Species: the concept, category and taxon

The term species by itself is vague because it refers to the species concept, the species category and the species taxon, all of which are distinct although related to one another. The species concept is not primarily a part of systematics, but has always been an integral part of basic biological theory, It is based on evolutionary theory and applies only to sexually reproducing organisms. The species concept and the phyletic lineage concept are quite distinct although they are related to one another. The important aspect of the species concept is lack of gene flow between different species, and hence the defining criterion of the species is genetic isolation. The species concept is often considered as non‐dimensional, both in time and space. Species possess three different major properties, namely genetic isolation, reproductive isolation and ecological isolation; these properties evolve at different times and under the effect of different causes during the speciation process. Speciation requires an external isolating barrier during the initial allopatric phase in which genetic isolation evolves and must reach 100% efficiency. The subsequent sympatric phase of speciation occurs after the disappearance of the external isolating barrier when members of the two newly evolved species can interact with one another and exert mutual selective demands on one another. Much of the reproductive and ecological isolation evolves during this secondary sympatric phase. The species category is a rank in the taxonomic hierarchy and serves as the basis on which the diversity of organisms is described; it is not the same as the species concept. The species category applied to all organisms, sexually and asexually reproducing. The species taxon is the practical application of the species category in systematics with the recognition of species taxa requiring many arbitrary decisions. No single set of rules exist by which the species category can be applied to all organisms. Recognition of species taxa in asexually reproducing organisms is based on amount of variation and gaps in the variation of phenotypic features associated with ecological attributes of these organisms as compared with similar attributes in sympatric species taxa of sexually reproducing organisms. Species taxa are multidimensional in that they exist over space–time and often have fuzzy borders. Because recognition of species taxa, including those in sexually reproducing organisms, depends on many arbitrary decisions especially when dealing with broad geographical and temporal ranges, species taxa cannot be used as the foundation for developing and testing theoretical concepts in evolutionary theory which can only be done with the non‐dimensional species concept.     

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。     

Species concepts in agamic complexes: Applications in theRanunculus auricomus complex and general perspectives

The application of different current species concepts to the predominantly apomicticR. auricomus complex (goldilocks) is discussed. As with other uniparental reproducing organisms, biological species concepts are hardly applicable in apomictic groups. Information on reproductive systems, phenetic and ecological differentation, and evolutionary traits favour an “agamospecies” concept. It is argued that agamic lineages in goldilocks can be treated neither as subspecific taxa, nor as hybrids. A general viewpoint is proposed that species are stable phases within a continuous process of diversification of ancestral-descendent lineages. Constancy of progeny, similarity of phenotype, and ecogeographical niches of organisms are regarded as the most important operational criteria for grouping and ranking of species. Mode of reproduction is seen as a feature of a species — not as a criterion for its definition. Internal stability of features is regarded as more important for species definition than the features themselves.     

The cladistic solution to the species problem

The correct explanation of why species, in evolutionary theory, are individuals and not classes is the cladistic species concept. The cladistic species concept defines species as the group of organisms between two speciation events, or between one speciation event and one extinction event, or (for living species) that are descended from a speciation event. It is a theoretical concept, and therefore has the virtue of distinguishing clearly the theoretical nature of species from the practical criteria by which species may be recognized at any one time. Ecological or biological (reproductive) criteria may help in the practical recognition of species. Ecological and biological species concepts are also needed to explain why cladistic species exist as distinct lineages, and to explain what exactly takes place during a speciation event. The ecological and biological species concepts work only as sub-theories of the cladistic species concept and if taken by themselves independently of cladism they are liable to blunder. The biological species concept neither provides a better explanation of species indivudualism than the ecological species concept, nor, taken by itself, can the biological species concept even be reconciled with species individualism. Taking the individuality of species seriously requires subordinating the biological, to the cladistic, species concept.     

