Rational taxonomy and the natural system

Since Darwin's theory of evolution by natural selection, the idea of descent with modification came to dominate systematics, and so the study of morphology became subgugated to the reconstruction of phylogenies. Reinstating the organism in the theory of evolution (Ho &; Saunders, 1979; Webster &; Goodwin, 1982) leads to a project inrational taxonomy (Ho, 1986, 1988a), which attempts to classify biological forms on the basis of transformations on a given dynamical structure. Does rational taxonomy correspond to thenatural system that Linnaeus and his contemporaries as well as all pre-Darwinian morphologists had in mind? Here, we examine how rational taxonomy and the natural system can coincide in the dynamics of processes generating forms during development, which conferexclusivity, genericity androbustness to the forms that do exist. We use the example of segmentation, especially inDrosophila, as an illustration to explore the implications of rational taxonomy for evolution and systematics, and the relationship between ontogeny and phylogeny.     

Coherence, correspondence, and the renaissance of morphology in phylogenetic systematics

The decline in morphological phylogenies has become a pronounced trend in contemporary systematics due to a disregard for theoretical, methodological, conceptual, and philosophical approaches. The role and meaning of morphology in phylogenetic reconstruction and classification have been undermined by the following: (i) the ambiguous delineation of morphological characters; (ii) the putative “objectivity” of molecular data; (iii) that morphology has not been included in data matrices; (iv) that morphology has been mapped onto molecular cladograms; and (v) a separation of a paradigmatic relationship among morphology, phylogeny, and classification. Historical/philosophical arguments including the synthesis of coherence (coherentism) and correspondence (foundationalism) theories—i.e. “foundherentism” as a theory of epistemic justification—provide support for a renaissance of morphology in phylogenetic systematics. In the language of systematics, coherence theory corresponds to the logical/operational congruence of character states translated into a hierarchical/relational system of homologues and monophyletic groups as natural kinds. Correspondence theory corresponds to the empirical/causal accommodation of homologues and monophyletic groups as natural kinds grounded in the concept of semaphoront, and in developmental biology, genetics, inheritance, ontogenesis, topology, and connectivity. The role and meaning of morphology are also discussed in the context of separate and combined analyses, palaeontology, natural kinds, character concepts, semaphoront, modularity, and taxonomy. Molecular systematics suffers from tension between coherence and correspondence theories, and fails to provide a pragmatic language for predicates in science and in everyday life. Finally, the renaissance of morphology is not only dependent on a scientific/philosophical perspective but also depends on political, economic, social, and educational reforms in contemporary systematics. © The Willi Hennig Society 2009.     

Phylogeny, classification and taxonomy of European dragonflies and damselflies (Odonata): a review

Although Europe is the cradle of dragonfly systematics and despite great progress in the last 2 decades, many issues in naming its species and understanding their evolutionary history remain unresolved. Given the public interest, conservation importance and scientific relevance of Odonata, it is time that remaining questions on the species?? status, names and affinities are settled. We review the extensive but fragmentary literature on the phylogeny, classification and taxonomy of European Odonata, providing summary phylogenies for well-studied groups and an ecological, biogeographic and evolutionary context where possible. Priorities for further taxonomic, phylogenetic and biogeographic research are listed and discussed. We predict that within a decade the phylogeny of all European species will be known.     

Descriptions and phylogenetic systematics of Myxobolus spp. from cyprinids in Algonquin Park, Ontario

Eight species of Myxobolus were collected from four species of cyprinids in Algonquin Park, Ontario. On the basis of spore morphology, five of these species are described as new and two are redescribed. The evolutionary relationships among these eight species were studied using partial small subunit ribosomal DNA (ssu-rDNA) sequence data. The resulting cladograms, which were highly resolved and with strongly supported relationships, allowed for the evaluation of spore morphology, host specificity, and tissue tropism, criteria traditionally used in species identification. These criteria, recently criticized for creating artificial rather than natural taxonomic groupings, were evaluated for their reliability in the systematics of the species examined. The data showed that distantly related species often infect the same host and tissue, and that closely related species often occur in different hosts. Morphologically similar species are more closely related to each other and the taxonomy based on spore morphology is consistent with the relationships depicted in the phylogenies. These results suggest that spore morphology is better than host specificity and tissue tropism as a species character, as well as for determining evolutionary relationships among the species of Myxobolus examined.     

