末次盛冰期以来观光木的潜在地理分布变迁

观光木(Tsoongiodendron odorum)是木兰科的古老残遗物种, 目前正面临严峻的生存威胁, 属于极小种群濒危植物。通过生态位模型(ENM)能够重建观光木地理分布格局的历史变迁, 探究气候变化对该物种分布的影响, 并了解其地理分布与气候需求间的关系, 从而为全球变暖背景下观光木的保护提供理论基础。该文基于96条现代分布记录和8个环境变量, 采用最大熵(MaxEnt)模型模拟观光木在末次盛冰期、全新世中期、现代和未来(2061-2080年, RCP 8.5)的潜在分布区, 利用SDM toolbox分析观光木的地理空间变化, 并综合贡献率、置换重要值和Jackknife检验来评估气候因子的重要性。研究结果表明: (1)观光木的高度适生区在南岭地区, 末次盛冰期时没有大尺度向南退缩, 很可能在山区避难所原地存活; (2)在全新世中期和未来两个增温的气候情境下, 观光木的分布区均表现为缩减, 其中未来分布的减幅更大, 表明气候变暖对观光木的生长有一定的负面影响; (3)总体上看, 观光木各个时期的地理分布范围相对稳定, 说明观光木对气候变化有一定的适应能力, 人为活动或自身繁育问题可能是致濒的重要原因, 并建议对广东和广西群体进行优先保护。     

Coupling Genetic and Species Distribution Models to Examine the Response of the Hainan Partridge (Arborophila ardens) to Late Quaternary Climate

Understanding the historical dynamics of animal species is critical for accurate prediction of their response to climate changes. During the late Quaternary period, Southeast Asia had a larger land area than today due to lower sea levels, and its terrestrial landscape was covered by extensive forests and savanna. To date, however, the distribution fluctuation of vegetation and its impacts on genetic structure and demographic history of local animals during the Last Glacial Maximum (LGM) are still disputed. In addition, the responses of animal species on Hainan Island, located in northern Southeast Asia, to climate changes during the LGM are poorly understood. Here, we combined phylogeographic analysis, paleoclimatic evidence, and species distribution models to examine the response of the flightless Hainan Partridge (Arborophila ardens) to climate change. We concluded that A. ardens survived through LGM climate changes, and its current distribution on Hainan Island was its in situ refuge. Range model results indicated that A. ardens once covered a much larger area than its current distribution. Demographic history described a relatively stable pattern during and following the LGM. In addition, weak population genetic structure suggests a role in promoting gene flow between populations with climate-induced elevation shifts. Human activities must be considered in conservation planning due to their impact on fragmented habitats. These first combined data for Hainan Partridge demonstrate the value of paired genetic and SDMs study. More related works that might deepen our understanding of the responses of the species in Southeast Asia to late Quaternary Climate are needed.     

中国纳入一级保护的极小种群野生植物濒危机制

为科学有效地保护极小种群野生植物, 明确其濒危机制具有重要意义。本文通过分析中国28种极小种群一级保护野生植物的种群特征及其濒危的内在原因和受威胁因素等, 总结了极小种群野生植物的濒危机制。极小种群野生植物的种群特征表现为遗传多样性低(13种)、衰退型种群结构(11种)、聚集型分布(11种)且分布区域狭窄(20种)。极小种群野生植物濒危的内在原因主要是繁殖力低(21种)和竞争能力弱(16种)。受威胁因素主要包括过度采挖等人类活动导致的种群数量减少(15种)和生境破坏(25种)以及气候变化等。因此, 除了保护极小种群野生植物免遭人类活动破坏, 保护策略应加强关注种群规模的维持和遗传多样性的保护。     

Defining conservation units in a stocking‐induced genetic melting pot: unraveling native and multiple exotic genetic imprints of recent and historical secondary contact in Adriatic grayling

