基因组学技术在生物多样性保护研究中的应用

在分子生物学、细胞生物学、微生物学、遗传学等学科的推动下, 生物多样性研究从仅关注宏观表型的博物学, 迅速演化为涵盖生态系统、物种和遗传多样性等多个维度的综合性生命科学。组学技术, 尤其是DNA测序技术的更新和发展, 使获取DNA序列所需的成本大幅下降, 促进了近年来其在生物多样性研究中取得的一系列令人瞩目成就。本文将从物种水平的遗传多样性和群落水平的物种多样性两个层面总结和介绍与DNA相关的组学技术在生物多样性研究中的一些创新和应用。其中, 物种水平主要是总结单一个体的基因组和单物种多个体在时空多个维度上的群体遗传研究; 而群落水平的物种多样性层面主要总结现有的分子鉴定技术(metabarcoding, eDNA, iDNA等), 以及上述新技术在群落多样性评估、旗舰保护物种监测以及物种间相互作用关系等研究中的应用。     

群落构建的中性理论和生态位理论

物种共存和生物多样性维持一直是生态学研究的中心论题。基于物种生态位分化的群落构建理论已经发展了近一个世纪, 但我们对群落构建和生物多样性维持的机理仍然不清楚。近年来, 群落中性理论以其简约性和预测能力成为群落生态学研究的焦点, 但由于其“物种在生态功能上等价”的假设与大量研究结果相悖, 同时对自然群落结构的准确预测也只限于少数的生态系统, 因而饱受质疑。如今, 越来越多的生态学家认为群落构建的生态位理论与中性理论之争的最终归宿应该是二者的整合。 在本文中, 我们在简要回顾生态位理论和群落中性理论发展的基础上, 分析二者之间的主要分歧和互补性, 试图梳理二者整合的途径。我们认为, 尽管中性理论的发展极大地丰富了群落构建理论, 但二者的整合尚处于初级阶段; 群落构建零模型假说、中性—生态位连续体假说、随机生态位假说等都不失为有价值的尝试, 今后需要在其他类型的生态系统中进行实验验证, 以更好地理解确定性过程和随机过程在决定群落构建和生物多样性维持中的作用。     

中国森林生物多样性监测网络: 二十年群落构建机制探索的回顾与展望

中国森林生物多样性监测网络(CForBio)目前已经沿纬度梯度从寒温带到热带布设23个大型森林动态样地, 监测1,893种木本植物, 代表我国木本植物种类的近1/6。CForBio的主要目标之一是研究森林群落的构建机制。本文综述了近20年来CForBio在群落构建机制探索方面取得的进展, 包括生物多样性时空格局、生境过滤、生物相互作用、局域扩散和区域因素以及利用新技术取得的新认知等。CForBio研究发现: (1)生境过滤和扩散限制共同决定种-面积关系及β多样性等多样性格局, 但二者的相对作用在不同样地及不同尺度存在差异; (2)生境过滤对局域群落构建的作用广泛存在, 但很难量化其对群落构建的重要性; (3)同种负密度制约在不同气候带样地普遍存在, 负密度制约的强度主要由植物菌根类型介导, 并随植物生活史类型、功能性状及环境变化而变化; (4)扩散限制在局域群落构建中发挥关键作用, 而区域因素如区域地质历史、区域物种库大小等塑造不同生物地理区群落之间的生物多样性差异; (5)宏观和微观两个方面的新技术促进群落构建机制的研究。在宏观方面, 遥感技术以低成本使大范围、多尺度的连续群落生物多样性监测和时空比较研究成为可能; 另一方面, 叶绿体基因技术和代谢组学等微观技术能促进推导群落构建的分子机制。同时, 本文还总结了以往研究的不足, 并展望了基于森林动态样地开展群落构建机制研究的未来发展, 特别强调了: (1)关注群落构建研究中的尺度问题; (2)深入开展多维度(物种、功能和系统发育)、多营养级生物互作相关的研究; (3)拓展全球变化对群落构建影响的研究; (4)融合观测-实验-模型多种手段开展群落构建机制的研究; (5)连结“群落构建理论研究”和“森林管理实践”。总之, 中国森林生物多样性监测网络的长期监测和联网研究是森林群落构建机制研究的重要基础, 也是推动群落构建理论、解决森林管理难题的重要平台。     