Molecular evolution inferred from small subunit rRNA sequences: what does it tell us about phylogenetic relationships and taxonomy of the parabasalids?

The Parabasala are a primitive group of protists divided into two classes: the trichomonads and the hypermastigids. Until recently, phylogeny and taxonomy of parabasalids were mainly based on the comparative analysis of morphological characters primarily linked to the development of their cytoskeleton. Recent use of molecular markers, such as small subunit (SSU) rRNA has led to now insights into the systematics of the Parabasala and other groups of prolists. An updated phylogeny based on SSU rRNA is provided and compared to that inferred from ultrastructural data. The SSU rRNA phylogeny contradicts the dogma equating simple characters with pumitive characters. Hypermastigids, possessing a hyperdeveloped cytoskeleton, exhibit the most basal emergence in the parabasalid lineage. Other observations emerge from the SSU rRNA analysis, such as the secondary loss of some cytoskeleton structures in all representatives of the Monocercomonadidae, the existence of secondarily free living taxa (reversibility of parasitism) and the evidence against the co-evolution of the endobiotic parabasalids and their animal hosts. According to phylogenies based on SSU rRNA, all the trichomonad families are not monophyletic groups, putting into question the validity of current taxonomic assignments. The precise branching order of some taxa remains unclear, but this issue can possibly be addressed by the molecular analysis of additional parabasalids. The goal of such additional analyses would be to propose, in a near future, a revision of the taxonomy of this group of protists that takes into account both molecular and morphological data.     

Classification of organisms and structuralism in biology

Structuralism in biology is the oldest trend oriented to the search for natural "laws of forms" comparable with laws of growth of crystal, was revived at the end of 20th century on the basis of structuralist thought in socio-humanitarian sciences. The development of principal ideas of the linguistic structuralism in some aspects is similar to that of biological systematics, especially concerning the relationships between "system" and "evolution". However, apart from this general similarity, biological structuralism is strongly focused on familiar problems of the origin of diversity in nature. In their striving for the renovation of existing views, biological structuralists oppose the neo-darwinism emphasizing the existence of "law of forms", that are independent on heredity and genetic "determinism". The trend to develop so-called "rational taxonomy" is also characteristic of biological structuralism but this attempt failed being connected neither with Darwin's historicism nor with Plato's typology.     

猫科动物的分类——分子系统学框架和化石证据

猫科动物的演化关系传统上一直是富有争议的,这很大程度上造成了猫科在属一级的分类众说纷纭。新兴的分子生物学技术为我们理解猫科动物的系统发育提供了新的视角,本文回顾了近些年来的猫科分子系统学研究,以Johnson等（2006）和李钢等（2016）的研究结果为核心,同时结合确切的化石记录进行佐证,推断了猫科的演化历史。我们发现,分子系统学提出的现代猫科动物于晚中新世开始适应辐射、先后分化出了8个支系等观点,与化石证据基本吻合;但是分子系统学对部分支系起源的推断与化石证据存在差异。结合化石记录的分析,我们认为现代猫科8个支系中除狞猫支系和虎猫支系以外,其余均最有可能起源于亚洲,现代猫科动物在演化过程中至少经历了30次洲际迁徙。结合演化历史和形态学研究,我们遵循邱占祥等（2004）的观点,将现存的猫科动物全部归于猫亚科（Felinae）,并将现代猫亚科动物划分为15个属40个物种。     

Molecular phylogeny of the benthic shallow-water octopuses (Cephalopoda: Octopodinae)