The definition of conservation units is crucial for the sustainable management of endangered species, though particularly challenging when recent and past anthropogenic and natural gene flow might have played a role. The conservation of the European grayling, Thymallus thymallus, is particularly complex in its southern distribution area, where the Adriatic evolutionary lineage is endangered by a long history of anthropogenic disturbance, intensive stocking and potentially widespread genetic introgression. We provide mtDNA sequence and microsatellite data of 683 grayling from 30 sites of Adriatic as well as Danubian and Atlantic origin. We apply Bayesian clustering and Approximate Bayesian Computation (ABC) to detect microgeographic population structure and to infer the demographic history of the Adriatic populations, to define appropriate conservation units. Varying frequencies of indigenous genetic signatures of the Adriatic grayling were revealed, spanning from marginal genetic introgression to the collapse of native gene pools. Genetic introgression involved multiple exotic source populations of Danubian and Atlantic origin, thus evidencing the negative impact of few decades of stocking. Within the Adige River system, a contact zone of western Adriatic and eastern Danubian populations was detected, with ABC analyses suggesting a historical anthropogenic origin of eastern Adige populations, most likely founded by medieval translocations. Substantial river‐specific population substructure within the Adriatic grayling Evolutionary Significant Unit points to the definition of different conservation units. We finally propose a catalog of management measures, including the legal prohibition of stocking exotic grayling and the use of molecular markers in supportive‐ and captive‐breeding programs.     

Molecular and paleo-climatic data uncover the impact of an ancient bottleneck on the demographic history and contemporary genetic structure of endangered Pinus uliginosa

With the current rate of biodiversity loss, conservation management practices require a comprehensive understanding of eco-evolutionary relationships, history, and genetic structure of species. Assessments of genetic diversity are crucial, especially in rare, endemic, or threatened forest tree species with small and isolated populations, such as peat bog pine (Pinus uliginosa N.). Here, we used a novel approach, combining genetic diversity assessment, ecological niche modeling, and population demography inference to explore the complex history of a few remnant populations of this endangered pine. To asses the relative influence of isolation and fragmentation on genetic diversity in the taxonomic context, the patterns of genetic variation found in P. uliginosa were contrasted with those observed in its close relatives with much bigger distribution ranges and larger populations (Pinus sylvestris, Pinus mugo, and Pinus uncinata). We found a similar level of genetic diversity across the species at nuclear loci but contrasting patterns of variability distribution at chloroplast markers. We detected the signatures of an ancient genetic bottleneck dated at around 26 400 years ago, indicating a drastic reduction in the population size of P. uligionosa during the Last Glacial Maximum. In addition, we found substantial differentiation between current populations as a result of enhanced genetic drift during long-lasting isolation. The research suggests potential conservation management strategies for peat bog pine and emphasizes the importance of using complementary approaches for their successful development.     

Signature of a Pre-Human Population Decline in the Critically Endangered Reunion Island Endemic Forest Bird Coracina newtoni

The exceptional biodiversity of Reunion Island is threatened by anthropogenic landscape changes that took place during the 350 years of human colonization. During this period the human population size increased dramatically from 250 to 800,000. The arrival of humans together with the development of agriculture, invasive species such as rats and cats, and deforestation has lead to the extinction of more than half of the original vertebrate species of the island. For the remaining species, significant work is being carried out to identify threats and conservation status, but little genetic work has been carried on some of the most endangered species. In the last decade theoretical studies have shown the ability of neutral genetic markers to infer the demographic history of endangered species and identify and date past population size changes (expansions or bottlenecks). In this study we provide the first genetic data on the critically endangered species the Reunion cuckoo-shrike Coracina newtoni. The Reunion cuckoo-shrike is a rare endemic forest bird surviving in a restricted 12-km(2) area of forested uplands and mountains. The total known population consists of less than one hundred individuals out of which 45 were genotyped using seventeen polymorphic microsatellite loci. We found a limited level of genetic variability and weak population structure, probably due to the limited geographic distribution. Using Bayesian methods, we identified a strong decline in population size during the Holocene, most likely caused by an ancient climatic or volcanic event around 5000 years ago. This result was surprising as it appeared in apparent contradiction with the accepted theory of recent population collapse due to deforestation and predator introduction. These results suggest that new methods allowing for more complex demographic models are necessary to reconstruct the demographic history of populations.     

