The role of theories in biological systematics

The role of scientific theories in classifying plants and animals is traced from Hennig's phylogenetics and the evolutionary taxonomy of Simpson and Mayr, through numerical phenetics, to present-day cladistics. Hennig limited biological classification to sister groups so that this one relation can be expressed unambiguously in classifications. Simpson and Mayr were willing to sacrifice precision in representation in order to include additional features of evolution in the construction of classifications. In order to make classifications more objective, precise and quantitative, numerical pheneticists limited themselves to representing degrees of phenetic similarity. Finally, present-day cladists can be separated into phylogenetic cladists, who retain much of Hennig's theory of classification, and pattern cladists, who have stripped Hennig's system down to its bare essentials.     

Primary classification and phylogeny of the Polemoniaceae, with comments on molecular cladistics

The system of classification of the Polemoniaceae currently in use was published by Grant in 1959. Much new evidence concerning relationships in the family has been obtained by numerous workers since 1959, and the old system is in need of revision. A revised system down to the genus level, based on conventional and unconventional characters, including molecular evidence, is presented here. Nineteen genera are grouped into eight tribes and two subfamilies. Three new tribes are described: Acanthogilieae, Loeselieae, and Leptodactyloneae. Several genera are transferred to new groups. The phylogeny of the family is discussed in the light of both the older and new evidence. The approach used in constructing both the 1959 and new systems is that of evolutionary systematics. Two recent (1996, 1997) family-wide surveys of cpDNA and rDNA use cladistic methods of analysis to arrive at sets of major groups. Some of this molecular evidence has been adopted for the present revised system. However, much incongruence still exists between the new sets of clades, on the one hand, and the present revised system or the still-viable parts of the 1959 system on the other hand. The incongruences call for an examination and comparison of the contrasting methods of evolutionary systematics and molecular cladistics. A fundamental flaw in the 1996 and 1997 treatments is the attempt to classify plants on the basis of single-gene gene trees.     

Morphology,phylogeny and taxonomy of South American bothropoid pitvipers (Serpentes,Viperidae)

Carrasco, P.A., Mattoni, C.I., Leynaud, G.C. & Scrocchi, G.J. (2012). Morphology, phylogeny and taxonomy of South American bothropoid pitvipers (Serpentes, Viperidae). —Zoologica Scripta, 41, 109–124. South American bothropoids comprise a monophyletic and greatly diverse group of pitvipers that were initially included in the genus Bothrops and later assigned to five genera. Until recently, most phylogenetic analyses of bothropoids used exclusively mitochondrial DNA sequences, whereas few of them have included morphological traits. Moreover, the systematic affinities of some species remain unclear. In this study, we performed a parsimony analysis of morphological data obtained from the examination of 111 characters related to lepidosis, colour pattern, osteology, and hemipenial morphology of 35 of the 48 species that compose the bothropoid group. The morphological data analysed contain novel information about several species, including the incertae sedis. Morphology was analysed separately and combined with 2393 molecular characters obtained from published sequences of four mitochondrial genes. Five characters of the ecology were also included. A sensitivity analysis was performed using different weighting criteria for the characters. The congruence among different sources of evidence was evaluated through partitioned and total evidence analyses, the analyses of reduced datasets and the use of incongruence length difference test. With few exceptions, results showed groups of species similar to those obtained in previous studies; however, incongruences between morphological and molecular characters, and within the molecular partition, were revealed. This conflict affects the relationship between particular groups of species, leading to alternative phylogenetic hypotheses for bothropoids: hierarchical radiation or two major lineages within the group. The results also showed that Bothrops sensu stricto is paraphyletic. We discuss previous taxonomic approaches and, considering both phylogenetic hypotheses, we propose an arrangement that rectifies the paraphyly of Bothrops: maintaining Bothrocophias, assigning Bothrops andianus to this genus; and recognising the sister clade as Bothrops, synonymising Bothriopsis, Bothropoides and Rhinocerophis.     

