The median means of species concepts and species delimitation

半世纪以来,物种概念的定义备受关注,不同研究方向的生物学家提出24种不同或至少有分歧的物种概念,根据其不同的物种概念,物种的界定和物种的数量会出现很大的差异.人们普遍认同:物种是进化分离的微居群谱系,但把谱系分离过程中获得的特征如生殖隔离、可鉴定性、单系统发生等视为鉴定物种次级特征却有不同的声音.该文提出统一的物种概念,把谱系进化分离作为物种界定的唯一而又必要的特征,把谱系分离过程中获得的次级特征作为界定谱系分离的证据.鉴于此,物种概念间的分歧就会化解.其一,物种概念化与物种界定明显分开,不再混淆;其二,谱系的次级特征只与物种界定有关,在某种程度上为谱系分离提供证据;第三,若能把合理解释的任何一个特征作为某物种客观存在的证据,这样更多的特征更能确定谱系分离;最后最重要的是,统一物种概念使我们解放思想,扬弃传统的物种界定标准,探求物种界定的新思路.     

“整合物种概念”和“分化路上的物种”

已有的各个物种概念对物种的认识类似盲人摸象, 只包含了物种的某一个方面; 而一个分化后期的成熟物种应涵盖了所有的物种概念。但是, 尚未到达分化后期的物种往往又已开始新一轮的物种分化; 自然中存在的多数“物种”处于分化路上。这种循环往复连续分化产生的物种, 存在种间生殖隔离不彻底、基因流频繁发生、网状进化突出等现象。此外, 对于不同的物种对, 最早开始分化的基因以及不同物种概念所要求的条件的分化顺序不是统一的, 而是随机的。定义一个适合所有“分化路上的物种”概念存在较大困难。但是, 应采用尽可能多的物种概念来界定分化路上的物种、发表新种和进行分类处理; 也应承认种间可能广泛存在不完全的生殖隔离和有限的基因流, 即有不属于两个物种群体的杂交或回交个体的存在。这样划分的物种比只依据一个物种概念认定的物种具有更高的客观性和科学性。     

浅析物种概念的演变历史

本文是一篇关于物种概念演变的简述。生物学家用不同的方法或标准划分物种, 就形成了不同的物种概念, 如生物学物种、形态学物种、生态学物种、进化物种、系统发生或支序物种, 或它们的组合, 等等。它们都揭示了物种属性的特定侧面, 都是不同物种客观存在的真实反映, 但都无法令所有人满意。对真核生物来说, 无论它们在形态上的差别有多大, 生殖隔离(不能产生可育的后代)应该是两个群体能否真正分化成不同物种的关键, 这种隔离机制可以是地理的、行为的或其他方式; 而生殖隔离总会伴随着一些形态或遗传上的变化, 虽然这些特征可能与生殖隔离本身并无多大关系, 但往往成为分类学家或分子进化生物学家区分种的依据,对已经灭绝的化石物种来说, 生殖隔离的物种划分方式就无能为力了。如何准确定义一个物种依然充满着矛盾, 因为基于生殖隔离的物种概念不实用, 而实用的物种概念(如形态学物种)又被认为是人为的。     

康定湍蛙物种界定

康定湍蛙Amolops kangtingensis依据多地混合标本订立,其分类地位一直存在争议。本文从居群水平出发,涵盖其多个模式产地及分布区,联合染色体核型、形态数量性状、分子系统发育分析,对其有效性及物种进行界定。结果表明,以新都桥为模式产地的康定湍蛙成立,分布区域大致界定于折多山以西雅砻江流域,海拔3000 m及以上高原地区,而原康定湍蛙大渡河流域各居群应划归四川湍蛙A.mantzorum物种之中。     