Genetic population structure of the sagebrush Brewer’s sparrow, <Emphasis Type="Italic">Spizella breweri breweri</Emphasis>, in a fragmented landscape at the northern range periphery

Assessing the genetic consequences of habitat fragmentation is a crucial step in conservation planning for species in endangered habitats. We tested for the impact of natural habitat fragmentation on gene flow and genetic diversity in seven northern breeding locations of the sagebrush Brewer’s sparrow, Spizella breweri breweri. Genetic analyses using five highly variable DNA microsatellite loci suggested that individuals sampled within a sagebrush landscape fragmented by natural elements such as coniferous forest, comprise a single genetic population and that gene flow among them is unimpeded. We posit that juvenile dispersal links seemingly isolated breeding locales of this species, and discuss implications of our findings for conservation of migratory songbirds in the northern portion of their ranges in light of potential shifts in distribution due to climate change.     

Uncertain recovery of the North Atlantic right whale in a changing ocean

Human activities have placed populations of many endangered species at risk and mitigation efforts typically focus on reducing anthropogenic sources of mortality. However, failing to recognize the additional role of environmental factors in regulating birth and mortality rates can lead to erroneous demographic analyses and conclusions. The North Atlantic right whale population is currently the focus of conservation efforts aimed at reducing mortality rates associated with ship strikes and entanglement in fishing gear. Consistent monitoring of the population since 1980 has revealed evidence that climate‐associated changes in prey availability have played an important role in the population's recovery. The considerable interdecadal differences observed in population growth coincide with remote Arctic and North Atlantic oceanographic processes that link to the Gulf of Maine ecosystem. Here, we build capture‐recapture models to quantify the role of prey availability on right whale demographic transitional probabilities and use a corresponding demographic model to project population growth rates into the next century. Contrary to previous predictions, the right whale population is projected to recover in the future as long as prey availability and mortality rates remain within the ranges observed during 1980–2012. However, recent events indicate a northward range shift in right whale prey, potentially resulting in decreased prey availability and/or an expansion of right whale habitat into unprotected waters. An annual increase in the number of whale deaths comparable to that observed during the summer 2017 mass mortality event may cause a decline to extinction even under conditions of normal prey availability. This study highlights the importance of understanding the oceanographic context for observed population changes when evaluating the efficacy of conservation management plans for endangered marine species.     

Allopatric divergence,demographic history,and conservation implications of an endangered conifer <Emphasis Type="Italic">Cupressus chengiana</Emphasis> in the eastern Qinghai-Tibet Plateau

Isolation and demographic history are key factors that affect lineage divergence of tree species in topographic complex areas, such as the Qinghai-Tibet Plateau (QTP), yet few studies have evaluated these factors in a coalescent-based modeling framework. In the present study, we surveyed ten nuclear DNA sequence loci (nDNA) and six nuclear microsatellite loci (nSSR) for an endangered conifer, Cupressus chengiana, throughout its natural range in the eastern QTP. BARRIER analyses revealed a strong genetic barrier between Gansu and Sichuan populations of C. chengiana, and isolation with migration models detected limited gene flow between them, supporting the division of this species into two evolutionary significant units (ESUs). Two independent coalescent-based approaches suggest a Quaternary divergence between ESUs, their consensus age range ((0.09–) 0.59–1.53 (–2.71) Mya) largely overlaps with the time period when the largest glaciation occurred in the QTP. Both demographic inferences, IMa2 and DIYABC, suggest that both ESUs may have experienced a bottleneck or population contraction event during the late Quaternary. A documented massive recent anthropogenic habitat loss and fragmentation may have led to further decrease of the natural distribution of this conifer. We propose that the conservation and management of both natural stands and plantations of C. chengiana should be reconsidered in the light of our findings.     

Ancient Demographics Determine the Effectiveness of Genetic Purging in Endangered Lizards

The purging of deleterious alleles has been hypothesized to mitigate inbreeding depression, but its effectiveness in endangered species remains debatable. To understand how deleterious alleles are purged during population contractions, we analyzed genomes of the endangered Chinese crocodile lizard (Shinisaurus crocodilurus), which is the only surviving species of its family and currently isolated into small populations. Population genomic analyses revealed four genetically distinct conservation units and sharp declines in both effective population size and genetic diversity. By comparing the relative genetic load across populations and conducting genomic simulations, we discovered that seriously deleterious alleles were effectively purged during population contractions in this relict species, although inbreeding generally enhanced the genetic burden. However, despite with the initial purging, our simulations also predicted that seriously deleterious alleles will gradually accumulate under prolonged bottlenecking. Therefore, we emphasize the importance of maintaining a minimum population capacity and increasing the functional genetic diversity in conservation efforts to preserve populations of the crocodile lizard and other endangered species.     

