基于生物学物种定义探讨物种形成理论与验证的研究进展

物种形成是进化生物学研究的一个永恒主题, 由于生物群体进化是连续和动态的, 物种界限变得难于界定。本文首先讨论了3种地理物种形成模式(同域、邻域及异域), 并分析了近期报道的研究证据。其次, 评述了合子后生殖隔离机制的分子遗传基础和应用群体基因组数据分析的证据, 包括BDMI模型(Bateson-Dobzhansky-Muller incompatibility)、QTLs (quantitative trait loci)、霍尔丹法则及大X染色体效应。最后, 探讨了交配系统作为合子前隔离机制之一与物种形成的关系, 认为近交或自交通过扩大种群遗传结构分化, 增强不同交配系统的种群间不对称基因渐渗, 或种群间无基因渐渗等途径, 促进新物种形成。已知植物交配系统的演化更倾向于从异交(或自交不亲和)向自交(或近交亲和)方式, 花性状和基因组的分化推动形成所谓的自交综合征, 研究交配系统驱动或强化物种形成模式对认识植物物种形成机制有重要意义。     

生态物种形成及其研究进展

物种形成是基本的进化过程, 也是生物多样性形成的基础。自然选择可以导致新物种的产生。生态物种形成是指以生态为基础的歧化选择使不同群体分化产生生殖隔离的物种形成过程。本文首先回顾了生态物种形成的研究历史, 并详细介绍了生态物种形成的3个要素, 即歧化选择的来源、生殖隔离的形式以及关联歧化选择与生殖隔离的遗传机制。歧化选择的来源主要包括不同的环境或生态位、不同形式的性选择, 以及群体间的相互作用。生殖隔离的形式多种多样, 我们总结了合子前和合子后隔离的遗传学机制以及在生态物种形成中起到的作用。控制适应性性状的基因与导致生殖隔离的基因可以通过基因多效性或连锁不平衡相互关联起来。借助于第二代测序技术, 研究者可以对生态物种形成的遗传学与基因组学基础进行研究。此外, 本文还总结了生态物种形成领域最新的研究进展, 包括平行进化的全基因组基础, 以及基因流影响群体分化的理论基础。通过归纳比较由下至上和由上至下这两种不同的研究思路, 作者认为这两种思路的结合可以为生态物种形成基因的筛选提供更有力也更精确的方法。同时, 作者还提出生态物种形成的研究应该基于更好的表型描述以及更完整的基因组信息, 研究的物种也应该具有更广泛的代表性。     

物种形成基因及其功能

什么是物种?新物种是如何形成的？这些问题是生命科学研究的重大问题.物种的形成是在生殖隔离的基础上某些新的生物学性状的形成和保留,是生物进化的最基本过程,其实质是基因结构突变的积累与功能的分化. 地理隔离使群体中的基因不能交流,基因突变也会影响个体间交配趣向,从而造成交配隔离或者交配后杂合体的基因组不亲和、杂交不育甚至杂交不活,使不同的群体逐渐分化为新物种. 随着分子生物学与基因组学的飞速发展,进化生物学家已经发现一些与物种形成有关的基因-物种形成基因（speciation genes）,鉴定并了解这些基因的功能,不仅能使我们在分子水平上理解新物种形成的实质和规律、而且对于我们突破种间屏障进行远缘杂交育种也有重要的理论指导意义.本文综述了目前对几个物种形成基因及其功能的研究进展,为该领域的进一步研究提供资料.     