Octopus has been regarded as a "catch all" genus, yet its monophyly is questionable and has been untested. We inferred a broad-scale phylogeny of the benthic shallow-water octopuses (subfamily Octopodinae) using amino acid sequences of two mitochondrial DNA genes: Cytochrome oxidase subunit III and Cytochrome b apoenzyme, and the nuclear DNA gene Elongation Factor-1alpha. Sequence data were obtained from 26 Octopus species and from four related genera. Maximum likelihood and Bayesian approaches were implemented to estimate the phylogeny, and non-parametric bootstrapping was used to verify confidence for Bayesian topologies. Phylogenetic relationships between closely related species were generally well resolved, and groups delineated, but the genes did not resolve deep divergences well. The phylogenies indicated strongly that Octopus is not monophyletic, but several monophyletic groups were identified within the genus. It is therefore clear that octopodid systematics requires major revision.     

Random sampling of constrained phylogenies: conducting phylogenetic analyses when the phylogeny is partially known

Statistical randomization tests in evolutionary biology often require a set of random, computer-generated trees. For example, earlier studies have shown how large numbers of computer-generated trees can be used to conduct phylogenetic comparative analyses even when the phylogeny is uncertain or unknown. These methods were limited, however, in that (in the absence of molecular sequence or other data) they allowed users to assume that no phylogenetic information was available or that all possible trees were known. Intermediate situations where only a taxonomy or other limited phylogenetic information (e.g., polytomies) are available are technically more difficult. The current study describes a procedure for generating random samples of phylogenies while incorporating limited phylogenetic information (e.g., four taxa belong together in a subclade). The procedure can be used to conduct comparative analyses when the phylogeny is only partially resolved or can be used in other randomization tests in which large numbers of possible phylogenies are needed.     

Ontogeny, systematics, and phylogenetics: Perspectives of future synthesis and a new model of the evolution of bilateria

Ontogeny is considered as a process that allows linking two key components of biological systematics in an objective way: historically independent character attribution and phylogeny. It is proposed to designate the general theory that unifies the ??static?? traditional taxonomy and the dynamic evolutionary process on the basis of ontogenetic transformation of shapes of organisms as the ontogenetic systematics. One of the important practical applications is a new model of the evolution of bilaterian animals, which supposes an ancestral status of clonal asexual reproduction and its multiple reduction in different lines of Bilatera.     

Phylogenetic analyses of marine sponges within the order Verongida: a comparison of morphological and molecular data

Abstract. Because the taxonomy of marine sponges is based primarily on morphological characters that can display a high degree of phenotypic plasticity, current classifications may not always reflect evolutionary relationships. To assess phylogenetic relationships among sponges in the order Verongida, we examined 11 verongid species, representing six genera and four families. We compared the utility of morphological and molecular data in verongid sponge systematics by comparing a phylogeny constructed from a morphological character matrix with a phylogeny based on nuclear ribosomal DNA sequences. The morphological phylogeny was not well resolved below the ordinal level, likely hindered by the paucity of characters available for analysis, and the potential plasticity of these characters. The molecular phylogeny was well resolved and robust from the ordinal to the species level. We also examined the morphology of spongin fibers to assess their reliability in verongid sponge taxonomy. Fiber diameter and pith content were highly variable within and among species. Despite this variability, spongin fiber comparisons were useful at lower taxonomic levels (i.e., among congeneric species); however, these characters are potentially homoplasic at higher taxonomic levels (i.e., between families). Our molecular data provide good support for the current classification of verongid sponges, but suggest a re-examination and potential reclassification of the genera Aiolochroia and Pseudoceratina . The placements of these genera highlight two current issues in morphology-based sponge taxonomy: intermediate character states and undetermined character polarity.     