生态学的多样性指数:功能与系统发育

生物多样性是生态学的核心问题。传统的多样性指数仅包含物种数和相对多度的信息,这类基于分类学的多样性指数并不能很好地帮助理解群落构建和生态系统功能。不同物种对群落构建和生态系统功能所起到的作用类型和贡献也不完全相同,且物种在生态过程中的作用和贡献往往与性状密切相关,因此功能多样性已经成为反映物种群落构建、干扰以及环境因素对群落影响的重要指标。同时,由于亲缘关系相近的物种往往具有相似的性状,系统发育多样性也可以作为功能多样性的一个替代。功能多样性和系统发育多样性各自具有优缺点,但二者均比分类多样性更能揭示群落和生态系统的构建、维持与功能。     

群落生态学的中性理论

生物多样性的分布格局和维持机制一直是群落生态学研究的核心问题,其中的关键是物种的共存机制。长期以来,生态位分化的思想在这一研究领域占据着主导地位。然而这一理论在解释热带雨林很高的物种多样性时遇到了困难。而以Hubbell为代表提出的群落中性漂变理论则假定在同一营养级物种构成的群落中不同物种的不同个体在生态学上可看成是完全等同的;物种的多度随机游走,群落中的物种数取决于物种灭绝和物种迁入/新物种形成之间的动态平衡。在这一假定之下,该理论预言了两种统计分布。一种是集合群落在点突变形成新物种的模式下其各个物种相对多度服从对数级数分布,而受扩散限制的局域群落以及按照随机分裂为新物种模式形成的集合群落则服从零和多项式分布。与生态位理论相反,中性理论不以种间生态位差异作为研究群落结构的出发点,而是以物种间在个体水平上的对等性作为前提。该理论第一次从基本生态学过程(出生、死亡、迁移、物种分化)出发,给出了群落物种多度分布的机理性解释,同时其预测的物种多度分布格局在实际群落中也得到了广泛的印证。因此,中性理论自诞生以来便在生态学界引发了极大的反响,也包括一些反对的声音。该文重点综述了关于中性理论的假设、预测和物种形成模式等方面的最新研究进展,包括中性理论本身的发展、关于中性理论的假设和预测的合理性检验以及在集合群落尺度上物种分化模式的讨论;并指出未来发展方向可能是在生态位理论和中性理论之间架起一座桥梁,同时发展包含随机性的群落生态位模型,以及允许种间差异的近中性模型。     

生物多样性理论最新进展

生物多样性是生态系统复杂性的重要特征, 理解多样性的形成和维持机制一直是理论生态学研究的核心议题。本文从三方面概述了生物多样性理论的最新进展。一是物种共存和群落构建, 总结了现代共存理论和基于过程的群落构建理论的新进展。二是物种相互作用, 综述了利用经验数据推断物种相互作用关系和强度的最新方法。三是生态-进化动态, 介绍了生态-进化模型的一般框架及其在生物多样性研究中的应用。最后对生物多样性理论的发展趋势做了展望, 特别是多尺度整合理论和全球变化下的预测理论。     

植物群落物种多样性研究综述

物种多样性是生物多样性在物种水平上的表现形式 ,包括两方面的含义 ,一是指一定区域内物种的总和 ,主要从分类学、系统学和生物地理学角度对一个区域内物种的状况进行研究 ,也称区域物种多样性 ;二是指生态学方面物种分布的均匀程度 ,常常是从群落组织水平上进行研究 ,也称为生态多样性或群落多样性[1] 。本文所涉及物种多样性即为群落组织水平上的物种多样性。植物群落物种多样性的研究是其它多样性 (遗传多样性、生态系统多样性等 )的基础 ,有大量的研究成果相继报道 ,也有一些综述对植物群落物种多样性某一领域的研究进行总结。Ｍａｇｕ…     