协同物种形成及其生物学意义

自达尔文与华莱士以来的每位生物学家都承认种间生态学作用对进化的意义。1964年,埃利希和雷文提出了协同进化理论。它反映了生态学相关的不同物种之间的相互作用引起的相互进化。这一理论引起了研究者的广泛重视。近年来,随着进化生态研究的深入发展,学者们对进化过程的生态机制以及生态特性与生态关系进化规律、种间生态学作用引起的物种形成有了进一步的认识。本文仅从协同物种形成的概念出发,对协同物种形成的生态机制以及生物学意义作一简要概述。协同物种形成的概念进化在本质上是一种生态过程,是生物与环境、生物与生物之间相互作用的结果。种群分化的生态机制和物种形成的本质在于对生存条件的逐步适应。按照协同进化理论,物种间的相互作用引起的协同适应     

基因流存在条件下的物种形成研究述评:生殖隔离机制进化

物种形成过程是生物多样性形成的基础, 长期以来一直是进化生物学的中心议题之一。传统的异域物种形成理论认为, 地理隔离是物种分化的主要决定因子, 物种形成只有在种群之间存在地理隔离的情况下才能发生。近年来, 随着种群基因组学的发展和溯祖理论分析方法的完善, 种群间存在基因流情况下的物种形成成为进化生物学领域新的研究焦点。物种形成过程中是否有基因流的发生?基因流如何影响物种的形成与分化?基因流存在条件下物种形成的生殖隔离机制是什么?根据已发表的相关文献资料, 作者综述了当前物种形成研究中基因流的时间和空间分布模式、基因流对物种分化的影响以及生殖隔离机制形成等问题, 指出基因流存在条件下的物种形成可能是自然界普遍发生的一种模式。     

叶绿体DNA标记在谱系地理学中的应用研究进展

谱系地理学研究旨在探究历史上发生的影响目前遗传谱系系统发育和空间分布格局关系的生态与进化过程。叶绿体DNA具有单亲遗传、低突变率、单倍体等特征, 其分子标记不同程度地保留着植物长期进化的历史遗传痕迹, 有助于深度解析谱系地理变异的形成机制。本文探讨了上述特征是怎样影响分子标记的选择、扩大或缩小群体遗传结构分化、延长或缩短空间基因溯祖时间、促进或阻碍种间基因渐渗及谱系分选(复系、并系和单系形成)进程, 重点阐述了这些影响过程的理论基础, 并结合实际例子阐述谱系地理研究进展。由于位点间在突变率、选择强度及它们与漂变互作等方面存在异质性, 今后一个研究重点就是基于叶绿体全基因组序列分析谱系地理变化格局, 包括分析DNA位点间的基因渐渗或基因流动程度差异分布及沿着叶绿体DNA序列上谱系分选差异分布。     

蟋蟀严格择偶进化快

夏威夷群岛的Laupala蟋蟀被科学家认为是世界上进化最快的物种之一。Laupala蟋蟀进化速度达到每100万年产生4．17个新物种,比非脊椎动物平均值高10倍。科学家认为严格的交配行为是Laupala蟋蟀快速物种形成的幕后决定力量。这项研究发表在《自然》杂志上。     

编委推荐

<正>Science|杂交物种形成导致金丝猴属的物种与表型多样性演化关于物种与表型多样性演化的分子机制一直都是进化生物学领域的核心命题。杂交物种形成，即两个近缘物种通过杂交而导致一个或多个新物种和新表型快速产生的过程，已被认为是植物、昆虫、鱼类以及鸟类中适应性辐射类群快速形成的重要机制。然而哺乳动物中的杂交物形成事件及其分子机制却鲜有报道。     

动物物种形成的生殖隔离机制研究进展

物种形成过程及其机制不仅是理解自然界生物多样性现象的关键,也是长期困扰达尔文的“谜中之谜”,是进化生物学研究领域的核心命题之一。物种形成是指新物种从祖先物种中分化出来的演化过程,也是种群间生殖隔离效应或屏障建立的演化过程,对这一过程及其内在遗传机制的探究和揭示是我们理解生物多样性现象的关键所在。本文聚焦于动物类群,系统阐述了动物物种生殖隔离的产生方式及其分子机制,并探讨了目前动物物种生殖隔离相关研究所面临的瓶颈、挑战和潜在机遇,为后续动物物种形成相关研究提供参考和启发。     

