通过培训将逐步放归到隔离野生小种群中以改变其命运。     

卧龙圈养大熊猫遗传多样性现状及预测,

以中国最大的大熊猫圈养种群—四川卧龙中国大熊猫保护中心的圈养种群为对象,以８个大熊猫微卫星位点为分子标记, 探讨了大熊猫圈养种群的遗传多样性, 并与邛崃野生种群及其他７个濒危物种进行比较。微卫星数据表明, 圈养种群的遗传多样性水平(A＝5.5, He ＝0.620, Ho＝0.574) 低于邛崃野生种群(A＝9.8,He＝0.779,Ho＝0.581),但高于其他7 个濒危物种的种群(He＝0.13~0.46)。在此数据的基础上对未来100个世代内圈养种群遗传多样性的变化情况做出了预测。结果表明假设种群数量比现在扩大一倍, 经历100个世代后也只会使平均等位基因数少减少0.4。因此继续增加野生个体对保持遗传多样性的意义已经不大, 建议该圈养种群的保护策略应将重点放到制定更有效的繁殖计划以避免近交上。     

野生大熊猫种群数量调查方法研究进展

大熊猫(Ailuropodamelanoleuca)是中国特有珍稀野生动物,被誉为野生动物保护领域的"旗舰物种"。大熊猫种群数量的变化可以实时反应大熊猫种群动态,提供大熊猫分布区域、栖息地质量等最直接的信息,是制定大熊猫保护方案的基础,也是有效实施大熊猫保护措施的前提。综述了几种传统野生大熊猫种群数量调查方法(包括直接计数法、数学模型法、距离-咬节分析法及分子生物学方法),以及近年来最新应用于野生动物种群数量调查的红外相机技术、足迹鉴定法,讨论了传统方法中可能存在的问题、分析新方法的应用前景,并针对今后的野生大熊猫种群数量调查提出了一些建议与展望。     

Giant pandas are losing their edge: Population trend and distribution dynamic drivers of the giant panda

Comprehending the population trend and understanding the distribution range dynamics of species are necessary for global species protection. Recognizing what causes dynamic distribution change is crucial for identifying species' environmental preferences and formulating protection policies. Here, we studied the rear-edge population of the flagship species, giant pandas (Ailuropoda melanoleuca), to (1) assess their population trend using their distribution patterns, (2) evaluate their distribution dynamics change from the second (1988) to the third (2001) survey (2–3 Interval) and third to the fourth (2013) survey (3–4 Interval) using a machine learning algorithm (eXtremely Gradient Boosting), and (3) decode model results to identify driver factors in the first known use of SHapley Additive exPlanations. Our results showed that the population trends in Liangshan Mountains were worst in the second survey (k = 1.050), improved by the third survey (k = 0.97), but deteriorated by the fourth survey (k = 0.996), which indicates a worrying population future. We found that precipitation had the most significant influence on distribution dynamics among several potential environmental factors, showing a negative correlation between precipitation and giant panda expansion. We recommend that further research is needed to understand the microenvironment and animal distribution dynamics. We provide a fresh perspective on the dynamics of giant panda distribution, highlighting novel focal points for ecological research on this species. Our study offers theoretical underpinnings that could inform the formulation of more effective conservation policies. Also, we emphasize the uniqueness and importance of the Liangshan Mountains giant pandas as the rear-edge population, which is at a high risk of population extinction.     

Does one size fit all? A multispecies approach to regional landscape corridor planning

Aim

The practical value of the single‐species approach to conserve biodiversity could be minimal or negligible when sympatric species are limited by factors that are not relevant to the proposed umbrella species. In this study, we quantitatively evaluated as follows: (1) habitat suitability and potential movement corridors of a single umbrella species, giant panda (Ailuropoda melanoleuca); (2) habitat suitability of sympatric mammals; and (3) the potential effectiveness of the single‐species corridor planning to preserve suitable habitat and its connectivity of other focal species.

Location

Qinling Mountains, central part of China (15,000 km²).

Methods

We collected species distribution, environmental and anthropogenic data and conducted species occupancy modelling for giant panda and six other sympatric species (i.e., takin Budorcas taxicolor, tufted deer Elaphodus cephalophus, Chinese goral Naemorhedus griseus, Reeve's muntjac Muntiacus reevesi, leopard cat Prionailurus bengalensis and yellow‐throated marten Martes flavigula). We then conducted circuit models to identify potential corridors for each species and evaluated the effectiveness of giant panda corridors to restore the habitat connectivity for these sympatric mammals.

