HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees

MOTIVATION: Numerous database management systems have been developed for processing various taxonomic data bases on biological classification or phylogenetic information. In this paper, we present an integrated system to deal with interacting classifications and phylogenies concerning particular taxonomic groups. RESULTS: An information-theoretic view (taxon view) has been applied to capture taxonomic concepts as taxonomic data entities. A data model which is suitable for supporting semantically interacting dynamic views of hierarchic classifications and a query method for interacting classifications have been developed. The concept of taxonomic view and the data model can also be expanded to carry phylogenetic information in phylogenetic trees. We have designed a prototype taxonomic database system called HICLAS (HIerarchical CLAssification System) based on the concept of taxon view, and the data models and query methods have been designed and implemented. This system can be effectively used in the taxonomic revisionary process, especially when databases are being constructed by specialists in particular groups, and the system can be used to compare classifications and phylogenetic trees. AVAILABILITY: Freely available at the WWW URL: http://aims.cps.msu.edu/hiclas/ CONTACT: pramanik@cps.msu.edu; lotus@wipm.whcnc.ac.cn     

Stems,nodes, crown clades,and rank‐free lists: is Linnaeus dead?

Recent radical proposals to overhaul the methods of biological classification are reviewed. The proposals of phylogenetic nomenclature are to translate cladistic phylogenies directly into classifications, and to define taxon names in terms of clades. The method has a number of radical consequences for biologists: taxon names must depend rigidly on the particular cladogram favoured at the moment, familiar names may be reassigned to unfamiliar groupings, Linnaean category terms (e.g. phylum, order, family) are abandoned, and the Linnaean binomen (e.g. Homo sapiens) is abandoned. The tenets of phylogenetic nomenclature have gained strong support among some vocal theoreticians, and rigid principles for legislative control of clade names and definitions have been outlined in the PhyloCode. The consequences of this semantic maelstrom have not been worked out. In pratice, phylogenetic nomenclature will bc disastrous, promoting confusion and instability, and it should be abandoned. It is based on a fundamental misunderstanding of the difference between a phylogeny (which is real) and a classification (which is utilitarian). Under the new view, classifications are identical to phlylogenies, and so the proponents of phylogenetic nomenclature will end up abandoning classifications altogether.     

Who's related to whom? Recent results from molecular systematic studies

Similarities among model systems can lead to generalizations about plants, but understanding the differences requires systematic data. Molecular phylogenetic analyses produce results similar to traditional classifications in the grasses (Poaceae), and relationships among the cereal crops are quite clear. Chloroplast-based phylogenies for the Solanaceae show that tomato is best considered as a species of Solanum, closely related to potatoes. Traditional classifications in the Brassicaceae are misleading with regard to true phylogenetic relationships and data are only now beginning to clarify the situation. Molecular data are also being used to revise our view of relationships among flowering plant families. Phylogenetic data are critical for interpreting hypotheses of the evolution of development.     

Evolution of Craniodental Correlates of Diet in African Bovidae

Establishing the relationship between craniodental morphology and dietary ecology in extant species permits inferences to be made about the ecology and biology of fossil species and the habitats they inhabited. Previous work linking diet and craniodental morphology has historically relied upon categorical classifications of diet and has not considered the phylogenetic signal (i.e., non-independence) of morphology due to shared evolutionary history. Here we use phylogenetic comparative methods to analyze the relationship between diet and eight craniodental indices for 40 species of African Bovidae using both categorical and continuous (stable carbon isotopes of enamel, δ¹³C) classifications of diet. In addition, we examine three modes of evolution that best explain interspecific variation in each of these indices, including: Brownian Motion (BM), Early Burst (EB), and Ornstein-Uhlenbeck (OU). Our results show that the hypsodonty index (HI), the length of the masseteric fossa relative to facial depth (MAS-F), and the length of the diastema relative to the total toothrow length (DIAS-TR) are the best predictors of diet among African bovids. These indices are best explained by either a BM or OU mode of evolution. Our findings have important implications for understanding the evolution of craniodental traits and reconstructing the diet of fossil mammals, especially bovids.     

Evolution,actuality and species concept: a need for a palaeontological tool

Species concept was developed to fit neontological necessities in ordering biological variability. Transversal (horizontal, synchronic) taxonomy shows hierarchical requirements quite different from those involved in longitudinal (vertical, diachronic) classifications. Furthermore, limitations within the species concept itself make it scarcely available in many paleontological contexts. Classical species definitions are often limited by theoretic and logic constraints, that are seldom available to describe practical situations. Morphology is an uncertain source of phylogenetic information, but it is still the main ground of biological comparison for extinct populations. Therefore, efforts in species recognition should be devoted to making taxonomy a useful tool for communication. First, inferences in systematics have to be led upon the available information about characters and processes. If this information is missing or not developed, no detailed conclusions can be supported. Secondly, definitions should be sufficiently elastic and generalised to allow an adaptation to each different case-study. The final target is to synthesise actual evolutionary histories, and not biological potentialities.     