生物多样性起源与进化研究进展

生物多样性的起源与进化是生命科学领域最重要的科学问题之一。多组学数据的积累和相关分析技术的发展, 极大地推动了人们对生物多样性起源与进化的理解和研究, 使得阐明生物进化事件发生的过程与机制成为可能。值此《生物多样性》创刊30周年之际, 本文简要回顾生物多样性起源与进化相关研究在近年来取得的重要研究进展, 以期帮助读者了解该研究方向的发展现状。过去10年中, 生物多样性起源与进化相关研究在生命之树重建、生物多样性时空分布格局、物种概念、物种形成与适应性进化以及新性状起源与多样化等方面取得了许多重要进展, 并在此基础上厘清了许多分类单元间的系统发育关系、揭示了生物多样性分布格局的部分历史成因、提出了新的物种概念和物种形成模型、阐明了新性状和新功能发生的部分分子机制。我们认为, 更精准地重建生命之树、深入挖掘基因组数据以及多学科交叉融合将是今后生物多样性研究的主要趋势。     

THE BIOLOGY OF SPECIATION

Since Darwin published the “Origin,” great progress has been made in our understanding of speciation mechanisms. The early investigations by Mayr and Dobzhansky linked Darwin's view of speciation by adaptive divergence to the evolution of reproductive isolation, and thus provided a framework for studying the origin of species. However, major controversies and questions remain, including: When is speciation nonecological? Under what conditions does geographic isolation constitute a reproductive isolating barrier? and How do we estimate the “importance” of different isolating barriers? Here, we address these questions, providing historical background and offering some new perspectives. A topic of great recent interest is the role of ecology in speciation. “Ecological speciation” is defined as the case in which divergent selection leads to reproductive isolation, with speciation under uniform selection, polyploid speciation, and speciation by genetic drift defined as “nonecological.” We review these proposed cases of nonecological speciation and conclude that speciation by uniform selection and polyploidy normally involve ecological processes. Furthermore, because selection can impart reproductive isolation both directly through traits under selection and indirectly through pleiotropy and linkage, it is much more effective in producing isolation than genetic drift. We thus argue that natural selection is a ubiquitous part of speciation, and given the many ways in which stochastic and deterministic factors may interact during divergence, we question whether the ecological speciation concept is useful. We also suggest that geographic isolation caused by adaptation to different habitats plays a major, and largely neglected, role in speciation. We thus provide a framework for incorporating geographic isolation into the biological species concept (BSC) by separating ecological from historical processes that govern species distributions, allowing for an estimate of geographic isolation based upon genetic differences between taxa. Finally, we suggest that the individual and relative contributions of all potential barriers be estimated for species pairs that have recently achieved species status under the criteria of the BSC. Only in this way will it be possible to distinguish those barriers that have actually contributed to speciation from those that have accumulated after speciation is complete. We conclude that ecological adaptation is the major driver of reproductive isolation, and that the term “biology of speciation,” as proposed by Mayr, remains an accurate and useful characterization of the diversity of speciation mechanisms.     

Sculpin hybrid zones: natural laboratories for the early stages of speciation

Firmly rooted as we are in the genomic era, it can seem incredible that as recently as 1974, Lewontin declared, 'we know virtually nothing about the genetic changes that occur in species formation'. To the contrary, we now know the genetic architecture of phenotypic differences and reproductive isolation between species for many diverse groups of plants, animals, and fungi. In recent years, detailed genetic analyses have produced a small but growing list of genes that cause reproductive isolation, several of which appear to have diverged by natural selection. Yet, a full accounting of the speciation process requires that we understand the reproductive and ecological properties of natural populations as they begin to diverge genetically, as well as the dynamics of newly evolved barriers to gene flow. One promising approach to this problem is the study of natural hybrid zones, where gene exchange between divergent populations can produce recombinant genotypes in situ . In such individuals, genomic variation might be shaped by introgression at universally adaptive or neutral loci, even as regions associated with local adaptation or reproductive isolation remain divergent. In Nolte et   al . (2009) , the authors take advantage of two independent, recently formed hybrid zones between sculpin species to investigate genome-wide patterns of reproductive isolation. Using a recently developed genomic clines method, the authors identify marker loci that are associated with isolation, and those that show evidence for adaptive introgression. Remarkably, Nolte et   al . (2009) find little similarity between the two hybrid zones in patterns of introgression, a fact that might reflect genetic variation within species or heterogeneous natural selection. In either case, their study system has the potential to provide insight into the early stages of speciation.     

