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.     

Phylogenetic definitions and taxonomic philosophy

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names.     

The Species Concept as a Cognitive Tool for Biological Anthropology

Taxonomy is caught between the search for the “perfect” theory and an elusive biological variability. The lack of major advances in issues related to how “species” and other taxonomic categories are defined suggests that perhaps we should avoid excessively rigid formalism in this regard. The risk is a separation between elegant but useless theories and confusing applications of the taxonomic tools. Communication is one of the main functions of taxonomy, and stability one of the main parameters that taxonomy users should be sensitive to. An excess of stability may generate anachronistic consequences while continuous revisions may make the tool of taxonomy scarcely practical. The current tendency pushes toward more and more fragmentation of biologically valid taxa. While taxonomy specialists enjoy such challenges, many taxonomy users feel a bit nervous and discouraged when trying to use a tool that is constantly changing. Debates over taxonomy would seem particularly unrewarding for fields with limited samples and scarce biological diversity, such as palaeoanthropology. In this context, where the information available is rarely sufficient to supply consistent taxonomical evidence, there are frequently excessive efforts to create debate on species separations. The risk is that we maintain the debate on a purely theoretical level, or else we distrust a reliable use of taxonomy. A compromise (and recommended) choice between these two extremes would be to rely on shared and reasonable interpretations of homogeneous evolutionary units, without diving into fine‐grained issues that will remain, however, unresolved. Taxonomy should be a tool, not the goal, of the evolutionary biologist. Our mind needs discrete and recognizable objects to structure our perception of reality. There is no reason to expect that nature works the same way. Am. J. Primatol. 75:10‐15, 2013. © 2012 Wiley Periodicals, Inc.     

Towards a prokaryotic genomic taxonomy

One of the most interesting developments in the field of modern-day microbiology is the ever increasing number of whole-genome sequences that is publicly available. There is an increasing interest in the use of these genome sequences to assess evolutionary relationships among microbial taxa, as it is anticipated that much additional taxonomic information can be extracted from these sequences. In a first part of the present review, mechanisms that are responsible for the evolution of genomes will be discussed. Subsequently, we will give an overview of approaches that are presently available to assess the taxonomic relationships between prokaryotic species based on complete genome sequences, followed by a brief discussion of the potential implications of these novel approaches for bacterial taxonomy in general and our thinking about the bacterial species concept in particular.     

珍稀蝴蝶的亚种分类问题及保护意义：以喙凤蝶属为例

亚种是种的一个亚单位,由于分类学上的不同定义和主观性而受到质疑。然而,在分类学实践中,所有试图用不同的术语取代亚种或完全放弃亚种的尝试都是不可接受的。亚种同样是生物多样性的重要组成,有一定独特性,为自然进程的一部分,具有保护研究价值。本文基于亚种概念、特征认为亚种分类需参考地理隔离(如异域分布)与表型差异2个原则。我们以珍稀喙凤蝶属Teinopalpus为例,系统收集亚种分类文献,采集该属亚种的地理分布、形态描述与差异等信息,综合分析该属蝶类的亚种分类现状、问题与原因。1843-2007年喙凤蝶属金带喙凤蝶T. imperialis及其姊妹种金斑喙凤蝶T. aureus各自记录了8个亚种。然而,部分亚种记录于同一行政区,如金带喙凤蝶T. i. imperialis, T. i. himalaicus与T. i. behludinii 均在中国四川有记录,而金斑喙凤蝶在中国浙江有2个亚种记录,这显示名称应用的不确定性。考虑到两姊妹种同域分布在亚洲东南部,通过比对亚种正模所在地植被群落(biome)、生态区(ecoregion)的一致性判定地理隔离,发现金带喙凤蝶(覆盖3个植被群落)比金斑喙凤蝶(仅覆盖1个)的种下生态位分化程度更高。而据所处生态区的一致性,建议将金带喙凤蝶亚种分类修订为T. i. imperialis, T. i. himalaicus, T. i. miecoae, T. i. behludinii, T. i. imperatrix(含T. i. bhumipholi), T. i.gillesi和T. i. gerritesi 7个;金斑喙凤蝶亚种分类修订为T. a. aureus(含T. a. wuyiensis, T. a. guangxiensis与T. a. nagaoi), T. a. eminens(含T. a. laotiana), T. a. shinkaii与T. a. hainani 4个。由于可参考标本少,喙凤蝶属亚种确立时可用形态比对信息有限、不完整(如只依据单性的形态比对结果等),易“过度亚种化”。珍稀亚种分类问题(如“过度亚种化”、信息不确定性等)影响其保护措施,因为管理者常需权衡投入成本与成效、明确优先保护区域或对象,并以此做出决策。因此,在更多确定信息未获得前,不建议进行亚种分类。     

FBIS: A regional DNA barcode archival & analysis system for Indian fishes

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics. AVAILABILITY: The database is available for free at http://mail.nbfgr.res.in/fbis/     