基于系统保护规划的三江平原湿地保护网络体系优化

综合三江平原湿地不同层次、不同维度的生物多样性特征,在系统保护规划方法(Systematic Conservation Planning,SCP)框架下,以集水区为规划单元,计算研究区域不可替代性指数,确定高保护价值网络体系,通过保护空缺分析对现有保护网络进行优化,并评估优化体系的有效性。结果表明:三江平原湿地高保护价值区域的分布呈现沿河流分布的特点;现有保护区中湖泊和目标物种的保护状态比较好;保护网络体系优化后,沼泽湿地在保护网络中的比重由22.88%重增加到50%以上;河流湿地由16.20%增加到33.92%;地下水资源在现有保护网络中的比重非常低,仅为2.01%,优化后保护网络中保护比重增加到12.05%,因此在今后的保护区规划中,应该重视对地下水资源的保护和管理。另外本研究结合生态脆弱性对高保护价值的空缺设计3个情景方案,并根据生态威胁的种类和强度提出各优先保护方案的保护建议,为保护管理决策提供依据。     

Comparison of population genetic diversity between a rare, narrowly distributed species and a common, widespread species of Alnus (Betulaceae)

Comparisons of population genetic diversity between related rare and widespread species provide valuable insights to the consequences of rarity and are critical for conservation planning. Population genetic diversity of A. maritima, a rare species, was compared with its common, widespread congener A. serrulata to evaluate the impacts of small population size and high isolation on genetic diversity in A. maritima and to provide population genetic data to be used in conservation planning for A. maritima. Genetic data were also used to evaluate whether the disjunct distribution of A. maritima was due to range reduction or anthropogenic dispersal. Genetic diversity was lower in A. maritima (H(e) = 0.217) than in A. serrulata (H(e) = 0.268), and there is also higher inbreeding within A. maritima populations (f = 0.483) than A. serrulata populations (f = 0.269). The partitioning of genetic variation was also higher among A. maritima populations (Θ = 0.278), but not significantly different from that of A. serrulata (Θ = 0.197). Significant genetic differences among A. maritima populations support using local populations as seed sources for regional conservation efforts. The results also indicate that the highly disjunct distribution of A. maritima is due to natural range reduction in the past and not anthropogenic establishment of Oklahoma and Georgia populations.     

湖北省珍稀濒危植物现状及其就地保护

本文论述了湖北省珍稀濒危植物的数量、分布及就地保护现状,并提出了保护的建议和措施。经调查研究,湖北省天然分布有62种珍稀濒危植物,占全国同类总数的15.97％;鄂西南和鄂西北为珍稀濒危植物的分布中心; 全省22个野生植物和森林生态系统自然保护区（点）现已就地保护55种,占总数的88.7％;在评价就地保护现状的基础上,提出了合理调整和布局自然保护区、大力发展自然保护小区、自然保护点和禁伐区以及将就地保护和其它手段相结合等建议。     

亚洲虎种群恢复的机遇与挑战

虎(Panthera tigris)作为顶级捕食者, 对维持森林生态系统服务和结构完整性有着重要作用, 是研究和保护工作的旗舰物种。历史上, 虎曾广泛分布于亚洲大部分地区, 如今仅分布于南亚、东南亚和东北亚的破碎化栖息地, 各区域种群处于濒危或极度濒危状态。准确了解野生虎的种群状态和生态需求信息对于科学开展保护和恢复工作至关重要。本文通过综述近几十年的研究文献, 总结了野生虎种群现状和主要威胁因素, 评价了已有研究的重点与不足, 为未来亚洲虎种群的研究和保护提出了建议。目前与虎相关的研究主要集中在分布范围最广的孟加拉虎(P. t. tigris)和东北虎(P. t. altaica) 2个亚种, 而最急需关注的其他亚种仍研究不足。经过近十几年的努力和保护投入, 目前野生虎种群数量已从2010年的大约3,200只恢复到现在约4,500只, 但在越南、柬埔寨和老挝3个国家已经灭绝。虎面临的主要威胁包括持续的栖息地破坏和隔离、猎物缺乏、近交衰退、人虎冲突、贸易与盗猎和疾病威胁等。未来的研究和保护工作需要加强种群和栖息地连通性恢复、个体重引入、疾病管控以及加强跨境合作和反盗猎等。     