生物多样性保护廊道构建方法研究进展

生物多样性保护廊道对遏制生态系统退化及生物多样性丧失,改善生态系统服务功能,消除生境破碎化对生物多样性的影响,恢复珍稀濒危物种的种群数量,维护自然生态系统平衡稳定具有极为重要的作用。在近20年(1997—2017)国内外生物多样性保护廊道的相关研究分析的基础上,对廊道的概念、构建理论及方法应用进行了系统总结与探讨,分析了廊道构建理论的发展过程及适用性,分类总结了现有的廊道构建方法和17种廊道构建模型工具。研究分析表明,廊道作为一种新的生物多样性保护模式,已成为目前国际生态领域研究的热点之一,随着对物种景观运动过程认识的加深,廊道构建理论逐渐趋于成熟,与之匹配的廊道构建方法及模型工具进展迅速。借助遥感与地理信息技术,大范围,高精度的获取廊道模拟数据,并集成综合模型实现目标物种廊道的构建、保护和管理是今后生物多样性保护廊道构建研究的发展方向。最后,对当前该领域的研究现状和不足展开讨论并展望了未来发展,为我国生物多样性保护廊道的应用与实践及国家生态廊道体系的建设完善提供借鉴与参考。     

局域和区域过程共同控制着群落的物种多样性:种库假说

解释群落的物种多样性大小是生态学研究的一个重要的理论和实践问题。人们提出了群落物种多样性的多种假说, Zobel等人提出的种库假说(species pool hypothesis)是生物多样性理论研究的重要发展。该假说认为, 一个群落的物种多样性不仅与环境条件和生态过程(ecological process)(如竞争、捕食)有关, 也受区域种库(regional species pool)的限制。区域种库是指一个地区可进入某一群落的潜在物种数量, 它由地史过程(如冰期、地质年代)和区域过程(物种形成、迁移扩散以及消亡)所决定。按照种库假说, 某一生境类型的面积越大, 地质年代越古老, 物种形成的机会也就越多, 因而能适应和分布于该生境的物种也就越多, 实际群落中的物种丰富度也就越高。种库在空间上主要有两个层次: 区域种库和实际种库, 前者指某一生境所拥有的潜在物种数量, 主要由生物地理过程(biogeographic processes)所决定; 后者则为调查的群落中实际出现的物种数量, 主要由竞争等生态过程和区域种库共同决定。本文对种库假说的基本概念、主要内容、种库确定方法等作了介绍, 并阐述了作者对这些问题的理解和认识。     

长白山暗针叶林群落物种多样性维持机制

植物群落物种多样性维持机制一直是生态学研究的热点话题,其中生态位理论和中性理论是被普遍接受的两种理论观点,但是目前关于生态位理论和中性理论在群落物种多样性维持中的相对重要性还没有统一定论。基于长白山暗针叶林群落数据,采用单物种-面积关系模型探究特定树种对邻域物种丰富度的影响,并借助同质性和异质性泊松零模型检验其显著性。(1)群落水平上,在3—15 m空间尺度上,促进种占据优势地位,在>15 m空间尺度上,中性种逐渐取代促进种起主导作用,抑制种比例较低,并且随着空间尺度变化幅度不大。(2)物种水平上,采用同质性泊松零模型检验树种对邻域物种丰富度的影响,臭冷杉、花楷槭、青楷槭在0—20 m空间尺度上对邻域物种丰富度增加起促进作用,黄花落叶松、鱼鳞云杉在0—20 m空间尺度上抑制了邻域物种丰富度增加。花楸树、黑桦和硕桦在全部研究尺度上表现为中性种,髭脉槭、大青杨、红松等在不同研究尺度上表现为不同的作用效果。剔除了生境过滤作用的异质性泊松零模型检验结果与同质性泊松零模型结果差异不显著,表明研究样地内生境过滤作用对多样性格局形成影响不大,各树种间的相互作用对群落物种组成影响较大,进一步证明...     