Results

Occupancy modelling revealed that each species had a unique set of environmental variables associated with its distribution in the Qinling Mountains. We found that giant panda and all other focal species had some degree of fragmentation to their suitable habitat that required restoring habitat connectivity. Among the eight potential giant panda corridors, conservation efforts to reduce anthropogenic impacts would significantly improve the effectiveness of six corridors, while the other two corridors would require altering the vegetation. Five proposed giant panda corridors had remarkable overlap with corridors proposed for other species. We suggest two giant panda corridors as a priority due to their potential to maximize the benefits to both giant panda and a broader suite of mammals.

Main conclusions

Corridor planning in this region of China will likely continue using the single‐species policy, but our results highlight that not all potential giant panda corridors have equal effectiveness for other wildlife species. When offered multiple alternative actions, conservation planners can prioritize corridor development based on a multispecies perspective without loss of connectivity for the priority species. This approach has strong implications to the conservation of wildlife communities in China, and elsewhere, where conservation plans developed for a single‐species garner most available funding and institutional support.

     

An improved,chromosome-level genome of the giant panda (Ailuropoda melanoleuca)

BackgroundThe iconic giant panda (Ailuropoda melanoleuca), as both a flagship and umbrella species endemic to China, is a world famous symbol for wildlife conservation. The giant panda has several specific biological traits and holds a relatively small place in evolution. A high-quality genome of the giant panda is key to understanding the biology of this vulnerable species.FindingsWe generated a 2.48-Gb chromosome-level genome (GPv1) of the giant panda named “Jing Jing” with a contig N50 of 28.56 Mb and scaffold N50 of 134.17 Mb, respectively. The total length of chromosomes (n = 21) was 2.39-Gb, accounting for 96.4% of the whole genome. Compared with the previously published four genomes of the giant panda, our genome is characterized by the highest completeness and the correct sequence orientation. A gap-free and 850 kb length of immunoglobulin heavy-chain gene cluster was manually annotated in close proximity to the telomere of chromosome 14. Additionally, we developed an algorithm to predict the centromere position of each chromosome. We also constructed a complete chromatin structure for “Jing Jing”, which includes inter-chromosome interaction pattern, A/B compartment, topologically associated domain (TAD), TAD-clique and promoter-enhancer interaction (PEI).ConclusionsWe presented an improved chromosome-level genome and complete chromatin structure for the giant panda. This is a valuable resource for the future genetic and genomic studies on giant panda.     

微卫星标记在大熊猫研究中的应用进展

大熊猫是我国保护最为成功、研究最为深入的珍稀动物之一,可以为其它珍稀濒危物种的保护研究工作提供参考。20世纪70年代末期借助无线电颈圈,大熊猫的生态学研究工作取得了突破性进展,近20年来微卫星标记和非损伤性遗传取样技术的联合使用,将大熊猫的保护研究工作提升到一个崭新的高度。本文在综合所有已发表大熊猫微卫星标记的基础上,梳理了微卫星标记在圈养大熊猫亲子鉴定与遗传管理,野生大熊猫个体识别与种群数量调查、遗传多样性评估、扩散和种群遗传结构研究中的应用情况,并着重介绍了其中29个重要的微卫星标记。同时指出目前微卫星标记的使用存在标记选择不统一、等位基因读数无统一规程等问题,并对应用前景进行了前瞻。     

我国濒危哺乳动物保护生物学研究进展

本文简要论述了2010-1015年间,我国濒危哺乳动物（主要是食肉类、灵长类、有蹄类和鲸类) 保护生物学的研究进展,涉及进化保护生物学、保护生态学、保护行为学、保护生理学、保护遗传学、保护基因组学与宏基因组学和保护政策建议与实践等诸多领域。以大熊猫和金丝猴为代表的濒危动物保护生物学研究成绩显著。各项研究结果表明,大熊猫并非是一个已走到“进化尽头”的物种,仍具进化潜力。虽然大熊猫仍然面临栖息地破碎等环境问题,总的来看其种群数量在逐渐增长,栖息地面积在逐渐扩大,已走出困境并脱离“濒危”的状态,可降为“易危”。我国大熊猫的保护为世界生物多样性保护树立了成功的范例。根据国内研究进展和国际发展动态,该文还对未来保护生物学的研究提出了一些建议,包括加强长期定点监测与系统性的研究工作,加强新理论、新方法和新技术的研发及应用,加强宏微观研究手段的结合从机制上揭示科学问题,加强动物对食物、高原极端环境和水生生态环境的适应性进化分子机制的揭示,加强理论与实践相结合积极推动研究成果的应用,为濒危动物的有效保护保驾护航。     

