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。     

Wohin steuert die Taxonomie?

In taxonomy, the organisms may be grouped into species according to different criteria, e.g. according to phenotypic and genetic characteristics or according to reproductive connections. In nature, there is no universal unit that can be called “species”, because different biological mechanisms are responsible for how individuals are grouped together or delimitated from each other. Different species concepts do not necessarily define the same entity existing in nature. One and the same individual can be assigned to different species depending on the species concept. In the last two decades, the barcode taxonomy has played a dominant role. A major advantage of the barcode taxonomy is the time‐saving automated mass detection of species without the need for taxonomically trained experts. Especially in evolutionarily young species, however, there are considerable discrepancies between the classification according to the barcode concept and the classification according to reproductive communities or phenotypic characteristics. The barcode species must therefore be understood as a species in addition to other species concepts.     

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.     

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.     

Empirical and philosophical problems with the subspecies rank

Species‐level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species “concepts.” These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what “kind” of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.     

Increasing numbers of bird species result from taxonomic progress,not taxonomic inflation

The impact and significance of modern taxonomy on other fields in biology have been subjects of much debate. It has been proposed that increasing numbers of vertebrate species are largely owing to ‘taxonomic inflation’. According to this hypothesis, newly recognized species result from reinterpretations of species limits based on phylogenetic species concepts (PSCs) rather than from new discoveries. Here, I examine 747 proposals to change the taxonomic rank of birds in the period 1950–2007. The trend to recognize more species of birds started at least two decades before the introduction of PSCs. Most (84.6%) newly recognized species were supported by new taxonomic data. Proposals to recognize more species resulted from application of all six major taxonomic criteria. Many newly recognized species (63.4%) were not based exclusively on PSC-based criteria (diagnosability, monophyly and exclusive coalescence of gene trees). Therefore, this study finds no empirical support for the idea that the increase in species is primarily epistemological rather than data-driven. This study shows that previous claims about the causes and effects of taxonomic inflation lack empirical support. I argue that a more appropriate term for the increase in species is ‘taxonomic progress’.     

An integrative approach to species delineation incorporating different species concepts: a case study of Limnadopsis (Branchiopoda: Spinicaudata)

The unambiguous delineation and identification of species remain central problems in systematic and taxonomic studies. Species delineation depends on the data utilized and the species concept applied. In recent years, morphology‐based species delineation has been complemented by DNA sequence data, leading to an integrative taxonomy. Such integrative approaches, however, are hampered by the partial incongruence of the various data types with certain species concepts. In this study, we delineated Australian Limnadopsis species employing one mitochondrial (cytochrome c oxidase subunit I, COI) and one nuclear (elongation factor 1α, EF1α) marker and a morphological character apparently part of the specific mate recognition complex, and therefore potentially indicative of reproductive isolation. By integrating the data over various species concepts (e.g. the ‘biological’, ‘Hennigian’, ‘recognition’, ‘phylogenetic’ and ‘evolutionary’ species concepts), the delineation of most species becomes straightforward and unambiguous. Conflicts are particularly interesting as they reveal different aspects of speciation considering the various species concepts. Our study emphasizes the benefits of a truly integrative approach to taxonomy. By combining molecular data with morphological characters indicative of reproductive isolation, it is possible to delineate species integrating not only different data types, but also different underlying species concepts. Overall, 11 Limnadopsis species could be delineated, including all eight currently recognized species, and three so far undescribed species. Most species were congruently delineated under all species concepts. A strict application of the evolutionary species concept, however, would have further split L. parvispinus into two species on the basis of the COI data. In addition, Limnadopsis tatei is consistently split into two sympatrically occurring species under all applied species concepts. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 575–599.     