Species concepts and the ontology of evolution

Biologists and philosophers have long recognized the importance of species, yet species concepts serve two masters, evolutionary theory on the one hand and taxonomy on the other. Much of present-day evolutionary and systematic biology has confounded these two roles primarily through use of the biological species concept. Theories require entities that are real, discrete, irreducible, and comparable. Within the neo-Darwinian synthesis, however, biological species have been treated as real or subjectively delimited entities, discrete or nondiscrete, and they are often capable of being decomposed into other, smaller units. Because of this, biological species are generally not comparable across different groups of organisms, which implies that the ontological structure of evolutionary theory requires modification. Some biologists, including proponents of the biological species concept, have argued that no species concept is universally applicable across all organisms. Such a view means, however, that the history of life cannot be embraced by a common theory of ancestry and descent if that theory uses species as its entities.These ontological and biological difficulties can be alleviated if species are defined in terms of evolutionary units. The latter are irreducible clusters of reproductively cohesive organisms that are diagnosably distinct from other such clusters. Unlike biological species, which can include two or more evolutionary units, these phylogenetic species are discrete entities in space and time and capable of being compared from one group to the next.     

From Anomaly to Unification: Tracy Sonneborn and the Species Problem in Protozoa, 1954--1957

This article examines the critique of the biological species concept advanced by protozoan geneticist Tracy Sonneborn at the 1955 AAAS symposium on “the species problem,” published subsequently in 1957. Although Sonneborn was a strong proponent of a population genetical conception of species, he became critical of the biological species concept for its failure to incorporate asexual and obligatory inbreeding organisms. It is argued that Sonneborn's intimate knowledge of the ciliate protozoan Paramecium aurelia species complex brought him into conflict with a growing pressure in the biological sciences to emphasize universal principles of life. Faced with the need to defend the value of P. aurelia as an investigative tool, Sonneborn argued that the sharp break in nature between sexual and asexual organisms posited by proponents of the biological species concept was not an existential feature of the living world, but rather the misleading consequence of an operational definition of species based only upon sexual organisms. Drawing upon his knowledge of the immense variability of P. aurelia, he proposed instead a continuum of breeding systems from obligatory outbreeding to asexual organisms, and a more broadly unifying definition of species that incorporated asexual as well as sexual organisms. Paradoxically, the push for unification that then characterized the evolutionary synthesis served to debar critical consideration of Sonneborn's more unificatory alternative, and his underlying contention that biological anomaly could serve as an important source of conceptual unification. This revised version was published online in July 2006 with corrections to the Cover Date.     

Organisms in evolution

Organisms constitute one of the most remarkable features of our living world. However, they have not yet received any accepted characterization within the framework of the evolutionary theory. The reasons for this contrast between the saliency of organisms in the biological landscape and their theoretical status are multiple and they are analyzed in the first part of this paper. Starting from this contrast, I argue for a theoretically grounded concept of organism within the framework of evolutionary theory itself. To this effect I argue that the theory of major transitions in evolution (Maynard Smith and Szathmáry 1995; Michod 1999) provides us with the theoretical basis for an understanding of the individuality of organisms and I propose a first characterization of organisms as evolutionary units structured by a division of reproductive labor among their parts. I also discuss one of the most important implications of this definition, namely that some colonial entities are to be counted as superorganisms. Finally, I show that though theoretically satisfying, this definition does not suffice in order fully to individuate the organisms and superorganisms in practice. To this end, physiology is needed, because it offers us some criteria for their individuation in ecological space. These criteria, however, are not immune to errors through misidentification and their shortcomings are discussed in the last section. In conclusion, I emphasize the positive implications of these criteria concerning the ecological significance of organisms.     