小叶栎分布格局对末次盛冰期以来气候变化的响应

小叶栎(Quercus chenii)是华东植物区系的代表树种, 具有很高的生态、经济价值。为重建冰期以来小叶栎地理分布格局的变迁历史、了解环境因子对潜在地理分布的制约机制, 为小叶栎种质资源保护和管理提供科学依据, 该研究基于55条分布记录和8个环境变量, 利用MaxEnt模型模拟小叶栎在末次盛冰期、全新世中期、现代和2070年(温室气体排放情景为典型浓度目标8.5)的潜在分布区, 利用多元环境相似度面和最不相似变量分析探讨气候变迁过程中环境异常区域和引起潜在地理分布改变的关键因素, 综合应用贡献率及置换重要值比较、Jackknife检验评估制约现代地理分布的主要因子, 采用响应曲线确定环境变量的适宜区间。研究结果表明: MaxEnt模型的预测准确度极高, 受试者工作特征曲线下的面积(AUC值)达0.9869 ± 0.0045; 现代高度适宜区在安徽南部、浙江西部、江西东北部和湖北东部; 影响小叶栎地理分布的主要气候因子为气温和降水量, 气温更重要; 最干季平均气温可能是制约小叶栎向北分布的关键因素; 末次盛冰期时, 小叶栎高度适宜区位于东海大陆架内; 全新世中期适宜分布区轮廓已与现代近似; 2070年适宜分布区向北移, 高度适宜区面积增大, 与末次盛冰期、全新世中期和现代相比, 这一时期的气候异常程度最高。气温季节变化和降水季节变化可能是引起地理分布变迁的重要气候因素。     

Black and white and read all over: the past,present and future of giant panda genetics

Few species attract much more attention from the public and scientists than the giant panda (Ailuropoda melanoleuca), a popular, enigmatic but highly endangered species. The application of molecular genetics to its biology and conservation has facilitated surprising insights into the biology of giant pandas as well as the effectiveness of conservation efforts during the past decades. Here, we review the history of genetic advances in this species, from phylogeny, demographical history, genetic variation, population structure, noninvasive population census and adaptive evolution to reveal to what extent the current status of the giant panda is a reflection of its evolutionary legacy, as opposed to the influence of anthropogenic factors that have negatively impacted this species. In addition, we summarize the conservation implications of these genetic findings applied for the management of this high‐profile species. Finally, on the basis of these advances and predictable future changes in genetic technology, we discuss future research directions that seem promising for giant panda biology and conservation.     

Natural and anthropogenic determinants of genetic structure in the largest remaining population of the endangered golden-brown mouse lemur, Microcebus ravelobensis

Genetic differentiation between natural populations is best understood as a result of both natural and anthropogenic factors. Genetic studies on large populations still living under relatively undisturbed conditions are extremely valuable to disentangle these influences. The effect of three natural (geographic distance, landscape, dispersal) factors and two anthropogenic factors (road, savannah) on gene flow was analyzed in the largest remaining forest region in the range of the endangered golden-brown mouse lemur in Madagascar. A total of 187 individuals from 12 sites were sampled and genotyped at eight polymorphic microsatellite loci. All sites exhibited similar levels of genetic variation. The level of genetic differentiation was low to moderate with pairwise F(ST) values ranging from -0.002 to 0.12, but most were significant and all sites exhibited high self-assignment rates. A spatial autocorrelation analysis was performed at two geographic scales revealing a pattern of isolation-by-distance and suggesting that no clear differences exist between male and female local dispersal. Two Bayesian approaches revealed that a stretch of savannah represented a significant barrier to movement, whereas the influence of the road on gene flow was less clear. Finally, we found that landscape characteristics, in particular altitude, play a role in the functional connectivity of the sites. The study underlines the importance of studies in relatively undisturbed conditions for the interpretation of population genetics data in fragmented environments. The results are discussed in terms of their conservation relevance for forest-dwelling animals such as most primate species.     