生物多样性事业需要科学、可操作的物种概念

物种概念(species concept)是生物学家们持续关注的中心问题。物种概念决定物种划分, 而物种划分的合理性关系到生物多样性的研究、保护和可持续利用。本文把现有较流行的物种概念分为6类, 并对它们予以述评后指出: 虽然生物学物种概念、遗传学物种概念、进化物种概念、系统发生物种概念等从不同方面认识了物种的客观真实性和物种的本质, 但在实践中都难以操作。绝大多数物种是由分类学家划分的, 但目前所有的分类学物种概念都包含有不同程度的主观因素, 从而造成物种划分的人为性, 对生物多样性研究造成负面影响。因此, 生物多样性事业需要科学、可操作的物种概念。本文在吸收了生物学物种概念、遗传学物种概念、进化物种概念以及系统发生物种概念等的长处, 也分析了它们的不足和问题的基础上提出一个新的物种概念, 即形态-生物学物种概念。最后, 以芍药属(Paeonia)几个物种的处理为例, 说明这一新的物种概念是可操作的, 划分的物种在形态上区别分明, 易于鉴别。更重要的是, 其结果得到基于25或26个单拷贝或寡拷贝核基因DNA序列所作的系统发生分析的强有力支持。各个物种在系统发生树上形成单系和独立的谱系, 表明其间各自形成独立的基因库, 没有基因交换, 它们独立进化, 有各自的生态位和独立的分布区。因此, 利用这一新的物种概念能够达到预期目标。     

菌物分类学研究中常见的物种概念

物种是生物多样性与分类学研究的基本单元, 物种识别是生物学研究的基本问题之一。物种的划分一直以来都没有一个明确统一的标准, 这使得分类学多少带有主观的色彩, 并经常被看作艺术而不完全是科学的研究。本文简要概述了菌物分类学研究中常见的3个物种概念, 即形态学种、生物学种和系统发育学种的背景和应用现状, 并通过实例讨论了这3个物种概念的特点及应用中存在的问题, 特别是各个物种概念之间的交错, 以期为菌物分类学研究和物种概念探讨提供参考。     

物种与物种多样性

本文首先讨论生物物种的科学概念和生物学本质，分析物种客观存在的自然属性和物种概念的局限性，认为物种的生物学属性和物种多样性的科学属性之间有着本质联系。物种多样性研究的实质是研究生物物种的生物学多样性。度量物种多样性程度有多种方法，但物种数目是物种多样性程度最直接、也是最基本的表达，估计物种多样性数目是当前国际上物种多样性研究的核心与热点内容。物种多样性产生的根源是物种形成，物种绝灭速率是维持物种多样性的关键因素。本文简要总结了物种形成与绝灭的基本模式和机制，通过分析生物地理区系与物种多样性研究的密切关系，说明物种的区系成份分析是物种多样性大尺度格局研究的重要内容。     

生物学物种概念在化石物种鉴定中的应用问题北大核心CSCD

物种概念是生物学的核心问题,而在化石鉴定中的应用存在诸多困难和分歧。本文介绍生物学物种概念在古生物学研究中的优点、难点与必要性。近年来,生物学物种概念已被古生物学家们广泛接受,居群和种内变异的重要性越来越受到重视。文章以二叠纪牙形类和腕足类化石种等为例,探讨如何在厘定物种、建立新种和使用亚种概念时,运用生物学物种概念及其延伸出来的各个标准。文章还讨论生物学物种在不同门类中的适用情况。认为在后生动物中,生物学物种可以得到较好的验证,在化石鉴定中,要尽量识别每一个种的发育序列和充分考虑种内变异,这样鉴定的化石种具有较高的地层对比价值,应当尽量避免仅仅根据个别标本的形态特征鉴定化石物种。     

论物种的客观真实性

关于物种的概念和本质的争论由来已久。大多数学者认为种是自然界客观存在的真实单位,是形态上和生殖上间断的群体体系,与种内连续的群体体系——宗,有着本质的区别。少数学者则认为种是主观意识的产物,是为了分类的目的而任意确定的人为的分类阶元,与宗只有程度的不同而无本质的区别;只有个体才是客观真实的单位。以形态标准为主的分类学种概念和以生殖隔离为标准的生物学种概念只能说代表了自然界有机体类群不连续性的两个不尽相符,但部分一致的侧面,而不能说就是客观物种的反映。自然界的生命有机体有两重性。它们既不是一群乱七八糟的乌合之众,也不是秩然不紊的鳞次栉比,而是以群体的组织形式适应于各自分布区内的生态位,在表型和基因型的变异式样上具有一定规律的遗传多样性。物种的客观本质也有两重性。物种作为有机体组合的单位既存在又不存在。说物种客观存在是因为按形态或生殖的不连续性标准划分的“种”在自然界具有一定的普遍性;说物种并非客观存在是因为至今还没有一个能把所有的生命有机体都划分成统一的生物学单位的不连续性标准。     