Gen‐morph species concept—A new and integrative species concept for outbreeding organisms

The present article briefly reviewed the prevailing species concepts, especially biological, genetic, evolutionary, phylogenetic, ecological, and several taxonomic species concepts. The former five reflect the properties of species from diverse aspects and in different degrees, while taxonomic species concepts all contain more or less subjective elements, except for Hedberg's taxonomic method (not species concept). So far, there is no species concept that is both theoretically rational and practically operable. The present article outlined recent studies on the genus Paeonia L. (Paeoniaceae) in biology, particularly in morphology, biogeography, molecular phylogeny, and reproductive behavior, which provided insight into the relationship between variation of morphological characteristics and phylogeny. Taking the study on Paeonia L. as a case, referring to studies on some other plant groups, and incorporating the merits of the prevailing species concepts into our consideration, “gen‐morph species concept” is proposed here formally as new for outbreeding organisms. The new species concept has three special features: (i) a bridge linking morphological aspect with genetic and other aspects of species; (ii) proposal of a concrete morphological criterion for species definition, and (iii) considering quantitative and qualitative characteristics as equally valuable for species definition and introducing statistics into the concept to handle such characteristics. Therefore, the gen‐morph species concept is an integrative species concept, both theoretically objective and practically operable.     

ANDROGENETICS AND TRIPLOIDS FROM AN INTERACTING PARTHENOGENETIC HYBRID AND ITS ANCESTORS IN STICK INSECTS

Populations of unisexual organisms are often assumed to be genetically invariant (clones) and destined to a short existence on an evolutionary timescale. Unisexual organisms are most often obligate parthenogens and, by definition, ought to be completely isolated reproductively from related bisexual organisms. The assumption of complete reproductive isolation between amphimictic ancestors and thelytokous hybrids is common to most hypotheses on the evolution of sex and its adaptive significance. Stick insects of the genus Bacillus however provide evidence for reproductive interactions between allodiploid parthenogens and their ancestors, because pure species progeny (androgenetics) and triploid descendants are produced. These findings demonstrate that, through androgenesis, offspring of parthenogenetic hybrid females can contribute specimens of both sexes to the fathering species when fertilized by syntopic ancestral males and the parthenogenetic egg of strictly clonal females, when fertilized, allows a third genome to be added to the allodiploid chromosome set. These triploid genomes promote further genetic diversification and evolution of the unisexual populations through the formation of new clones by recombination during the changed maturation mode of allotriploid eggs. All this argues for much more complex breeding systems and evolutionary pathways than are usually assumed for hybrid unisexual organisms.     

An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer--Brachionus plicatilis

Since the advent of molecular phylogenetics, there is increasing evidence that many small aquatic and marine invertebrates--once believed to be single, cosmopolitan species--are in fact cryptic species complexes. Although the application of the biological species concept is central to the identification of species boundaries in these cryptic complexes, tests of reproductive isolation do not frequently accompany phylogenetic studies. Because different species concepts generally identify different boundaries in cryptic complexes, studies that apply multiple species concepts are needed to gain a more detailed understanding of patterns of diversification in these taxa. Here we explore different methods of empirically delimiting species boundaries in the salt water rotifer Brachionus plicatilis by comparing reproductive data (i.e., the traditional biological species concept) to phylogenetic data (the genealogical species concept). Based on a high degree of molecular sequence divergence and largely concordant genetic patterns in COI and ITS1, the genealogical species hypothesis indicates the existence of at least 14 species--the highest estimate for the group thus far. A test of the genealogical species concept with biological crosses shows a fairly high level of concordance, depending on the degree of reproductive success used to draw boundaries. The convergence of species concepts in this group suggests that many of the species within the group may be old. Although the diversity of the group is higher than previously understood, geographic distributions remain broad. Efficient passive dispersal has resulted in global distributions for many species with some evidence of isolation by distance over large geographic scales. These patterns concur with expectations that micro-meiofauna (0.1-1mm) have biogeographies intermediate to microbial organisms and large vertebrates. Sympatry of genetically distant strains is common.     