An evaluation of the systematic value of skull morphology in the Trimeresurus radiation (Serpentes: Viperidae: Crotalinae) of Asian pitvipers

Trimeresurus (in its widest sense) is a very diverse and widespread radiation of Asian pitvipers, which has been subject to numerous taxonomic revisions, some of which have been based on characteristics of the skull. In order to evaluate the taxonomic utility of such characters, we conducted a comparison of the skulls of 57 specimens representing nine genera, and two currently unassigned species that are very closely related to each other. A canonical variate analysis reveals three distinct phenetic groups: the Protobothrops group, a group containing Ovophis monticola , ' Ovophis ' okinavensis , and ' Trimeresurus ' gracilis , and finally a group comprising the remaining species and characterized by considerable overlap between most genera with the exception of the monotypic Peltopelor and Himalayophis . Agreement between phenetic similarity based on skull characteristics and phylogenetic relationships based on molecular evidence varies between different groups: the morphological similarity of the skull of Protobothrops sieversorum to the other Protobothrops species is congruent with their recent synonymization while the phenetic similarity among the species within the second group does not reflect current molecular phylogenetic relationships and indicates that convergent or parallel evolution may be responsible for at least some of the phenetic similarity detected among skulls of the Asian pit vipers examined. A test of phylogenetic independence, however, indicates that there is still a significant phylogenetic signal that can be recovered from several skull characteristics. Thus, we conclude that skull morphology can contribute to an overall understanding of pitviper taxonomy, but that it would be unwise to rely on skull characteristics alone.     

Integration of conflict into integrative taxonomy: fitting hybridization in species delimitation of Mesocarabus (Coleoptera: Carabidae)

In species differentiation, characters may not diverge synchronously, and there are also processes that shuffle character states in lineages descendant from a common ancestor. Species are thus expected to show some degree of incongruence among characters; therefore, taxonomic delimitation can benefit from integrative approaches and objective strategies that account for character conflict. We illustrate the potential of exploiting conflict for species delimitation in a study case of ground beetles of the subgenus Carabus (Mesocarabus), where traditional taxonomy does not accurately delimit species. The molecular phylogenies of four mitochondrial and three nuclear genes, cladistic analysis of the aedeagus, ecological niche divergence and morphometry of pronotal shape in more than 500 specimens of Mesocarabus show that these characters are not fully congruent. For these data, a three‐step operational strategy is proposed for species delimitation by (i) delineating candidate species based on the integration of incongruence among conclusive lines of evidence, (ii) corroborating candidate species with inconclusive lines of evidence and (iii) refining a final species proposal based on an integrated characterization of candidate species based on the evolutionary analysis of incongruence. This procedure provided a general understanding of the reticulate process of hybridization and introgression acting on Mesocarabus and generated the hypothesis of seven Mesocarabus species, including two putative hybrid lineages. Our work emphasizes the importance of incorporating critical analyses of character and phylogenetic conflict to infer both the evolutionary history and species boundaries through an integrative taxonomic approach.     

Methods of systematic analysis: the relative superiority of phylogenetic systematics

The superiority of cladistic methods to both synthetic and phenetic methods is briefly advanced and reviewed. Cladistics creates testable hypotheses of phylogeny that also give a highly informative summary of available data. Thus it best fits the criteria for a method for determining the general reference classification in biology. For protistologists in particular, cladistics is especially useful. Inundated by an abundance of ultrastructural, biochemical, and cell biological information, protistologists could be greatly helped by the informative way in which cladistics orders and summarizes the data. In addition to classifying protist taxa, hypotheses about the evolution of cell organelles and cellular could be scientifically formulated and tested by cladistics . Because cladistic classifications best summarize the data, they would also be best for making predictions about taxa and characters. They would, for the same reason, be the most stable. Widespread adoption of cladistic methods would serve to stabilize the now fluid state of protist taxonomy. It is for all of these reasons that such methods best suit the needs of the evolutionary protistologist .     

Methods of systematic analysis: The relative superiority of phylogenetic systematics

The superiority of cladistic methods to both synthetic and phenetic methods is briefly advanced and reviewed. Cladistics creates testable hypotheses of phylogeny that also give a highly informative summary of available data. Thus it best fits the criteria for a method for determining the general reference classification in biology.For protistologists in particular, cladistics is especially useful. Inundated by an abundance of ultrastructural, biochemical, and cell biological information, protistologists could be greatly helped by the informative way in which cladistics orders and summarizes the data. In addition to classifying protist taxa, hypotheses about the evolution of cell organelles and cellular could be scientifically formulated and tested by cladistics. Because cladistic classifications best summarize the data, they would also be best for making predictions about taxa and characters. They would, for the same reason, be the most stable. Widespread adoption of cladistic methods would serve to stabilize the now fluid state of protist taxonomy. It is for all of these reasons that such methods best suit the needs of the evolutionary protistologist.     