From diversity indices to community assembly processes: a test with simulated data

Ecological theory suggests that spatial distribution of biodiversity is strongly driven by community assembly processes. Thus the study of diversity patterns combined with null model testing has become increasingly common to infer assembly processes from observed distributions of diversity indices. However, results in both empirical and simulation studies are inconsistent. The aim of our study is to determine with simulated data which facets of biodiversity, if any, may unravel the processes driving its spatial patterns, and to provide practical considerations about the combination of diversity indices that would produce significant and congruent signals when using null models. The study is based on simulated species’ assemblages that emerge under various landscape structures in a spatially explicit individual‐based model with contrasting, predefined assembly processes. We focus on four assembly processes (species‐sorting, mass effect, neutral dynamics and competition colonization trade‐off) and investigate the emerging species’ distributions with varied diversity indices (alpha, beta and gamma) measured at different spatial scales and for different diversity facets (taxonomic, functional and phylogenetic). We find that 1) the four assembly processes result in distinct spatial distributions of species under any landscape structure, 2) a broad range of diversity indices allows distinguishing between communities driven by different assembly processes, 3) null models provide congruent results only for a small fraction of diversity indices and 4) only a combination of these diversity indices allows identifying the correct assembly processes. Our study supports the inference of assembly processes from patterns of diversity only when different types of indices are combined. It highlights the need to combine phylogenetic, functional and taxonomic diversity indices at multiple spatial scales to effectively infer underlying assembly processes from diversity patterns by illustrating how combination of different indices might help disentangling the complex question of coexistence.     

Dispersal and neutral sampling mediate contingent effects of disturbance on plant beta‐diversity: a meta‐analysis

A major challenge in ecology, conservation and global‐change biology is to understand why biodiversity responds differently to similar environmental changes. Contingent biodiversity responses may depend on how disturbance and dispersal interact to alter variation in community composition (β‐diversity) and assembly mechanisms. However, quantitative syntheses of these patterns and processes across studies are lacking. Using null‐models and meta‐analyses of 22 factorial experiments in herbaceous plant communities across Europe and North America, we show that disturbance diversifies communities when dispersal is limited, but homogenises communities when combined with increased immigration from the species pool. In contrast to the hypothesis that disturbance and dispersal mediate the strength of niche assembly, both processes altered β‐diversity through neutral‐sampling effects on numbers of individuals and species in communities. Our synthesis suggests that stochastic effects of disturbance and dispersal on community assembly play an important, but underappreciated, role in mediating biotic homogenisation and biodiversity responses to environmental change.     

A taxonomic and phylogenetic perspective on plant community assembly along an elevational gradient in subtropical forests

亚热带森林植物群落沿海拔梯度的分类与系统发育研究 生物多样性沿海拔梯度的分布格局已受到广泛关注。然而,生物多样性格局沿海拔梯度的变异及其潜在机制尚不清楚。整合生物多样性的多维度信息为理解群落构建机制提供了新思路。本研究在我国东部亚热带森林沿海拔270–1470 m的梯度上设置了17个木本植物固定样地,分析了沿海拔梯度植物群落 构建的生态和进化驱动力。基于样地内物种出现(0–1数据)和多度信息,计算群落内被子植物的物种和系统发育alpha和beta多样性、系统发育结构等,并量化多样性指标与微气候和地形之间的关系。研究发现,不论多度加权与否,物种alpha多样性均沿海拔升高而增加,物种和系统发育的相似性随海拔距离的增加而呈衰减趋势。然而,多度加权与否会形成不同的系统发育alpha多样性格局。对于系统发育结构而言,沿海拔增加并无明显趋势。地形和微气候是多样性格局和系统发育结构的主要驱动力。与未考虑物种多度的多样性指标相比,多度加权的指标与坡度和胸高断面积相关性更高。这些结果表明,由局域物种多度介导的确定性过程对沿海拔梯度的植物群落构建具有一定影响。     