Species concepts and species reality: salvaging a Linnaean rank

The validity of the species category (rank) as a distinct level of biological organization has been questioned. Phenetic, cohesion and monophyletic species concepts do not delimit species-level taxa that are qualitatively distinct from lower or higher taxa: all organisms throughout the tree of life exhibit varying degrees of similarity, cohesion, and monophyly. In contrast, interbreeding concepts delimit species-level taxa characterized by a phenomenon (regular gene flow) not found in higher taxa, making the species category a distinct level of biological organization. Only interbreeding concepts delimit species-level taxa that are all comparable according to a biologically meaningful criterion and qualitatively distinct from entities assigned to other taxonomic categories. Consistent application of interbreeding concepts can result in counterintuitive taxonomies--e.g. many wide polytypic species in plants and narrow cryptic species in animals. However, far from being problematic, such differences are biologically illuminating--reflecting differing barriers to gene flow in different clades. Empirical problems with interbreeding concepts exist, but many of these also apply to other species concepts, whereas others are not as severe as some have argued. A monistic view of species using interbreeding concepts will encounter strong historical inertia, but can save the species category from redundancy with other categories, and thus justify continued recognition of the species category.     

Species and paleoanthropology

The biotic world is self-evidently “packaged” into units, of which the most basic is the species. It is necessary to develop an accurate understanding of what species are and how they are to be identified before we can proceed to more complex analyses of the evolutionary histories and relationships of extinct and extant taxa at all levels of the systematic hierarchy. In this article, we review the major species concepts current today among paleoanthropologists, and examine the limitations of their applicability to practical studies of extant and extinct faunas. The primary such limitation for paleoanthropologists is the fact that all major species definitions stress reproductive continuity (whether by exclusionary or inclusionary mechanisms), a quality that is inferential at best among forms known only as fossils (and, in many cases, in the extant fauna as well). The only reliable signal as to species status in the fossil record is morphology, yet speciation carries with it no specifiable quantity of morphological innovation. Some groups with autapomorphies are not species, and some species do not bear autapomorphies. How, then, are we to recognize species in the hominid and other fossil records? Noting that osteodental differences among congeneric primate species tend to be subtle, and that when consistent identifiable “morphs” can be found at least as many species are present, we recommend equating morphs based on several characters with species—realizing that only one or two distinctive characters may not make a morph. In this way, our views of the phylogenetic histories of higher taxa may be oversimplified, but their essential patterns will not be distorted.     

Perspectives: Towards a language for mapping relationships among taxonomic concepts

Abstract

Taxonomic concepts (sensu Berendsohn) embody the underlying meanings of scientific names as stated in a particular publication, thus offering a new way to resolve semantic ambiguities that result from multiple revisions of a taxonomic name. This paper presents a comprehensive and powerful language for representing the relationships among taxonomic concepts. The language features terms and symbols for concept relationships within a single taxonomic hierarchy, or between two related but independently published hierarchies. Taxonomic concepts pertaining to a single hierarchy are characterised by parent/child relationships, whereas those pertaining to two independent hierarchies may have the following basic relationships: congruence, inclusion (non‐symmetrical, relative to the side of comparison), overlap, and exclusion. The relationships are asserted by specialists who have the option to add or subtract concepts on one or both sides of a relationship equation in order to reconcile differences between non‐congruent taxonomic perspectives. The terms ‘and’, ‘or’ and ‘not’ are available, respectively, to connect multiple simultaneously or alternatively valid relationship assessments, or to explicitly negate the validity of a relationship. The language also permits the decomposition of a relationship according to the intensional (property referencing) and ostensive (member pointing) aspects of the compared taxonomic concepts. Adopting the concept relationship language will facilitate a more precise documentation of similarities and differences in multiple succeeding taxonomic perspectives, thereby preparing the stage for an ontology‐based integration of taxonomic and related biological information.     

Using average nucleotide identity (ANI) to evaluate microsporidia species boundaries based on their genetic relatedness