Molecular data confirm family status for the Tryonicus-Lauraesilpha group (Insecta: Blattodea: Tryonicidae)

Family status was recently proposed for the Tryonicus-Lauraesilpha group (Insecta: Blattodea: Tryonicidae), which had been assigned to Blattidae before. In order to test this hypothesis, a molecular phylogenetic analysis of Blattodea was conducted using the 12S and H3 genes. The results show that Tryonicidae indeed form a lineage distinct from Blattidae. The results are compared to the previous classifications and phylogenetic hypotheses (morphology- and molecular-based). It is suggested that the Polyzosteriinae tribe Methanini should remain in Polyzosteriinae (Blattodea: Blattidae).     

Principles of biological comparison

The problems of comparative analyses in biology have been discussed, showing that a single comparative method does not exist. Several principles of comparison are elucidated, which include that comparisons do not have to possess a phylogenetic basis, can be horizontal or vertical, and can be genetic or nongenetic. Biological comparisons can be grouped roughly into historical and nonhistorical ones. Historical comparisons depend on the details of evolutionary theory, and include: (a) comparisons on which phylogenies and classifications are based; and (b) comparative studies using these phylogenies and classifications. Nonhistorical comparisons require pertinent nomological relationships between two or more variables, and include: (a) comparisons between variables used to elucidate these law-like relationships; and (b) comparisons in which unknown properties of one variable are deduced from the known properties of other variables - extrapolations made in biology.     

Numerical and comparative analyses of the modern systems of classification of the flowering plants

The modern classifications of Cronquist, Dahlgren, Takhtajan, and Thorne have been compared with one another and also with those published at the beginning of the 20th century, which comprise the ones by Bessey, Engler, Gobi, and Hallier. Mantel and consensus tests have been used to compare the different matrices taken from the above classifications. Results indicate that all four modern classifications do not differ from one another statistically. Ordinal delimitation has not changed significantly for a century at least: Orders of the modern classifications are similar to those of the past classifications. However, the topology or structure of Cronquist’s and Takhtajan’s classifications differs from that of Bessey’s. Also, Engler’s dicotyledon classification is statistically different from those of the modern systems. Among past classifications, that of Hallier resembles the modern ones most. The resemblance among the modern classifications and, in general, with the past ones can be explained by the similarity in taxonomic principles and in the practice used. Two other factors help in explaining similarities among classifications: cognitive constraint and historical inertia. For instance, the Linnean scheme—upon which all botanical classifications are based—imposes on the latter a structure which allows only with difficulty and approximation the representation of taxon evolution. Moreover, not only have modern authors mutually influenced one another (particularly Cronquist/Takhtajan, Dahlgren/Thorne), but also they have been influenced by past authors. Indeed, modern classifications are a reshuffling of past ones. Also, Engler’s influence is great, especially at the ordinal level. For changes and modifications to become effective in future classifications of flowering plants, one will have to minimize, if not avoid, the implicit influence of the modern systems as standard systems, and to count on, among others, molecular data in redefining taxonomic concepts founded on classical morphology, and consequently to remove the prudence that makes us look at classification as a useful convention for which one of the basic criteria remains the stability of taxa recognized long ago.     

The opsins

The photosensitive molecule rhodopsin and its relatives consist of a protein moiety - an opsin - and a non-protein moiety - the chromophore retinal. Opsins, which are G-protein-coupled receptors (GPCRs), are found in animals, and more than a thousand have been identified so far. Detailed molecular phylogenetic analyses show that the opsin family is divided into seven subfamilies, which correspond well to functional classifications within the family: the vertebrate visual (transducin-coupled) and non-visual opsin subfamily, the encephalopsin/tmt-opsin subfamily, the G_q-coupled opsin/melanopsin subfamily, the G_o-coupled opsin subfamily, the neuropsin subfamily, the peropsin subfamily and the retinal photoisomerase subfamily. The subfamilies diversified before the deuterostomes (including vertebrates) split from the protostomes (most invertebrates), suggesting that a common animal ancestor had multiple opsin genes. Opsins have a seven-transmembrane structure similar to that of other GPCRs, but are distinguished by a lysine residue that is a retinal-binding site in the seventh helix. Accumulated evidence suggests that most opsins act as pigments that activate G proteins in a light-dependent manner in both visual and non-visual systems, whereas a few serve as retinal photoisomerases, generating the chromophore used by other opsins, and some opsins have unknown functions.     