鳇亚科似鳇属鱼类的物种界定和系统发育关系

逗亚科似逗属鱼类的物种界定保持争议, 系统发育关系尚待解决。研究取样似逗属鱼类所有种, 使用核基因多位点序列重建似逗属鱼类的系统发育关系, 运用分子的物种界定方法并结合形态特征分析厘定我国似逗属鱼类的分类。贝叶斯系统发育树结果表明: 桂林似逗与平江似逗是单系种; 似逗与扁嘴似逗是多系种, 前者包括五个谱系A至E, 后者包括两个谱系A与B。POFAD距离分析和Structurama分析的结果表明似逗和扁嘴似逗的每个谱系是独立遗传种群, BP & P分析结果强烈支持它们是不同种。*Beast物种树结果揭示: 扁嘴似逗谱系B位于似逗属鱼类的基部位置; 似逗谱系A与B是姊妹群关系, 似逗谱系C是扁嘴似逗谱系A的姊妹群, 它们一起与桂林似逗形成姊妹群关系; 似逗谱系D与E是姊妹群关系, 它们一起是平江似逗的姊妹群。结合形态证据, 对我国似逗属鱼类分类厘定如下: 限定严格意义似逗包括似逗谱系A+B; 恢复长吻似逗(Pseudogobio longirostris Mori, 1934)给予似逗谱系C分类名; 似逗谱系D与E是隐存种, 桂林似逗与平江似逗是有效种。     

The species concept as an emergent property of population biology

Resurgent interest in the genetics of population divergence and speciation coincides with recent critical evaluation of species concepts and proposals for species delimitation. An important result of these parallel trends is a slight but important conceptual shift in focus away from species diagnoses based on prior species concepts or definitions, and toward analyses of the processes acting on lineages of metapopulations that eventually lead to differences recognizable as species taxa. An advantage of this approach is that it identifies quantitative metapopulation differences in continuous variables, rather than discrete entities that do or do not conform to a prior species concept, and species taxa are recognized as an emergent property of population-level processes. The tension between species concepts and diagnosis versus emergent recognition of species taxa is at least as old as Darwin, and is unlikely to be resolved soon in favor of either view, because the products of both approaches (discrete utilitarian taxon names for species, process-based understanding of the origins of differentiated metapopulations) continue to have important applications.     

How to fail at species delimitation

Species delimitation is the act of identifying species‐level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting species. However, most recent investigations only utilize a handful (i.e. 2–3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.     

Phylogeny and species delimitation of the C-genome diploid species in Oryza

The diploid Oryza species with C-genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C-genome (BBCC,CCDD).Despite extensive studies,the phylogenetic relationship among the C-genome species and the taxonomic status of some taxa remain controversial.In this study,we reconstructed the phylogeny of three diploid species with C-genome (Oryza officinalis,O.rhizomatis,and O.eichingeri) based on sequences of 68 nuclear single-copy genes.We obtained a fully resolved phylogenetic tree,clearly indicating the sister relationship of O.officinalis and O.rhizomatis,with O.eichingeri being the more divergent lineage.Incongruent phylogenies of the C-genome species found in previous studies might result from lineage sorting,introgression/hybridization and limited number of genetic markers used.We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O.eichingeri.Analyses of two datasets (68 genes with a single sample,and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O.eichingeri.In addition,we evaluated the impact of the number of sampled individuals and loci on species delimitation.Our simulation suggests that sampling multiple individuals is critically important for species delimitation,particularly for closely related species.     

SpedeSTEM: a rapid and accurate method for species delimitation

We describe a software package (SpedeSTEM) that allows researchers to conduct a species delimitation analysis using intraspecific genetic data. Our method operates under the assumption that a priori information regarding group membership is available, for example that samples are drawn from some number of described subspecies, races or distinct morphotypes. SpedeSTEM proceeds by calculating the maximum likelihood species tree from all hierarchical arrangements of the sampled alleles and uses information theory to quantify the model probability of each permutation. SpedeSTEM is tested here against empirical and simulated data; results indicate that evolutionary lineages that diverged as few as 0.5N generations in the past can be validated as distinct using sequence data from little as five loci. This work enables speciation investigations to identify lineages that are evolutionarily distinct and thus have the potential to form new species before these lineages acquire secondary characteristics such as reproductive isolation or morphological differentiation that are commonly used to define species.     