Important population viability analysis parameters for giant pandas (Aliuropoda melanoleuca)

Population viability analysis(PVA) is a tool to evaluate the risk of extinction for endangered species and aid conservation decision-making.The quality of PVA output is dependent on parameters related to population dynamics and life-history;however,it has been difficult to collect this information for the giant panda(Aliuropoda melanoleuca),a rare and endangered mammal native to China,confined to some 30 fragmented habitat patches.Since giant pandas are long-lived,mature late,have lower reproductive rates,and show little sexual dimorphism,obtaining data to perform adequate PVA has been difficult.Here,we develop a parameter sensitivity index by modeling the dynamics of six giant panda populations in the Minshan Mountains,in order to determine the parameters most influential to giant panda populations.Our data shows that the giant panda populations are most sensitive to changes in four female parameters:initial breeding age,reproductive rate,mortality rate between age 0 and 1,and mortality rate of adults.The parameter sensitivity index strongly correlated with initial population size,as smaller populations were more sensitive to changes in these four variables.This model suggests that demographic parameters of females have more influence on the results of PVA,indicating that females may play a more important role in giant panda population dynamics than males.Consequently,reintroduction of female individuals to a small giant panda population should be a high priority for conservation efforts.Our findings form a technical basis for the coming program of giant panda reintroduction,and inform which parameters are crucial to successfully and feasibly monitoring wild giant panda populations.     

Integrating population size analysis into habitat suitability assessment: implications for giant panda conservation in the Minshan Mountains,China

Compared to conventional approaches, the integration of population size analysis with habitat suitability assessment on a large scale can provide more evidence to explain the mechanisms of habitat isolation and fragmentation, and thus make regional conservation plans. In this paper, we analyzed the habitat suitability for giant pandas in the Minshan Mountains, China, using the ecological-niche factor analysis (ENFA) method, and then evaluated the current conservation status of this endangered species. The results showed that (1) giant pandas were distributed in a narrow altitudinal range in which vegetation cover was dominated by coniferous forest, mixed coniferous and deciduous broadleaf forest, and deciduous broadleaf forest with scattered bamboo understory, and (2) roads and human settlements had strong negative effects on the panda habitat selection. According to habitat analysis, the total habitat area of giant panda in the Minshan Mountains was 953,173 ha, which was fragmented into 12 habitat units by major roads, rivers, and human settlements. The habitat of the mid-Minshan was less fragmentized, but was seriously fragmented in the north. The panda population size estimation showed that 676 individuals inhabited the study area, and 94.53% of them were in the mid-Minshan, but small panda populations less than 30 individuals inhabited the isolated and fragmented habitat patches in the north. The nature reserves in the Minshan Mountains have formed three conservation groups, which covered 41.26% of panda habitat and protected 70.71% of panda population of the study area, but there still exists two conservation gaps, and the connectivity among these reserves is still weak. Due to habitat isolation and extensive human disturbances, giant pandas in the north (i.e., Diebu, Zhouqu, and Wudou) are facing threats of local extinction. In order to protect pandas and their habitats in this area, some effective conservation approaches, such as establishing new reserves in gap areas, creating corridors among patches, and seasonally controlling traffic flux in key roads, should be implemented in the future to link these isolated habitats together.     