Microsporidia are obligatory intracellular parasites related to fungi and since their discovery their classification and origin has been controversial due to their unique morphology. Early taxonomic studies of microsporidia were based on ultrastructural spore features, characteristics of their life cycle and transmission modes. However, taxonomy and phylogeny based solely on these characteristics can be misleading. SSU rRNA is a traditional marker used in taxonomical classifications, but the power of SSU rRNA to resolve phylogenetic relationships between microsporidia is considered weak at the species level, as it may not show enough variation to distinguish closely related species. Overall genome relatedness indices (OGRI), such as average nucleotide identity (ANI), allows fast and easy-to-implement comparative measurements between genomes to assess species boundaries in prokaryotes, with a 95% cutoff value for grouping genomes of the same species. Due to the increasing availability of complete genomes, metrics of genome relatedness have been applied for eukaryotic microbes taxonomy such as microsporidia. However, the distribution of ANI values and cutoff values for species delimitation have not yet been fully tested in microsporidia. In this study we examined the distribution of ANI values for 65 publicly available microsporidian genomes and tested whether the 95% cutoff value is a good estimation for circumscribing species based on their genetic relatedness.     

Species concepts and the recognition of ancestors

Whether or not ancestral species can be recognised depends on the species concept adopted. A “metaspecies”; is a species that completely lacks autapomorphies, and which might (or might not) be ancestral to other species. Such taxa have been identified among both living and fossil organisms. Under the most commonly‐used species concepts (biological, evolutionary, phenetic, phylogenetic, ecological, recognition and cohesion), “metaspecies”; can be assumed to be ancestral. Even if the known members of a metaspecies are not ancestral to anything, parsimony dictates that the (as yet unknown) ancestral lineage is identical to the metaspecies and, under these species concepts, assignable to the same species. Only the cladistic and monophyletic species concepts would deny “metaspecies”; ancestral status, but these species concepts are problematical and have never been used by practising systematists.     

16S and 23S plastid rDNA phylogenies of Prototheca species and their auxanographic phenotypes

Because algae have become more accepted as sources of human nutrition, phylogenetic analysis can help resolve the taxonomy of taxa that have not been well studied. This can help establish algal evolutionary relationships. Here, we compare Auxenochlorella protothecoides and 23 strains of Prototheca based on their complete 16S and partial 23S plastid rDNA sequences along with nutrient utilization (auxanographic) profiles. These data demonstrate that some of the species groupings are not in agreement with the molecular phylogenetic analyses and that auxanographic profiles are poor predictors of phylogenetic relationships.     

“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。     

Stepping stones towards a new prokaryotic taxonomy

Technological developments provide new insights into prokaryotic evolution and diversity and provoke a continuous need to update taxonomy and revise classification schemes. Our present species concept and definition are being challenged by the growing amount of whole genomic information, which should allow improvements in the natural species definition. The continuous quest for an objective and stable method for sorting strains into coherent homogeneous groups is inherent to prokaryotic systematics and nomenclature. Morphological, biochemical, physiological, phenotypic and chemotaxonomic criteria have been complemented by molecular data and pragmatic, purpose built, species definitions are being replaced by more natural ones based on evolutionary insights. It is imperative to give due consideration to both fundamental and applied aspects of future species concepts and definitions. The present paper discusses the present practice in prokaryotic taxonomy of how this system developed and how it may evolve in the future.     

Taxonomy of Lactobacilli and Bifidobacteria

Genera Lactobacillus and Bifidobacterium include a large number of species and strains exhibiting important properties in an applied context, especially in the area of food and probiotics. An updated list of species belonging to those two genera, their phylogenetic relationships and other relevant taxonomic information are reviewed in this paper. The conventional nature of taxonomy is explained and some basic concepts and terms will be presented for readers not familiar with this important and fast-evolving area, which importance is often underestimated. The analysis of biodiversity and its cataloguing, i.e. taxonomy, constitute the basis for applications and scientific communication: reliable identification and correct naming of bacterial strains are not only primary aims of taxonomic studies, but also fundamental elements in an applied context, for the tracking of probiotic strains and a non fraudulent labelling of fermented milks and pharmaceutical products containing probiotic microorganisms. A number of resources freely available have been listed and their use is suggested for people concerned with different aspects of taxonomy. Some perspectives in taxonomy have been outlined, in particular considering the role of culture independent analyses to reveal the still unknown and uncultured microorganisms. Finally, the impact of the availability of whole-genome sequences in taxonomy is briefly explained: they have already begun to give insights on bacterial evolution, which will surely have implications on taxonomy, even if the analysis of data for lactic acid bacteria is still limited to few species.