Systematics,reproductive isolation and species boundaries in monogonont rotifers

The typological concept of rotifer species and the morphological basis of rotifer systematics is reviewed and alternatives proposed. Occasional sexuality in the cyclical parthenogenetic life cycle of monogononts permits application of the biological species concept to this group. Data from cross-mating experiments with Asplanchna, Brachionus and Epiphanes illustrate the usefulness of reproductive isolation as a criterion for species boundaries. Populations from different geographic regions are often interfertile indicating that rotifer species are genetically integrated over wide areas. The main types of isolating mechanisms operating in monogononts are reviewed. The role of behavioral reproductive isolation in maintaining species boundaries is examined. The use of a mate recognition bioassay which estimates the probability of copulation and quantifies the degree of isolation is described. Recent work of the mechanism of mate recognition is reviewed. It is concluded that the biological species concept is applicable to rotifers and that a more experimental approach to determining species boundaries is both feasible and desirable.     

On the integrated frameworks of species concepts: Mayden’s hierarchy of species concepts and de Queiroz’s unified concept of species

Richard L. Mayden and Kevin de Queiroz have devised and developed ‘a hierarchy of species concepts’ and ‘a unified species concept’, respectively. Although their integrated frameworks of species concepts are rather different as to how to integrate the diverse modern concepts of species, the end result is that they are likely to agree on species recognition in nature, because they virtually share the same major components (i.e. evolutionary or lineage concept of species; same way of delimiting species), and have the same important consequences. Both the hierarchical and unified frameworks, however, are interpreted to have shortcoming regarding the way of integrating the modern species concepts. I reformulate these ideas into a framework of species concepts as follows: It treats the idea of species as population‐level evolutionary lineages (sensu Wiley 1978 ) as the concept for species category, and it adopts the contingent biological properties of species (e.g. internal reproductive isolation, diagnosability, monophyly) as operational criteria in delimiting species. I also suggest that existing and revised versions of the integrated framework of species concepts all are not new species concepts, but versions of the evolutionary species concept, because they treat the evolutionary (or lineage) species concept as the concept for species category.     

为什么在物种概念上难以达成共识?

生物学家通常认为物种是生命多样性的基本单位。然而, 尽管近一个世纪以来生物学家们不断地讨论物种概念问题, 但到目前为止仍然难以形成共识。大多数生物学家关注如何定义物种主要是因为它有非常重要的实践意义, 所以, 不同学者提出的物种概念在很大程度上是基于实践应用上的可操作性, 并且其视角难免受其专业见地以及对形成新物种的进化过程的认识所影响。物种代表了进化过程的一个阶段, 而且不同的“物种”可能处于物种形成这个进化过程的不同阶段。鉴于“定义”实际上是一种类似协议的约定或界定, 任何定义都是一种带有局限性的概括, 因此我们可能很难建立一个与分类实践中千变万化的情况都能完全匹配协调的物种定义。已经提出来的那些物种概念或定义都有其合理性, 但是也没有一个是完美无缺的。认识到这一点很重要, 否则就可能会因为固执地坚持某一特定的物种概念而在物种界定和进化研究中自觉或不自觉地引入错误甚至制造混乱。     

Removing ambiguity from the biological species concept

The biological species concept (BSC) is a common way to define species although it is ambiguous even when strictly applied. I interpret it here syntactically in four different ways and show that one of them is more suitable than previously thought. The first interpretation (fully restricted) produces discrete, non-overlapping biological species with the inconvenience of being inapplicable when there is gradual evolution of reproductive isolation. The second (cohesion relaxed) and fourth (fully relaxed) interpretation are overly unrestricted to be useful. The third interpretation (isolation relaxed) overcomes the problem of gradual evolution of reproductive isolation at the cost of recognizing non-discrete, overlapping biological species. That is, some populations are members of more than one species. Non-discreteness, however, removes hand-waving in infamous difficulties of the BSC such as those with ring species, phyletic species, and syngameons. Moreover, it lets the BSC deal with introgression with no appeal to subjectivity. Therefore, precision in terms underlying the BSC provides an objective and still natural alternative to deal with gradual evolution of reproductive isolation.     

What is a fish species?