Propositions for a character-state-based biological taxonomy

A new procedure for defining taxa upon a single character state is developed. It is centred on the designation of two specimens, belonging to two distinct species, exhibiting the same given character state, as type material, and referred to as ‘cladotypes’. A taxon name/definition designates a monophyletic group until one of the following assumptions is falsified: (1) the character state typified by cladotypes is homologous in individuals that are designated as cladotypes, and (2) cohesion mechanisms isolated individuals exhibiting the type‐character‐state from those that do not. A taxon defined by a character state that is found to be a combination of several character states is to be redefined upon a character state shared by its cladotypes. If several character states are available, the character state that makes the taxon the least inclusive taxon including cladotypic species (i.e., species to which belong cladotypes) is to be preferred. Taxon names designate obsolete phylogenetic hypotheses if the first assumption is falsified (such names are to be kept for this purpose, i.e., they are not to be recycled in another definition). Rules governing adaptation of previously erected names are proposed. Main cases of taxa synonymy involve definitions based on different pairs of cladotypes but referring to the same type‐character‐state; and definitions based on the same character‐state initially hypothesised as acquired by convergence in cladotypic species pairs, but later demonstrated as originating from a unique ancestor. Taxa could be synonyms if a permanent splitting event did not segregate individuals exhibiting a new character state, qualified as type‐character‐state, from individuals already assigned to a previously erected taxon. This procedure accommodates potentially any species concept, but is not tied to any; it is an extension of the composite species concept. Species are treated in a different way than other taxa: they are defined as sets of individuals belonging to the same evolving (segments of) metapopulation lineages as a holotype specimen, and do not need a defining character state.     

The debate about the biological species concept - a review

The importance of the species concept in biology has led to a continuing debate about the definition of species. This paper summarizes the recent literature in relation to the ‘biological species concept’ (MAYR 1942). Among the general attributes demanded, possible limitations of the universality and applicability of a species definition are discussed. Three different areas of criticism of the biological species concept are considered: 1. The impracticability of the criterion of reproductive isolation. The demand for more practical criteria is rejected, because reproductive isolation is seen as the factor that produces and maintains species as discrete entities in nature. 2. The inapplicability to non-bisexual organisms. A brief survey of modes of uniparental reproduction and their relative importance suggests that obligatory apomicts are of little evolutionary significance. 3. The inapplicability to multidimensional situations. Despite practical difficulties, the biological species concept is held to apply to organisms separated in space. The impossibility to delimit species in time by reproductive isolation is recognized. Out of two ways to divide continuous evolutionary lineages in time, the phylogenetic approach, which considers only speciation events (cladogenesis), is preferred as it is more objective. A list of recently published alternative definitions of species, none of which is found acceptable, is given. It is concluded that the biological species concept needs not be changed or dismissed on the basis of the discussed criticisms.     

Does Biology Need an Organism Concept?

Among biologists, there is no general agreement on exactly what entities qualify as ‘organisms’. Instead, there are multiple competing organism concepts and definitions. While some authors think this is a problem that should be corrected, others have suggested that biology does not actually need an organism concept. We argue that the organism concept is central to biology and should not be abandoned. Both organism concepts and operational definitions are useful. We review criteria used for recognizing organisms and conclude that they are not categorical but rather continuously variable. Different organism concepts are useful for addressing different questions, and it is important to be explicit about which is being used. Finally, we examine the origins of the derived state of organismality, and suggest that it may result from positive feedback between natural selection and functional integration in biological entities.     

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.     

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。     

Taxonomie, écologie et lutte biologique

Summary It is impossible to study modern taxonomy without taking into consideration the population genetic and ecology. Thé Linnean concept of monotypic species should be replaced by the biometric study of the frequency of the variability of the biological characters (particularly morphological) used in taxonomy. The study of populations offers a larger scientific interest than the one of isolated types. It gives the possibility of caracterizing the evolution stability of the species. So, Taxonomy can help considerably in biological control. By revealing large variability species, it gives a criterion of their adjusting plasticity. But, by definition, the biological control is based on the adjusting capacity of the entomophagous insects either to a new host or to a new environment. Information given by the taxonomist on the species stability has consequently a great value in the choice and use of the Entomophagous insects. — Ecologists using biological control, expect from the taxonomist to lie more than a label, which implies the use of biometric analysis methods in Entomophagous taxonomy.      

The second internal transcribed spacer of nuclear ribosomal DNA as a tool for Latin American anopheline taxonomy - a critical review

Among the molecular markers commonly used for mosquito taxonomy, the internal transcribed spacer 2 (ITS2) of the ribosomal DNA is useful for distinguishing among closely-related species. Here we review 178 GenBank accession numbers matching ITS2 sequences of Latin American anophelines. Among those, we found 105 unique sequences corresponding to 35 species. Overall the ITS2 sequences distinguish anopheline species, however, information on intraspecific and geographic variations is scarce. Intraspecific variations ranged from 0.2% to 19% and our analysis indicates that misidentification and/or sequencing errors could be responsible for some of the high values of divergence. Research in Latin American malaria vector taxonomy profited from molecular data provided by single or few field capture mosquitoes. However we propose that caution should be taken and minimum requirements considered in the design of additional studies. Future studies in this field should consider that: (1) voucher specimens, assigned to the DNA sequences, need to be deposited in collections, (2) intraspecific variations should be thoroughly evaluated, (3) ITS2 and other molecular markers, considered as a group, will provide more reliable information, (4) biological data about vector populations are missing and should be prioritized, (5) the molecular markers are most powerful when coupled with traditional taxonomic tools.     