Molecular phylogeny of the family Pectinidae (Mollusca: Bivalvia) based on mitochondrial 16S and 12S rRNA genes

Pectinidae is a large bivalve family characterised by almost circular, flat shells. Species are distributed worldwide and fall into three life-styles: swimming, byssally attached to hard substrates, and cemented to rocks with one valve. Despite these very different life strategies, pectinid shells are highly conservative in shape and offer few clues for the unravelling of phylogenetic issues. Consequently, phylogenetic studies based on morphological features have not yielded conclusive results. We thus set out to analyse partial sequences of mitochondrial 12S and 16S rRNA genes from 23 species of 16 genera with molecular techniques. The results are largely in contrast, both at the genus and the subfamily level, with the systematic classifications based on adult morphological characters, whereas they agree with the morphological classifications based on the more conserved non-adaptive features.     

MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method

Background  

A phylogenetic network is a generalization of phylogenetic trees that allows the representation of conflicting signals or alternative evolutionary histories in a single diagram. There are several methods for constructing these networks. Some of these methods are based on distances among taxa. In practice, the methods which are based on distance perform faster in comparison with other methods. The Neighbor-Net (N-Net) is a distance-based method. The N-Net produces a circular ordering from a distance matrix, then constructs a collection of weighted splits using circular ordering. The SplitsTree which is a program using these weighted splits makes a phylogenetic network. In general, finding an optimal circular ordering is an NP-hard problem. The N-Net is a heuristic algorithm to find the optimal circular ordering which is based on neighbor-joining algorithm.     

Trees before and after Darwin

Phylogenetic trees published before Darwin’s On the Origin of Species are scarce. Lamarck (1809) and Barbançois (1816; J Phys Chim Hist Nat Arts 82, 444) are the first and only trees devoted to illustrating the genealogical connections between organisms of different species and different higher taxa. In the late 18th and early 19th centuries, most of the trees depicted in papers dealing with natural history were classifications; classifications in the shape of trees, but classifications nonetheless. Those published by Bronn (1858) are a good example. After Darwin, phylogenetic trees incorporating the time dimension flourished. In the first half of the 20th century, the Modern Synthesis failed to renew and rejuvenate the intuitive construction of trees. It wasn’t until the appearance of Hennig’s phylogenetic systematics that the real nature of the connection between phylogeny and the pre‐Darwinian concept of homology was made clear.     

丝核菌的分类系统：现状及存在问题

以重要植物病原菌为特征的丝核菌是一类在土壤中广泛分布的丝状真菌,通常不产孢,以菌丝或菌核的形式存在,多样性非常丰富。本文基于国内外最新研究进展,对依据菌丝体的细胞核数目、菌丝融合、有性生殖和系统进化等方面的基本特征展开的丝核菌分类体系及分类现状进行了综述。基于菌丝的细胞核数目,丝核菌被分为单核、双核和多核丝核菌三大类群。自然界中单核丝核菌数量极少,多核和双核丝核菌在全球分布广泛,占丝核菌的绝大多数。基于菌丝融合试验的结果,目前多核丝核菌被分为13个菌丝融合群,双核丝核菌被分为18个菌丝融合群。部分融合群内又根据一些稳定的特征分了亚群,但亚群的建立标准并不统一。目前的分子系统学研究结果基本支持丝核菌的菌丝融合群及亚群的分类。基于部分有性世代被发现的菌株的形态特征,多核和双核丝核菌分别被鉴定为亡革菌属和角担菌属。此外,目前已有分属重要植物病原菌和兰科菌根菌类群的至少9个融合群或亚群的17个菌株完成了基因组测序,比较基因组学和线粒体组学开始在丝核菌分类和进化研究中发挥作用。丝核菌分类系统特殊且复杂,作者在文末提出了目前丝核菌分类学研究面临的问题和今后研究的趋势,期待更多的学者参与到这个重要菌...     

Molecular phylogenetics of subtribe Aeridinae (Orchidaceae): insights from plastid matK and nuclear ribosomal ITS sequences

We conducted phylogenetic analyses using two DNA sequence data sets derived from matK, the maturase-coding gene located in an intron of the plastid gene trnK, and the internal transcribed spacer region of 18S–26S nuclear ribosomal DNA to examine relationships in subtribe Aeridinae (Orchidaceae). Specifically, we investigated (1) phylogenetic relationships among genera in the subtribe, (2) the congruence between previous classifications of the subtribe and the phylogenetic relationships inferred from the molecular data, and (3) evolutionary trends of taxonomically important characters of the subtribe, such as pollinia, a spurred lip, and a column foot. In all, 75 species representing 62 genera in subtribe Aeridinae were examined. Our analyses provided the following insights: (1) monophyly of subtribe Aeridinae was tentatively supported in which 14 subclades reflecting phylogenetic relationships can be recognized, (2) results are inconsistent with previous classifications of the subtribe, and (3) repeated evolution of previously emphasized characters such as pollinia number and apertures, length of spur, and column foot was confirmed. It was found that the inconsistencies are mainly caused by homoplasy of these characters. At the genus level, Phalaenopsis, Cleisostoma, and Sarcochilus are shown to be non-monophyletic.     