四种淡水缘毛类纤毛虫的形态学研究

通过活体显微观察及银染法对采自武汉东湖的4种固着缘毛类纤毛虫: 粗茎睫纤虫Ophrydium crassicaule Penard, 1922, 念珠伪钟虫Pseudovorticella monilata (Tatem, 1870) Foissner & Schiffmann, 1974, 垂盖虫Opercularia nutans (Ehrenberg, 1831) Stein, 1854和一个鞘居虫未定种Vaginicola sp.的活体、纤毛图式、银线系以及细胞核的形态学特征进行详细的描述, 补充和完善了缘毛类纤毛虫的形态学资料, 为纤毛虫分类和系统发育学的研究提供重要信息。此外, 首次在伪钟虫中观察到有性生殖现象, 为纤毛虫生殖进化的研究提供了基础资料。     

Discordant mtDNA and cpDNA phylogenies indicate geographic speciation and reticulation as driving factors for the diversification of the genus Picea

The phylogeny of the genus Picea was investigated by sequencing three loci from the paternally inherited chloroplast genome (trnK, rbcL and trnTLF) and the intron 2 of the maternally transmitted mitochondrial gene nad1 for 35 species. Significant topological differences were found between the trnK tree and the rbcL and trnTLF phylogenetic trees, and between cpDNA and mtDNA phylogenies. None of the phylogenies matched morphological classifications. The mtDNA phylogeny was geographically more structured than cpDNA phylogenies, reflecting the different inheritance of the two cytoplasmic genomes in the Pinaceae and their differential dispersion by seed only and seed and pollen, respectively. Most North American taxa formed a monophyletic group on the mtDNA tree, with topological patterns suggesting geographic speciation by range fragmentation or by dispersal and isolation. Similar patterns were also found among Asian taxa. Such a trend towards geographic speciation is anticipated in other Pinaceae genera with similar life history, autecology and reproductive system. Incongruences between organelle phylogenies suggested the occurrence of mtDNA capture by invading cpDNA. Incongruences between cpDNA partitions further suggested heterologous recombination presumably also linked to ancient reticulate evolution. Whilst cpDNA appears potentially valuable for molecular taxonomy and systematics purposes, these results emphasize the reduced value of cpDNA to infer vertical descent and the speciation history for plants with paternal transmission and high dispersal of their chloroplast genome.     

Molecular phylogeny of the diatom genera Amphora and Halamphora (Bacillariophyta) with a focus on morphological and ecological evolution

The taxonomic history of the diatom genus Amphora is one of a broad early morphological concept resulting in the inclusion of a diversity of taxa, followed by an extended period of revision and refinement. The introduction of molecular systematics has increased the pace of revision and has largely resolved the relationships between the major lineages, indicating homoplasy in the evolution of amphoroid symmetry. Within the two largest monophyletic lineages, the genus Halamphora and the now taxonomically refined genus Amphora, the intrageneric morphological and ecological relationships have yet to be explored within a phylogenetic framework. Critical among this is whether the range of morphological features exhibited within these diverse genera are reflective of evolutionary groupings or, as with many previously studied amphoroid features, are nonhomologous when examined phylogenetically. Presented here is a four‐marker molecular phylogeny that includes 31 taxa from the genus Amphora and 77 taxa from the genus Halamphora collected from fresh, brackish, and salt waters from coastal and inland habitats of the United States and Japan. These phylogenies illustrate complex patterns in the evolution of frustule morphology and ecology within the genera and the implications of this on the taxonomy, classification, and organization of the genera are discussed.     

En route to a genome-based classification of Archaea and Bacteria?

Given the considerable promise whole-genome sequencing offers for phylogeny and classification, it is surprising that microbial systematics and genomics have not yet been reconciled. This might be due to the intrinsic difficulties in inferring reasonable phylogenies from genomic sequences, particularly in the light of the significant amount of lateral gene transfer in prokaryotic genomes. However, recent studies indicate that the species tree and the hierarchical classification based on it are still meaningful concepts, and that state-of-the-art phylogenetic inference methods are able to provide reliable estimates of the species tree to the benefit of taxonomy. Conversely, we suspect that the current lack of completely sequenced genomes for many of the major lineages of prokaryotes and for most type strains is a major obstacle in progress towards a genome-based classification of microorganisms. We conclude that phylogeny-driven microbial genome sequencing projects such as the Genomic Encyclopaedia of Archaea and Bacteria (GEBA) project are likely to rectify this situation.     