中国濒危兽类保护基因组学和宏基因组学研究进展与展望

揭示濒危兽类的演化历史、濒危机制及适应性演化策略,是保护生物学关注的重大科学问题。近十几年来,高通量测序技术的不断发展以及多学科交叉融合,为揭示濒危物种的演化历史、遗传结构、适应性演化及其与肠道微生物的协同演化的分子机制提供了重要的技术支撑,由此产生了保护基因组学和保护宏基因组学两个分支学科,为野生动物尤其是濒危动物的保护生物学研究提供了新的方向与思路。本文综述了我国在保护基因组学和保护宏基因组学领域取得的重要进展,并展望未来的发展趋势,以期进一步推动我国濒危兽类保护生物学的发展。     

A study on giant panda recognition based on images of a large proportion of captive pandas

1. As a highly endangered species, the giant panda (panda) has attracted significant attention in the past decades. Considerable efforts have been put on panda conservation and reproduction, offering the promising outcome of maintaining the population size of pandas. To evaluate the effectiveness of conservation and management strategies, recognizing individual pandas is critical. However, it remains a challenging task because the existing methods, such as traditional tracking method, discrimination method based on footprint identification, and molecular biology method, are invasive, inaccurate, expensive, or challenging to perform. The advances of imaging technologies have led to the wide applications of digital images and videos in panda conservation and management, which makes it possible for individual panda recognition in a noninvasive manner by using image‐based panda face recognition method.
2. In recent years, deep learning has achieved great success in the field of computer vision and pattern recognition. For panda face recognition, a fully automatic deep learning algorithm which consists of a sequence of deep neural networks (DNNs) used for panda face detection, segmentation, alignment, and identity prediction is developed in this study. To develop and evaluate the algorithm, the largest panda image dataset containing 6,441 images from 218 different pandas, which is 39.78% of captive pandas in the world, is established.
3. The algorithm achieved 96.27% accuracy in panda recognition and 100% accuracy in detection.
4. This study shows that panda faces can be used for panda recognition. It enables the use of the cameras installed in their habitat for monitoring their population and behavior. This noninvasive approach is much more cost‐effective than the approaches used in the previous panda surveys.

     

Genetic viability and population history of the giant panda, putting an end to the "evolutionary dead end"?

The giant panda (Ailuropoda melanoleuca) is currently threatened by habitat loss, fragmentation, and human persecution. Its dietary specialization, habitat isolation, and reproductive constraints have led to a perception that this is a species at an "evolutionary dead end," destined for deterministic extinction in the modern world. Here we examine this perception by a comprehensive investigation of its genetic diversity, population structure, and demographic history across its geographic range. We present analysis of 655 base pairs of mitochondrial (mt) control region (CR) DNA and 10 microsatellite loci for samples from its 5 extant mountain populations (Qinling, Minshan, Qionglai, Liangshan, and Lesser Xiangling). Surprisingly, extant populations display average to high levels of CR and microsatellite diversity compared with other bear species. Genetic differentiation among populations was significant in most cases but was markedly higher between Qinling and the other mountain ranges, suggesting, minimally, that the Qinling population should comprise a separate management unit for conservation purposes. Recent demographic inference using microsatellite markers demonstrated a clear genetic signature for population decline starting several thousands years ago or even further back in the past, and being accelerated and enhanced by the expansion of human populations. Importantly, these data suggest that the panda is not a species at an evolutionary "dead end," but in common with other large carnivores, has suffered demographically at the hands of human pressure. Conservation strategies should therefore focus on the restoration and protection of wild habitat and the maintenance of the currently substantial regional genetic diversity, through active management of disconnected populations.     

Population genetics reveals high connectivity of giant panda populations across human disturbance features in key nature reserve

The giant panda is an example of a species that has faced extensive historical habitat fragmentation, and anthropogenic disturbance and is assumed to be isolated in numerous subpopulations with limited gene flow between them. To investigate the population size, health, and connectivity of pandas in a key habitat area, we noninvasively collected a total of 539 fresh wild giant panda fecal samples for DNA extraction within Wolong Nature Reserve, Sichuan, China. Seven validated tetra‐microsatellite markers were used to analyze each sample, and a total of 142 unique genotypes were identified. Nonspatial and spatial capture–recapture models estimated the population size of the reserve at 164 and 137 individuals (95% confidence intervals 153–175 and 115–163), respectively. Relatively high levels of genetic variation and low levels of inbreeding were estimated, indicating adequate genetic diversity. Surprisingly, no significant genetic boundaries were found within the population despite the national road G350 that bisects the reserve, which is also bordered with patches of development and agricultural land. We attribute this to high rates of migration, with four giant panda road‐crossing events confirmed within a year based on repeated captures of individuals. This likely means that giant panda populations within mountain ranges are better connected than previously thought. Increased development and tourism traffic in the area and throughout the current panda distribution pose a threat of increasing population isolation, however. Maintaining and restoring adequate habitat corridors for dispersal is thus a vital step for preserving the levels of gene flow seen in our analysis and the continued conservation of the giant panda meta‐population in both Wolong and throughout their current range.     