中国栎属植物的数量分类研究

在全面衡量中国栎属49种4变种性状特征的基础上,观测了25个定性性状和18个数量性状。通过聚类分析,可以将中国栎属分为5个特征明显的表征群,即5组:麻栎组(Section Aegilops)、槲栎组(Section Quercus)、高山栎组(Section Brachylepides)、巴东栎组(Section Engleriana)和橿子栎组(Section Echinolepides)。在主成分分析中,虽然性状的累积贡献率增长不明显,前3个主成分累积贡献率仅有50.4%,但结果仍然显示出和聚类分析同样的结果。说明栎属的分类性状仍存在主要方面,只不过在演化过程中由于性状变异的多样性,产生了多个不同的表征类群。分析结果对我们解决个别有疑问种的分类地位也有启示作用。因此,数量分类方法对解决栎属组间及种间的分类问题有重要的意义。     

More evidence for pervasive paraphyly in scleractinian corals: Systematic study of Southeast Asian Faviidae (Cnidaria; Scleractinia) based on molecular and morphological data

Coral taxonomy and systematics continue to be plagued by a host of problems. Due to high phenotypic variability within species, morphological approaches have often failed to recognize natural taxa, and molecular techniques have yet to be applied to many groups. Here, we summarize the levels of paraphyly found for scleractinian corals and test, based on new data, whether paraphyly is also a significant problem in Faviidae, the second-most speciose hermatypic scleractinian family. Using both DNA sequence and morphological data we find that, regardless of analysis technique (maximum parsimony, maximum likelihood and Bayesian likelihood), many conventional taxonomic groups are not monophyletic. Based on two mitochondrial markers (COI and a noncoding region) that we amplified for 81 samples representing 41 faviid species and 13 genera, five genera that are represented by more than one species are paraphyletic, as is the family Faviidae. The morphological characters currently used to identify these corals similarly fail to recover many genera. Furthermore, trees based on both data types are incongruent, and total evidence analysis does little to salvage conventional taxonomic groupings. Morphological convergence, phenotypic variability in response to the environment, and recent speciation are likely causes for these conflicts, which suggest that the present classification of corals is in need of a major overhaul. We propose more detailed studies of problematic faviid taxa using standardized morphological, mitochondrial, and nuclear genetic markers to facilitate combining of data.     

Pattern Cladistics and the ‘Realism–Antirealism Debate’ in the Philosophy of Biology

Despite the amount of work that has been produced on the subject over the years, the ‘transformation of cladistics’ is still a misunderstood episode in the history of comparative biology. Here, I analyze two outstanding, highly contrasting historiographic accounts on the matter, under the perspective of an influential dichotomy in the philosophy of science: the opposition between Scientific Realism and Empiricism. Placing special emphasis on the notion of ‘causal grounding’ of morphological characters (sensu Olivier Rieppel) in modern developmental biology’s (mechanistic) theories, I arrive at the conclusion that a ‘new transformation of cladistics’ is philosophically plausible. This ‘reformed’ understanding of ‘pattern cladistics’ entails retaining the interpretation of cladograms as ‘schemes of synapomorphies’, but in association to construing cladogram nodes as ‘developmental-genetic taxic homologies’, instead of ‘standard Darwinian ancestors’. The reinterpretation of pattern cladistics presented here additionally proposes to take Bas Van Fraassen’s ‘constructive empiricism’ as a philosophical stance that could properly support such analysis of developmental-genetic data for systematic purposes. The latter suggestion is justified through a reappraisal of previous ideas developed by prominent pattern cladists (mainly, Colin Patterson), which concerned a scientifically efficient ‘observable/non-observable distinction’ linked to the conceptual pair ‘ontogeny and phylogeny’. Finally, I argue that a robust articulation of Antirealist alternatives in systematics may provide a rational basis for its disciplinary separation from evolutionary biology, as well as for a critical reconsideration of the proper role of certain Scientific Realist positions, currently popular in comparative biology.     