植物群落构建机制研究进展

群落构建研究对于解释物种共存和物种多样性的维持是至关重要的,因此一直是生态学研究的中心论题。尽管近年来关于生态位和中性理论的验证研究已经取得了显著的成果,但对于局域群落构建机制的认识仍存在很大争议。随着统计和理论上的进步使得用功能性状和群落谱系结构解释群落构建机制变为可能,主要是通过验证共存物种的性状和谱系距离分布模式来实现。然而,谱系和功能性状不能相互替代,多种生物和非生物因子同时控制着群落构建,基于中性理论的扩散限制、基于生态位的环境过滤和竞争排斥等多个过程可能同时影响着群落的构建。所以,综合考虑多种方法和影响因素探讨植物群落的构建机制,对于预测和解释植被对干扰的响应,理解生物多样性维持机制有重要意义。试图在简要回顾群落构建理论及研究方法发展的基础上,梳理其最新研究进展,并探讨整合功能性状及群落谱系结构的研究方法,解释群落构建和物种多样性维持机制的可能途径。在结合功能性状和谱系结构研究群落构建时,除了考虑空间尺度、环境因子、植被类型外,还应该关注时间尺度、选择性状的种类和数量、性状的种内变异、以及人为干扰等因素对群落构建的影响。     

Tree diversity on islands: assembly rules,passive sampling and the theory of island biogeography

Aim Species diversity is distributed heterogeneously through space, for reasons that are poorly understood. We tested three hypotheses to account for spatial variation in coniferous tree species diversity in a temperate island archipelago. The theory of island biogeography (ToIB) predicts that island area affects species diversity both directly (by increasing habitat diversity) and indirectly (by increasing abundances, which in turn reduce extinction rates). The ToIB also predicts that island isolation directly affects species diversity by reducing immigration rates. The passive sampling hypothesis predicts that island area and isolation both affect species diversity indirectly, by increasing and decreasing abundances, respectively. Community assembly rules (i.e. even partitioning of conifer abundances among islands) might also reduce tree species diversity beyond the core predictions of ToIB and the passive sampling hypothesis. Location Barkley Sound, British Columbia, Canada. Methods The abundances of eight coniferous tree species were quantified on 34 islands and two (1 ha) mainland plots. The predictions of the ToIB and the passive sampling hypothesis were tested using path analysis, and null models were used to test for abundance‐based assembly rules and to further test the passive sampling hypothesis. Results Path analysis showed that island area and isolation did not have direct, statistical effects on tree species diversity. Instead, both geographic variables had direct statistical effects on total tree abundances, which in turn predicted tree diversity. Results from several passive sampling null models were correlated with observed patterns in species diversity, but they consistently overestimated the number of tree species inhabiting most islands. A different suite of null models showed support for community assembly rules, or that tree species often reached higher abundances on islands that housed fewer heterospecific trees. Main conclusions Results were inconsistent with the ToIB. Instead, patterns in tree diversity were best explained by a combination of stochastic (passive sampling) and deterministic (assembly rules) processes. Stochastic and deterministic processes are commonly considered to be exclusive explanations for island community structure, but results from this study suggest that they can work synergistically to structure island tree communities.     

Community disassembly under global change: Evidence in favor of the stress‐dominance hypothesis

Ecological theory suggests that communities are not random combinations of species but rather the results of community assembly processes filtering and sorting species that are able to coexist together. To date, such processes (i.e., assembly rules) have been inferred from observed spatial patterns of biodiversity combined with null model approaches, but relatively few attempts have been made to assess how these processes may be changing through time. Specifically, in the context of the ongoing biodiversity crisis and global change, understanding how processes shaping communities may be changing and identifying the potential drivers underlying these changes become increasingly critical. Here, we used time series of 460 French freshwater fish communities and assessed both functional and phylogenetic diversity patterns to determine the relative importance of two key assembly rules (i.e., habitat filtering and limiting similarity) in shaping these communities over the last two decades. We aimed to (a) describe the temporal changes in both functional and phylogenetic diversity patterns, (b) determine to what extent temporal changes in processes inferred through the use of standardized diversity indices were congruent, and (c) test the relationships between the dynamics of assembly rules and both climatic and biotic drivers. Our results revealed that habitat filtering, although already largely predominant over limiting similarity, became more widespread over time. We also highlighted that phylogenetic and trait‐based approaches offered complementary information about temporal changes in assembly rules. Finally, we found that increased environmental harshness over the study period (especially higher seasonality of temperature) led to an increase in habitat filtering and that biological invasions increased functional redundancy within communities. Overall, these findings underlie the need to develop temporal perspectives in community assembly studies, as understanding ongoing temporal changes could provide a better vision about the way communities could respond to future global changes.     