湖南省两栖、爬行动物物种多样性及其地理分布

物种多样性及其地理分布是制定野生动物保护对策的重要依据。两栖、爬行动物在生物演化的历史上占据着重要地位, 又是脊椎动物分类体系变动较大的类群。为了掌握湖南省两栖、爬行动物物种多样性现状, 促进湖南省生物多样性保护和野生动物管理工作, 我们参考分类学及分子生物系统学的最新研究成果, 系统地收集了近10多年来有关湖南省两栖、爬行动物分类的文献资料, 结合团队长期以来的野外调查数据, 对湖南省两栖、爬行动物名录进行了整理与更新(截止到2021年10月31日)。结果表明: 湖南省已记录两栖动物2目10科30属86种(含亚种), 爬行动物2目22科55属105种(含亚种), 其中中国特有种分别有62种和30种, 湖南省特有种分别有10种和4种。列入《国家重点保护野生动物名录》(2021)的两栖动物有11种, 爬行动物有10种; 列为《中国生物多样性红色名录》(2021)受威胁等级的两栖动物有20种, 爬行动物有30种。此外, 湖南省两栖、爬行动物区系特征明显, 以东洋界种类为主(81.2%), 广布种较少(18.8%), 无古北界种。在地理分布上, 湘南山地丘陵区、湘西北山地区是湖南省两栖、爬行动物物种丰富度较高的地区。     

Phylogenetic relationships among the Ithomiini (Lepidoptera: Nymphalidae) inferred from one mitochondrial and two nuclear gene regions

Abstract.  A phylogenetic hypothesis for the tribe Ithomiini (Lepidoptera: Nymphalidae: Danainae) is presented, based on sequences of the mitochondrial cytochrome oxidase subunits I and II (COI–COII) region and regions of the nuclear genes wingless and Elongation factor 1-alpha . Branch support for each clade is assessed, and a partition congruence index is used to explore conflict among gene regions. The monophyly of the clade is strongly supported, as are many of the traditionally recognized subtribes and genera. The data imply paraphyly of some genera and tribes, but largely support recent classifications and phylogenetic hypotheses based on morphological characters.     

Marginal Likelihood Estimate Comparisons to Obtain Optimal Species Delimitations in Silene sect. Cryptoneurae (Caryophyllaceae)

Coalescent-based inference of phylogenetic relationships among species takes into account gene tree incongruence due to incomplete lineage sorting, but for such methods to make sense species have to be correctly delimited. Because alternative assignments of individuals to species result in different parametric models, model selection methods can be applied to optimise model of species classification. In a Bayesian framework, Bayes factors (BF), based on marginal likelihood estimates, can be used to test a range of possible classifications for the group under study. Here, we explore BF and the Akaike Information Criterion (AIC) to discriminate between different species classifications in the flowering plant lineage Silene sect. Cryptoneurae (Caryophyllaceae). We estimated marginal likelihoods for different species classification models via the Path Sampling (PS), Stepping Stone sampling (SS), and Harmonic Mean Estimator (HME) methods implemented in BEAST. To select among alternative species classification models a posterior simulation-based analog of the AIC through Markov chain Monte Carlo analysis (AICM) was also performed. The results are compared to outcomes from the software BP&P. Our results agree with another recent study that marginal likelihood estimates from PS and SS methods are useful for comparing different species classifications, and strongly support the recognition of the newly described species S. ertekinii.     

Repeated evolution of dioecy from androdioecy in Acer

The evolution of breeding systems was studied in the genus Acer, with special attention to the origin of androdioecy and dioecy, using a phylogenetic approach. Parsimony and maximum-likelihood techniques were used to infer the ancestral character state and trends in the evolution of breeding systems. Information on breeding systems was obtained from the literature, and phylogenetic relationships were taken from three published phylogenies. Although a general trend from duodichogamy to dioecy through heterodichogamy has been proposed for the genus Acer, our results show that a general trend is not detected when phylogenetic relationships are taken into account. Dioecy appeared as a derived state that evolved at least three times and never reversed towards other states. Three different paths to dioecy have been followed in the genus Acer: from heterodichogamous androdioecy; from heterodichogamous trioecy; and from dichogamous subdioecy. Therefore, although the best documented cases of evolution of androdioecy indicate that this breeding system evolves from dioecy, in the genus Acer the opposite situation occurs (androdioecy leading to dioecy). Here we discuss the role of inbreeding avoidance and sexual specialization as selective forces driving the evolution of dioecy in the genus Acer.