Review. The strength and genetic basis of reproductive isolating barriers in flowering plants

Speciation is characterized by the evolution of reproductive isolation between two groups of organisms. Understanding the process of speciation requires the quantification of barriers to reproductive isolation, dissection of the genetic mechanisms that contribute to those barriers and determination of the forces driving the evolution of those barriers. Through a comprehensive analysis involving 19 pairs of plant taxa, we assessed the strength and patterns of asymmetry of multiple prezygotic and postzygotic reproductive isolating barriers. We then reviewed contemporary knowledge of the genetic architecture of reproductive isolation and the relative role of chromosomal and genic factors in intrinsic postzygotic isolation. On average, we found that prezygotic isolation is approximately twice as strong as postzygotic isolation, and that postmating barriers are approximately three times more asymmetrical in their action than premating barriers. Barriers involve a variable number of loci, and chromosomal rearrangements may have a limited direct role in reproductive isolation in plants. Future research should aim to understand the relationship between particular genetic loci and the magnitude of their effect on reproductive isolation in nature, the geographical scale at which plant speciation occurs, and the role of different evolutionary forces in the speciation process.     

Evolution of reproductive isolation in stickleback fish

To understand how new species form and what causes their collapse, we examined how reproductive isolation evolves during the speciation process, considering species pairs with little to extensive divergence, including a recently collapsed pair. We estimated many reproductive barriers in each of five sets of stickleback fish species pairs using our own data and decades of previous work. We found that the types of barriers important early in the speciation process differ from those important late. Two premating barriers—habitat and sexual isolation—evolve early in divergence and remain two of the strongest barriers throughout speciation. Premating isolation evolves before postmating isolation, and extrinsic isolation is far stronger than intrinsic. Completing speciation, however, may require postmating intrinsic incompatibilities. Reverse speciation in one species pair was characterized by significant loss of sexual isolation. We present estimates of barrier strengths before and after collapse of a species pair; such detail regarding the loss of isolation has never before been documented. Additionally, despite significant asymmetries in individual barriers, which can limit speciation, total isolation was essentially symmetric between species. Our study provides important insight into the order of barrier evolution and the relative importance of isolating barriers during speciation and tests fundamental predictions of ecological speciation.     

The accumulation of reproductive barriers during speciation: postmating barriers in two behaviorally isolated species of darters (Percidae: Etheostoma)

Identifying the manner in which reproductive barriers accumulate during lineage divergence is central to establishing general principles of species formation. One outstanding question is which isolating mechanisms form the first complete barrier to gene flow in a given lineage or under a particular set of conditions. To identify these initial reproductive barriers requires examining lineages in very early stages of divergence, before multiple reproductive barriers have evolved to completion. We quantified the strength of three postmating barriers in a pair of darter species and compared these estimates to each other and to the strength of behavioral isolation (BI) reported in a previous study. Results reveal no evidence of gametic incompatibility but intermediate levels of conspecific sperm precedence and hybrid inviability. As BI is nearly complete, our analysis comparing the strength of multiple reproductive barriers implicates the evolution of mate choice as central to both the origin and maintenance of these species. Further examination of ecological isolation and hybrid sterility is necessary to determine the role of these barriers in darter speciation.     