The formal processes of alpha-taxonomy ensure that species have uniquenames and can be identified. No similar process is mandatory forinfraspecific variation, so the species is a uniquely importantpractical term. At present, there is little agreement of the definitionof a species. In the last 30 years, numerous concepts have beenproposed. The nature of fish species is reviewed. Clonal inheritance ofnuclear genes occurs in several lineages. Hybridization is frequent,often leading to introgression, which may lead to extinction of species.Species may have hybrid origins. There is good evidence for parallelspeciation in similar habitats. There are clearly exceptions to thecladistic assumption of dichotomous branching during speciation. Siblingspecies may exist with no discernible niche differentiation.Basic assumptions are violated for the recognition, phylogenetic,ecological and some formulations of the evolutionary species concepts.The most satisfactory definitions are two of the earliest proposed inthe light of evolutionary theory. The Darwinian view is that species arerecognizable entities which are not qualitatively distinct fromvarieties. A restatement of this concept in genetic terms provides ameans of dealing with all forms of species known in present-day fishes.This modified Darwinian concept is operated through the application offuzzy logic rather than rigid definition. This involves a search fordiscontinuities between species, rather than an a priori definition ofhow boundaries are to be determined. A subset of Darwinian species areMayrian or biological species, which are characterized by theirdemonstrable reproductive isolation from other species. The status of apopulation as a Mayrian species is a testable hypothesis. Moleculartechniques allow this hypothesis to be tested more easily thanpreviously, at least when dealing with sympatric populations.     

2. Genome rearrangement and speciation in freshwater algae

Speciation problems are reviewed in the context of biogeography of fresh-water algae. Currently accepted species concept in phycology is based on morphological characters, and according to this concept, most freshwater algal species are considered cosmopolitan. This implies whether they have a highly efficient means of dispersal or their morphological characters are very static through a long evolutionary time. Recent studies of reproductive isolation show that some biological species of fresh-water algae are not so static or may not have such a high power of dispersal means, though some are indeed very static in morphological characters. The life cycle of most freshwater algae is composed of a vegetative cycle of growth and reproduction and a sexual cycle of gametic fusion and meiosis in the zygote, which forms a dormant spore-like structure. Since any freshwater habitat is ephemeral in terms of evolutionary time scale, each species has a capacity of forming germlings from a dormant cell in order to recycle its life history. The genome of freshwater algae, therefore, contains various coadapted gene systems, at least two, for the vegetative and for the sexual cycle. Homothallism and heterothallism are two contrasting mating systems that represent two opposing ways of life to harmonize antagonism between the vegetative stage of growth and reproduction and the sexual and dormant stage. Geographic and ecological distribution, polyploidy, and sex determination are discussed in conjunction with sexual and postzygotic isolating mechanisms.     

Genes versus phenotypes in the study of speciation

Despite persistent debate on the nature of species, the widespread adoption of Mayr’s biological species concept has led to a heavy emphasis on the importance of reproductive isolation to the speciation process. Equating the origin of species with the evolution of reproductive isolation has become common practice in the study of speciation, coincident with an increasing focus on elucidating the specific genetic changes (i.e.—speciation genes) underlying intrinsic reproductive barriers between species. In contrast, some have recognized that reproductive isolation is usually a signature effect rather than a primary cause of speciation. Here we describe a research paradigm that shifts emphasis from effects to causes in order to resolve this apparent contradiction and galvanize the study of speciation. We identify major elements necessary for a balanced and comprehensive investigation of the origin of species and place the study of so-called “speciation genes” into its appropriate context. We emphasize the importance of characterizing diverging phenotypes, identifying relevant evolutionary forces acting on those phenotypes and their role in the causal origins of reduced gene flow between incipient species, and the nature of the genetic and phenotypic boundaries that results from such processes. This approach has the potential to unify the field of speciation research, by allowing us to make better “historical” predictions about the fate of diverging populations regardless of taxon.     