鸣螽科(直翅目：螽亚目)昆虫研究历史与进展

鸣螽科Prophalangopsidae昆虫作为螽亚目少有的孑遗类群,对认识螽亚目系统发育和演化具有重要意义。本文综述鸣螽科的研究历史;考证并提出鸣螽科及相关类群的中文名;详述鸣螽科昆虫形态特征与生物学特性;介绍近年鸣螽科包括化石与现生属种的分类学及系统发育学研究进展,并讨论其存在的问题及对未来的展望。     

Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands

A well-resolved rhizobial species phylogeny with 51 haplotypes was inferred from a combined atpD + recA data set using Bayesian inference with best-fit, gene-specific substitution models. Relatively dense taxon sampling for the genera Rhizobium and Mesorhizobium was achieved by generating atpD and recA sequences for six type and 24 reference strains not previously available in GenBank. This phylogeny was used to classify nine nodule isolates from Sesbania exasperata, S. punicea and S. sericea plants native to seasonally flooded areas of Venezuela, and compared with a PCR-RFLP analysis of rrs plus rrl genes and large maximum likelihood rrs and nifH phylogenies. We show that rrs phylogenies are particularly sensitive to strain choice due to the high levels of sequence mosaicism found at this locus. All analyses consistently identified the Sesbania isolates as Mesorhizobium plurifarium or Rhizobium huautlense. Host range experiments on ten legume species coupled with plasmid profiling uncovered potential novel biovarieties of both species. This study demonstrates the wide geographic and environmental distribution of M. plurifarium, that R. galegae and R. huautlense are sister lineages, and the synonymy of R. gallicum, R. mongolense and R. yanglingense. Complex and diverse phylogeographic, inheritance and host-association patterns were found for the symbiotic nifH locus. The results and the analytical approaches used herein are discussed in the context of rhizobial taxonomy and molecular systematics.     

Three-dimensional analysis of mandibular dental root morphology in hominoids

Although often preserved in the fossil record, mandibular dental roots are rarely used for evolutionary studies. This study qualitatively and quantitatively characterizes the three-dimensional morphology of hominoid dental roots. The sample comprises extant apes as well as two fossil species, Khoratpithecus piriyai and Ouranopithecus macedoniensis. The morphological differences between extant genera are observed, quantified and tested for their potential in systematics. Dental roots are imaged using X-ray computerized tomography, conventional microtomography and synchrotron microtomography. Resulting data attest to the high association between taxonomy and tooth root morphology, both qualitatively and quantitatively. A cladistic analysis based on the dental root characters resulted in a tree topology congruent with the consensus phylogeny of hominoids, suggesting that tooth roots might provide useful information in reconstructing hominoid phylogeny. Finally, the evolution of the dental root morphology in apes is discussed.     

Parallelism,parsimony, and the phytogeny of the lemuridae

In spite of the increasing popularity of cladistic methods in studies of primate systematics, few authors have investigated the effects of parallel evolution when such methods are applied to empirical data. To counter the effects of parallelism, cladistic techniques rely on the principle of evolutionary parsimony. When parsimony procedures are used to reconstruct the phylogeny of the Lemuridae, nine highly parsimonious phylogenies can be deduced. Further choice among these competing hypotheses of relationship is determined by the extent to which one embraces the parsimony principle. The phylogeny obtained by the most rigorous adherence to the parsimony principle is one which is wholly consistent with traditional evolutionary classifications of the Lemuridae. Moderate levels of parallelism can lead to the generation of several plausible, alternative phylogenetic hypotheses; less than 25% of the characters analyzed here need have evolved in parallel, yet they are largely responsible for the ambiguity of the nine different lemurid phylogenies. This suggests that phylogeny reconstructions based entirely on cladistic methods do not provide a suitable basis for the construction of classifications for groups such as the order Primates, where the degree of parallelism is likely to be quite high.