WEAK CROSSABILITY BARRIER BUT STRONG JUVENILE SELECTION SUPPORTS ECOLOGICAL SPECIATION OF THE HYBRID PINE PINUS DENSATA ON THE TIBETAN PLATEAU

Determining how a new hybrid lineage can achieve reproductive isolation is a key to understanding the process and mechanisms of homoploid hybrid speciation. Here, we evaluated the degree and nature of reproductive isolation between the ecologically successful hybrid species Pinus densata and its parental species P. tabuliformis and P. yunnanensis. We performed interspecific crosses among the three species to assess their crossability. We then conducted reciprocal transplantation experiments to evaluate their fitness differentiation, and to examine how natural populations representing different directions of introgression differ in adaptation. The crossing experiments revealed weak genetic barriers among the species. The transplantation trials showed manifest evidence of local adaptation as the three species all performed best in their native habitats. Pinus densata populations from the western edge of its distribution have evolved a strong local adaptation to the specific habitat in that range; populations representing different directions of introgressants with the two parental species all showed fitness disadvantages in this P. densata habitat. These observations illustrate that premating isolation through selection against immigrants from other habitat types or postzygotic isolation through selection against backcrosses between the three species is strong. Thus, ecological selection in combination with endogenous components and geographic isolation has likely played a significant role in the speciation of P. densata.     

Thermal adaptation and ecological speciation

Ecological speciation is defined as the emergence of reproductive isolation as a direct or indirect consequence of divergent ecological adaptation. Several empirical examples of ecological speciation have been reported in the literature which very often involve adaptation to biotic resources. In this review, we investigate whether adaptation to different thermal habitats could also promote speciation and try to assess the importance of such processes in nature. Our survey of the literature identified 16 animal and plant systems where divergent thermal adaptation may underlie (partial) reproductive isolation between populations or may allow the stable coexistence of sibling taxa. In many of the systems, the differentially adapted populations have a parapatric distribution along an environmental gradient. Isolation often involves extrinsic selection against locally maladapted parental or hybrid genotypes, and additional pre- or postzygotic barriers may be important. Together, the identified examples strongly suggest that divergent selection between thermal environments is often strong enough to maintain a bimodal genotype distribution upon secondary contact. What is less clear from the available data is whether it can also be strong enough to allow ecological speciation in the face of gene flow through reinforcement-like processes. It is possible that intrinsic features of thermal gradients or the genetic basis of thermal adaptation make such reinforcement-like processes unlikely but it is equally possible that pertinent systems are understudied. Overall, our literature survey highlights (once again) the dearth of studies that investigate similar incipient species along the continuum from initial divergence to full reproductive isolation and studies that investigate all possible reproductive barriers in a given system.     

Population genomics and speciation

The process of speciation begins with genomically-localised barriers to gene exchange associated with loci for local adaptation, intrinsic incompatibility or assortative mating. The barrier then spreads until reproductive isolation influences the whole genome. The population genomics approach can be used to identify regions of reduced gene flow by detecting loci with greater differentiation than expected from the average across many loci. Recently, this approach has been used in several systems. I review these studies, concentrating on the robustness of the approach and the methods available to go beyond the simple identification of differentiated markers. Population genomics has already contributed significantly to understanding the balance between gene flow and selection during the evolution of reproductive isolation and has great future potential both in genome species and in non-model organisms.     

Ecological speciation in phytophagous insects

Divergent natural selection has been shown to promote speciation in a wide range of taxa. For example, adaptation to different ecological environments, via divergent selection, can result in the evolution of reproductive incompatibility between populations. Phytophagous insects have been at the forefront of these investigations of 'ecological speciation' and it is clear that adaptation to different host plants can promote insect speciation. However, much remains unknown. For example, there is abundant variability in the extent to which divergent selection promotes speciation, the sources of divergent selection, the types of reproductive barriers involved, and the genetic basis of divergent adaptation. We review these factors here. Several findings emerge, including the observation that although numerous different sources of divergent selection and reproductive isolation can be involved in insect speciation, their order of evolution and relative importance are poorly understood. Another finding is that the genetic basis of host preference and performance can involve loci of major effect and opposing dominance, factors which might facilitate speciation in the face of gene flow. In addition, we raise a number of other recent issues relating to phytophagous insect speciation, such as alternatives to ecological speciation, the geography of speciation, and the molecular signatures of speciation. Throughout, we aim to both synthesize what is known, as well as highlight areas where future work is especially needed.