THE SPECIES OF THE BIRDS-OF-PARADISE (PARADISAEIDAE): APPLYING THE PHYLOGENETIC SPECIES CONCEPT TO A COMPLEX PATTERN OF DIVERSIFICATION

Abstract The phylogenetic species concept is applied for the first time to a major radiation of birds, the birds-of-paradise (Paradisaeidae) of Australasia. Using the biological species concept, previous workers have postulated approximately 40–42 species in the family. Of these, approximately 13 are monotypic and 27 are polytypic with about 100 subspecies. Phylogenetic species are irreducible (basal) clusters of organisms (terminal taxa) that are diagnosably distinct from other such clusters. Within the context of this concept, approximately 90 species of paradisaeids are postulated to have diversified within Australasia. The phylogenetic species concept more accurately describes evolutionary diversity within the family and provides a better theoretical and empirical framework for analysing speciation, historical biogeography and patterns of morphological, behavioral and ecological diversification within this group than does the biological species concept.     

Genetic divergence and reproductive isolation in the Ochthebius (Calobius) complex (Coleoptera: Hydraenidae)

The reproductive isolation in hydrenid beetles of the Ochthebius complex was studied by analysing gene exchange in natural populations of O. quadricollis, Ochthebius sp. A and O. brevicollis steinbuehleri collected along the Mediterranean coasts. The ranges of these three species are largely allopatric, but sympatric areas were detected between contiguous taxa, ie, O. quadricollis and Ochthebius sp. A; Ochthebius sp. A and O. b. steinbuehleri. Three levels of reproductive isolation and genetic divergence were observed. One level involves extensive intraspecific genetic divergence within the biological species O. quadricollis, Ochthebius sp. A and O. brevicollis, associated with both physical barriers (eg, sea and sand stretches) and the low dispersal capacity of larvae and adults. The finding of transitional samples between the most differentiated population groups should indicate, however, that there is still some gene flow between the populations of the three taxa. Another level is found between Ochthebius sp. A and O. b. steinbuehleri, whose gene pools appear to be fairly distinct in spite of the fact that reproductive isolation is still incomplete: in their few syntopic sites, some F1 hybrids appeared indeed to have lower fitness, since backcrosses or recombinant genotypes were never observed. The final level in the evolution of reproductive isolation (full reproductive isolation) has been achieved by the species O. quadricollis and Ochthebius sp. A. No F1 or F(n) hybrids, nor backcrosses were found in their sympatric areas. The relative importance of ecological factors and evolutionary forces in the prevention of gene exchange between taxa are discussed.     

Ecological aspects of the evolutionary processes

Darwin in his On the Origin of species made it clear that evolutionary change depends on the combined action of two different causes, the first being the origin of genetically based phenotypic variation in the individual organisms comprising the population and the second being the action of selective agents of the external environment placing demands on the individual organisms. For over a century following Darwin, most evolutionists focused on the origin of inherited variation and its transmission; many workers continue to regard genetics to be the core of evolutionary theory. Far less attention has been given to the exact nature of the selective agents with most evolutionists still treating this cause imprecisely to the detriment of our understanding of both nomological and historical evolutionary theory. Darwin was vague in the meaning of his new concept of "Natural Selection," using it interchangeably as one of the causes for evolutionary change and as the final outcome (= evolutionary change). In 1930, natural selection was defined clearly as "non-random, differential reproduction of genes" by R. Fisher and J.B.S. Haldane which is a statement of the outcome of evolutionary process and which omits mention of the causes bringing about this change. Evolutionists quickly accepted this outcome definition of natural selection, and have used interchangeably selection both as a cause and as the result of evolutionary change, causing great confusion. Herein, the details will be discussed of how the external environment (i.e., the environment-phenotype interaction) serves as selective agents and exerts demands on the phenotypic organisms. Included are the concepts of fitness and of the components of fitness (= adaptations) which are respectively (a) survival, (b) direct reproductive and (c) indirect reproductive features. Finally, it will be argued that historical-narrative analyses of organisms, including classification and phylogenetic history, are possible only with a full understanding of nomological evolutionary theory and with functional/adaptive studies of the employed taxonomic features in addition to the standard comparative investigations.