利用数值模拟重构物种多样性格局的形成过程

生命形成的过程极其漫长, 经历了地球系统复杂的沧海桑田变化。当前人类所观察到的物种分布格局的形成除了由物种本身特征决定外, 还受到环境变化、人类活动以及各种随机事件的影响。受限于实验条件、时间、经费、人力等诸多因素, 我们尚无法完整地观察并记录到物种多样性形成的全过程, 只能通过片段化数据来推测该过程。信息科学中包括数值模拟在内的仿真技术以其高效、可控及全过程记录等优势, 能从某种程度上解决物种多样性格局形成过程中的部分数据黑箱问题。本文介绍了数值模拟的概念和工作原理及在物种多样性研究中应用的特点, 列举了物种生态位、扩散模式、种间互作及物种分布应对气候变化等方面的数值模拟研究, 基于已有研究系统地介绍了如何综合上述数值模拟研究构建虚拟物种、气候和场景来解释物种多样性的形成与维持机制, 并阐述了数值模拟在物种多样性研究中的优缺点及应用前景。     

Phylogenetic community structure metrics and null models: a review with new methods and software

Competitive exclusion and habitat filtering influence community assembly, but ecologists and evolutionary biologists have not reached consensus on how to quantify patterns that would reveal the action of these processes. Currently, at least 22 α‐diversity and 10 β‐diversity metrics of community phylogenetic structure can be combined with nine null models (eight for β‐diversity metrics), providing 278 potentially distinct approaches to test for phylogenetic clustering and overdispersion. Selecting the appropriate approach for a study is daunting. First, we describe similarities among metrics and null models across variance in phylogeny size and shape, species abundance, and species richness. Second, we develop spatially explicit, individual‐based simulations of neutral, competitive exclusion, or habitat filtering community assembly, and quantify the performance (type I and II error rates) of all 278 metric and null model combinations against each assembly process. Many α‐diversity metrics and null models are at least functionally equivalent, reducing the number of truly unique metrics to 12 and the number of unique metric + null model combinations to 72. An even smaller subset of metric and null model combinations showed robust statistical performance. For α‐diversity metrics, phylogenetic diversity and mean nearest taxon distance were best able to detect habitat filtering, while mean pairwise phylogenetic distance‐based metrics were best able to detect competitive exclusion. Overall, β‐diversity metrics tended to have greater power to detect habitat filtering and competitive exclusion than α‐diversity metrics, but had higher type 1 error in some cases. Across both α‐ and β‐diversity metrics, null model selection affected type I error rates more than metric selection. A null model that maintained species richness, and approximately maintained species occurrence frequency and abundance across sites, exhibited low type I and II error rates. This regional null model simulates neutral dispersal of individuals into local communities by sampling from a regional species pool. We introduce a flexible new R package, metricTester, to facilitate robust analyses of method performance.     

From species distributions to meta‐communities

The extent that biotic interactions and dispersal influence species ranges and diversity patterns across scales remains an open question. Answering this question requires framing an analysis on the frontier between species distribution modelling (SDM), which ignores biotic interactions and dispersal limitation, and community ecology, which provides specific predictions on community and meta‐community structure and resulting diversity patterns such as species richness and functional diversity. Using both empirical and simulated datasets, we tested whether predicted occurrences from fine‐resolution SDMs provide good estimates of community structure and diversity patterns at resolutions ranging from a resolution typical of studies within reserves (250 m) to that typical of a regional biodiversity study (5 km). For both datasets, we show that the imprint of biotic interactions and dispersal limitation quickly vanishes when spatial resolution is reduced, which demonstrates the value of SDMs for tracking the imprint of community assembly processes across scales.