浅评当今植物系统学中争论的三个问题——并系类群、谱系法规和系统发育种概念

一般来讲,进化学派承认分支学派对系统学的研究作出了有意义的贡献,如应用分支分析方法重建系统发育,应用共有衍征确定分类群之间的分支关系以及应用外类群方法来判断性状的极性等,都对系统学的方法有所改进。但分支学派的致命缺点是拒绝接受并系类群。我们属于进化学派,认为并系类群是可以接受的。例如,根据分子资料分析,Zabelia属可以包括于Abelia属内。Zabelia属不但在花粉上和Abelia属不同,可能由于它占有了新的生态位,获得了新的特征,如叶柄基部膨大两两联合,并宿存以保护腋芽。有理由认为它们应独立成属,并不由于Zabelia属从Abelia属分出而使后者成为一个并系类群而把它们合并。分支学派的一些学者认为生物名称作为交流的工具和生物信息储存系统应有明晰的、唯一的和稳定的特性。但具等级的林奈命名系统并不具有这些特性来命名分支和种。最后,PhyloCode被提出。PhyloCode对分支的命名方法有3种,即分支结点定义、分支基干定义和衍征定义。我们认为林奈命名系统作为传媒系统在生物学界的应用已近250年,若要废弃它而采用PhyloCode,必然会在命名方面引起一片混乱。但我们并不是说PhyloCode的拥护者所提出的建议一无是处,我们建议他们宜继续进行研究。由于应用生物学种概念于植物界产生了许多问题,因此多为植物系统学家所抛弃。分支学派的兴起,推动了系统发育种概念的提出。该概念基于3个特征,即自征、区别特征和基本排它,因此分别命名为自征种概念、特征种概念和谱系种概念。事实上,目前大多数植物系统学家仍然应用着形态–地理学种概念,但我们在划分种时,必须有尽可能多的资料,特别是要将传粉、繁育系统、分子系统学资料和形态学资料结合起来。     

Reverse taxonomy for elucidating diversity of insect-associated nematodes: a case study with termites

Background

The molecular operational taxonomic unit (MOTU) has recently been applied to microbial and microscopic animal biodiversity surveys. However, in many cases, some of the MOTUs cannot be definitively tied to any of the taxonomic groups in current databases. To surmount these limitations, the concept of “reverse taxonomy” has been proposed, i.e. to primarily list the MOTUs with morphological information, and then identify and/or describe them at genus/species level using subsamples or by re-isolating the target organisms. Nevertheless, the application of “reverse taxonomy” has not been sufficiently evaluated. Therefore, the practical applicability of “reverse taxonomy” is tested using termite-associated nematodes as a model system for phoretic/parasitic organisms which have high habitat specificity and a potential handle (their termite host species) for re-isolation attempts.

Methodology

Forty-eight species (from 298 colonies) of termites collected from the American tropics and subtropics were examined for their nematode associates using the reverse taxonomy method and culturing attempts (morphological identification and further sequencing efforts). The survey yielded 51 sequence types ( =  MOTUs) belonging to 19 tentatively identified genera. Within these, four were identified based on molecular data with preliminary morphological observation, and an additional seven were identified or characterized from successful culturing, leaving eight genera unidentified.

Conclusions

That 1/3 of the genera were not successfully identified suggests deficiencies in the depth of available sequences in the database and biological characters, i.e. usually isolated as phoretic/parasitic stages which are not available for morphological identification, and too many undiscovered lineages of nematodes. Although there still is the issue of culturability of nematodes, culturing attempts could help to make reverse taxonomy methods more effective. However, expansion of the database, i.e., production of more DNA barcodes tied to biological information by finding and characterizing additional new and known lineages, is necessary for analyzing functional diversity.     

The 3Cs provide a novel concept of bacterial species: messages from the genome as illustrated by Salmonella

A key issue troubling bacterial taxonomy and systematics is the lack of a biological species definition. Criteria to be used for defining bacterial species on genetic and biological bases should be able to reveal clear-cut boundaries among clusters of bacteria. To date, DNA–DNA re-association assays and ribosomal RNA sequence comparison have been useful in determining relative evolutionary distances among bacteria but the data are continuous and thus cannot define bacterial clusters as taxonomic units to be called species. Using Salmonella as models, we have looked for definite genetic and biologic uniqueness of clusters of bacteria. Based on our findings that each Salmonella lineage has a unique genome structure shared by strains of the same lineage but not overlapping with strains of other Salmonella lineages, we conclude that this is a result of genetic isolation following divergence of the bacteria. We propose that there should be genetic boundaries between different species of bacteria at the genomic level, which awaits further genomic information for validation.