Phylogeny and species delimitation of the C‐genome diploid species in Oryza

Abstract The diploid Oryza species with C‐genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C‐genome (BBCC, CCDD). Despite extensive studies, the phylogenetic relationship among the C‐genome species and the taxonomic status of some taxa remain controversial. In this study, we reconstructed the phylogeny of three diploid species with C‐genome (Oryza officinalis, O. rhizomatis, and O. eichingeri) based on sequences of 68 nuclear single‐copy genes. We obtained a fully resolved phylogenetic tree, clearly indicating the sister relationship of O. officinalis and O. rhizomatis, with O. eichingeri being the more divergent lineage. Incongruent phylogenies of the C‐genome species found in previous studies might result from lineage sorting, introgression/hybridization and limited number of genetic markers used. We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O. eichingeri. Analyses of two datasets (68 genes with a single sample, and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O. eichingeri. In addition, we evaluated the impact of the number of sampled individuals and loci on species delimitation. Our simulation suggests that sampling multiple individuals is critically important for species delimitation, particularly for closely related species.     

Process-based species delimitation leads to identification of more biologically relevant species*

Most approaches to species delimitation to date have considered divergence-only models. Although these models are appropriate for allopatric speciation, their failure to incorporate many of the population-level processes that drive speciation, such as gene flow (e.g., in sympatric speciation), places an unnecessary limit on our collective understanding of the processes that produce biodiversity. To consider these processes while inferring species boundaries, we introduce the R-package delimitR and apply it to identify species boundaries in the reticulate taildropper slug (Prophysaon andersoni). Results suggest that secondary contact is an important mechanism driving speciation in this system. By considering process, we both avoid erroneous inferences that can be made when population-level processes such as secondary contact drive speciation but only divergence is considered, and gain insight into the process of speciation in terrestrial slugs. Further, we apply delimitR to three published empirical datasets and find results corroborating previous findings. Finally, we evaluate the performance of delimitR using simulation studies, and find that error rates are near zero when comparing models that include lineage divergence and gene flow for three populations with a modest number of Single Nucleotide Polymorphisms (SNPs; 1500) and moderate divergence times (<100,000 generations). When we apply delimitR to a complex model set (i.e., including divergence, gene flow, and population size changes), error rates are moderate (∼0.15; 10,000 SNPs), and, when present, misclassifications occur among highly similar models.     

Species delimitation of North American Nyssa species

The development of next-generation sequencing technologies allows researchers to address complex problems in species delimitation, especially for non-model organisms. The taxonomic status of North American Nyssa species has long been debated and remains controversial. To elucidate the genetic structure and phylogenetic relationships of the five currently recognized North American Nyssa species, we conducted whole-genome sequencing of representative individuals and identified genome-wide single-nucleotide polymorphisms (SNPs) by utilizing the recently released chromosome-level assembly of Nyssa sinensis genome. Population genetic and phylogenetic analyses consistently inferred four well-supported genetic clusters from our sampled individuals, that is, N. aquatica, N. ogeche, N. sylvatica, and N. biflora–N. ursina. Although the identification of N. biflora and N. ursina is primarily based on the morphological characteristics of leaves and drupes, the present evidence, including our principal components analysis of leaf morphological traits, strongly supports the taxonomic designation of N. biflora and N. ursina as a single species. In addition, these four genetic clusters were grouped into two major clades, that is, clade 1 (N. aquatica and N. ogeche) and clade 2 (N. sylvatica and N. biflora–N. ursina). Despite the fact that no evidence of widespread gene flow was found between these two major clades, our analyses revealed the possibility of introgression from N. sylvatica into N. biflora, albeit at a relatively low frequency. This study demonstrates the use of whole-genome sequences as a promising avenue for delimiting species boundaries and further advocates for an integrative approach in the assessment of species delimitation.     

Revisiting species delimitation within the genus Oxystele using DNA barcoding approach

The genus Oxystele, a member of the highly diverse marine gastropod superfamily Trochoidea, is endemic to southern Africa. Members of the genus include some of the most abundant molluscs on southern African shores and are important components of littoral biodiversity in rocky intertidal habitats. Species delimitation within the genus is still controversial, especially regarding the complex O. impervia / O. variegata. Here, we assessed species boundaries within the genus using DNA barcoding and phylogenetic tree reconstruction. We analysed 56 specimens using the mitochondrial gene COI. Our analysis delimits five molecular operational taxonomic units (MOTUs), and distinguishes O. impervia from O. variegata. However, we reveal important discrepancies between MOTUs and morphology-based species identification and discuss alternative hypotheses that can account for this. Finally, we indicate the need for future study that includes additional genes, and the combination of both morphology and genetic techniques (e.g. AFLP or microsatellites) to get deeper insight into species delimitation within the genus.