Effect of anthropogenic landscape features on population genetic differentiation of Przewalski's gazelle: main role of human settlement

Anthropogenic landscapes influence evolutionary processes such as population genetic differentiation, however, not every type of landscape features exert the same effect on a species, hence it is necessary to estimate their relative effect for species management and conservation. Przewalski's gazelle (Procapra przewalskii), which inhabits a human-altered area on Qinghai-Tibet Plateau, is one of the most endangered antelope species in the world. Here, we report a landscape genetic study on Przewalski's gazelle. We used skin and fecal samples of 169 wild gazelles collected from nine populations and thirteen microsatellite markers to assess the genetic effect of anthropogenic landscape features on this species. For comparison, the genetic effect of geographical distance and topography were also evaluated. We found significant genetic differentiation, six genetic groups and restricted dispersal pattern in Przewalski's gazelle. Topography, human settlement and road appear to be responsible for observed genetic differentiation as they were significantly correlated with both genetic distance measures [F(ST)/(1-F(ST)) and F'(ST)/(1-F'(ST))] in Mantel tests. IBD (isolation by distance) was also inferred as a significant factor in Mantel tests when genetic distance was measured as F(ST)/(1-F(ST)). However, using partial Mantel tests, AIC(c) calculations, causal modeling and AMOVA analysis, we found that human settlement was the main factor shaping current genetic differentiation among those tested. Altogether, our results reveal the relative influence of geographical distance, topography and three anthropogenic landscape-type on population genetic differentiation of Przewalski's gazelle and provide useful information for conservation measures on this endangered species.     

Polyphyly and species delimitation of Picea brachytyla (Pinaceae) based on population genetic data

Accurate species delimitation is fundamental to biodiversity conservation. The endangered spruce Picea brachytyla (Franch.) E. Pritz. was suggested to be polyphyletic based on a limited number of samples in previous studies. To evaluate polyphyly of P. brachytyla, we sampled 139 individuals from 16 populations across most of its distributional range, plus representatives of two related species, Picea likiangensis (Franch.) E. Pritz. and Picea wilsonii Mast. We sequenced 13 nuclear loci and three chloroplast and two mitochondrial loci for the following species delimitation. Phylogenetic analyses of nuclear loci grouped all individuals of P. brachytyla from Sichuan and Chongqing into one distinct lineage and those from Yunnan and Tibet (southern distribution) nested within the P. likiangensis species complex. Structure analyses confirmed this result. Networks of chloroplast DNA haplotypes similarly showed that P. brachytyla from the southern distribution nested within the P. likiangensis species complex, whereas haplotypes for the northern distribution comprised a separate and well-supported lineage. These results suggest that P. brachytyla from the southern distribution is a part of the P. likiangensis species complex and should be removed from P. brachytyla. Our study highlights the utility of population genetic evidence in delimitating endangered species and understanding the conservation status of such species.     

High regional genetic differentiation of an endangered relict plant Craigia yunnanensis and implications for its conservation

Of the genus Craigia, widespread in the Tertiary, only two relict species survived to modern times. One species is now possibly extinct and the other one, Craigia yunnanensis, is severely endangered. Extensive surveys have located six C. yunnanensis populations in Yunnan province, southwest China. Using fluorescent amplified fragment length polymorphism (AFLP), the genetic diversity and population structure of these populations were examined. It was found that genetic diversity of C. yunnanensis was moderate at the species level, but low at regional and population levels. Analysis of population structure showed significant genetic differentiation between Wenshan and Dehong regions, apparently representing two geographically isolated for long time refuges. There are also clear indications of isolation between populations, which, together with anthropogenically caused decline of population size, will lead to general loss of the species genetic variation with subsequent loss of adaptive potential. To conserve the genetic integrity of C. yunnanensis, we recommend that ex-situ conservation should include representative samples from every population of the two differentiated regions (e.g. Wenshan and Dehong). The crosses between individuals originated from different regions should be avoided because of a high risk of outbreeding depression. As all the extant populations of C. yunnanensis are in unprotected areas with strong anthropogenic impact, there is no alternative to reintroduction of C. yunnanensis into suitable protected locations.