马边大风顶自然保护区大熊猫种群生存力模拟分析

采用漩涡模型Vortex mondel 713 , 模拟了马边大风顶自然保护区大熊猫种群在未来100年内的变动趋势。结果显示: 在无交配限制、无密度制约、无近亲交配衰退等条件下, 马边大风顶自然保护区大熊猫种群数量呈下降趋势; 在考虑近交衰退的影响后, 遗传多样性水平降低, 灭绝率提高; 竹子开花虽能加速大熊猫种群的绝灭, 但由于保护区分布有多个竹种,因此并不会对大熊猫种群产生灾难性影响; 但是人为捕杀可迅速减少大熊猫种群数量, 加速其灭绝过程。因此, 对该保护区大熊猫进行保护的最重要措施就是严格控制人为捕杀, 并保护栖息地及走廊带。     

Assessing vulnerability of giant pandas to climate change in the Qinling Mountains of China

Climate change might pose an additional threat to the already vulnerable giant panda (Ailuropoda melanoleuca). Effective conservation efforts require projections of vulnerability of the giant panda in facing climate change and proactive strategies to reduce emerging climate‐related threats. We used the maximum entropy model to assess the vulnerability of giant panda to climate change in the Qinling Mountains of China. The results of modeling included the following findings: (1) the area of suitable habitat for giant pandas was projected to decrease by 281 km² from climate change by the 2050s; (2) the mean elevation of suitable habitat of giant panda was predicted to shift 30 m higher due to climate change over this period; (3) the network of nature reserves protect 61.73% of current suitable habitat for the species, and 59.23% of future suitable habitat; (4) current suitable habitat mainly located in Chenggu, Taibai, and Yangxian counties (with a total area of 987 km²) was predicted to be vulnerable. Assessing the vulnerability of giant panda provided adaptive strategies for conservation programs and national park construction. We proposed adaptation strategies to ameliorate the predicted impacts of climate change on giant panda, including establishing and adjusting reserves, establishing habitat corridors, improving adaptive capacity to climate change, and strengthening monitoring of giant panda.     

Giant Panda (Ailuropoda melanoleuca) Buccal Mucosa Tissue as a Source of Multipotent Progenitor Cells

Since the first mammal was cloned, the idea of using this technique to help endangered species has aroused considerable interest. However, several issues limit this possibility, including the relatively low success rate at every stage of the cloning process, and the dearth of usable tissues from these rare animals. iPS cells have been produced from cells from a number of rare mammalian species and this is the method of choice for strategies to improve cloning efficiency and create new gametes by directed differentiation. Nevertheless information about other stem cell/progenitor capabilities of cells from endangered species could prove important for future conservation approaches and adds to the knowledge base about cellular material that can be extremely limited. Multipotent progenitor cells, termed skin-derived precursor (SKP) cells, can be isolated directly from mammalian skin dermis, and human cheek tissue has also been shown to be a good source of SKP-like cells. Recently we showed that structures identical to SKPs termed m-SKPs could be obtained from monolayer/ two dimensional (2D) skin fibroblast cultures. Here we aimed to isolate m-SKPs from cultured cells of three endangered species; giant panda (Ailuropoda melanoleuca); red panda (Ailurus fulgens); and Asiatic lion (Panthera leo persica). m-SKP-like spheres were formed from the giant panda buccal mucosa fibroblasts; whereas dermal fibroblast (DF) cells cultured from abdominal skin of the other two species were unable to generate spheres. Under specific differentiation culture conditions giant panda spheres expressed neural, Schwann, adipogenic and osteogenic cell markers. Furthermore, these buccal mucosa derived spheres were shown to maintain expression of SKP markers: nestin, versican, fibronectin, and P75 and switch on expression of the stem cell marker ABCG2. These results demonstrate that giant panda cheek skin can be a useful source of m-SKP multipotent progenitors. At present lack of sample numbers means that we can only postulate why we were unable to obtain m-SKPs from the lion and red panda cultures. However the giant panda observations point to the value of archiving cells from rare species, and the possibilities for later progenitor cell derivation.