THE QUANTIFICATION OF SOME PLANT-TAXA CIRCUMSCRIPTIONS

Intrataxon variability is estimated by the technique of numerical taxonomy. Taxa which had been determined by orthodox taxonomic methods are subjected to analyses by numerical phenetics. Comparisons are made of the amounts of cohesion among the members of different taxa in the Bromeliaceae at several taxonomic levels by computing the degrees of similarities between members of the same taxon and of different taxa. Results of these comparisons with several taxa reveal that the variability of a taxon in terms of phenetic distance computed with a large number of characters does not necessarily agree with a subjective appraisal of variability. The method facilitated difficult taxonomic determinations and provided an estimate of the relative evolutionary ages of different taxonomic groups.     

Classification of weevils as a data-driven science: leaving opinion behind

Data and explicit taxonomic ranking criteria, which minimize taxonomic change, provide a scientific approach to modern taxonomy and classification. However, traditional practices of opinion-based taxonomy (i.e., mid-20^th century evolutionary systematics), which lack explicit ranking and naming criteria, are still in practice despite phylogenetic evidence. This paper discusses a recent proposed reclassification of weevils that elevates bark and ambrosia beetles (Scolytinae and Platypodinae) to the ranks of Family. We demonstrate that the proposed reclassification 1) is not supported by an evolutionary systematic justification because the apparently unique morphology of bark and ambrosia beetles is shared with other unrelated wood-boring weevil taxa; 2) introduces obvious paraphyly in weevil classification and hence violates good practices on maintaining an economy of taxonomic change; 3) is not supported by other taxonomic naming criteria, such as time banding. We recommend the abandonment of traditional practices of an opinion-based taxonomy, especially in light of available data and resulting phylogenies.     

Catching the phylogenic history through the ontogenic hourglass: a phylogenomic analysis of Drosophila body segmentation genes

SUMMARY The phylogenetic information content of different developmental stages is a long‐standing issue in the study of development and evolution. We performed phylogenetic analyses of 51 body segmentation genes in 12 species of Drosophila in order to investigate the impact of the mode of evolution of development on phylogeny inference. Previous studies of these genes in Drosophila using pairwise phenetic comparisons at the species group level revealed the presence of an “hourglass model” (HG), wherein mid‐embryonic stages are the most evolutionarily constrained. We utilized two character‐based approaches: taxonomic congruence using the relative consensus fork index (RCFI), in which phylogenies are inferred from each gene separately and compared with a total evidence tree (TET), and partitioned simultaneous analysis using several indices such as branch support (BS) and localized incongruence length difference (LILD) test. We also proposed a new index, the recapitulatory index (R), which divides the number of synapomorphies on the total number of informative characters in a data set. Polynomial adjustment of both BS and R indices showed strong support for the hourglass model regardless of the taxonomic level (species subgroup vs. subgenera), showing less phylogenetic information content for mid‐developmental stages (mainly the zygotic segment polarity stage). Significant LILD scores were randomly distributed among developmental stages revealing the absence of differential selective constraints, but were significantly related to chromosomal location showing physical (linkage) impact on phylogenetic incongruence. RCFI was the most sensitive measure to taxonomic level, having a convex parabola at the species subgroup level in support of the hourglass model and a concave parabola at the subgeneric level in support of the adaptive penetrance model. This time‐dependent discrepancy of best fit developmental model parallels previous conflicting results from the vertebrates. Because of the quasi‐phenetic nature of this index, we argue that the discrepancy is due to the evolutionary rate heterogeneity of developmental genes rather than to fundamental differences among organisms. We suggest that simultaneous character‐based analyses give better macroevolutionary support to the hourglass model of the developmental constraints on genome evolution than pairwise phenetic comparisons.     

It is normal for classification approaches to be diverse

It is asserted that the postmodern concept of science, unlike the classical ideal, presumes necessary existence of various classification approaches (schools) in taxonomy, each corresponding to a particular aspect of consideration of the "taxic reality". They are set up by diversity of initial epistemological and ontological backgrounds which fix in a certain way a) fragments of that reality allowable for investigation, and b) allowable methods of exploration of the fragments being fixed. It makes it possible to define a taxonomic school as a unity of the above backgrounds together with consideration aspect delimited by them. Two extreme positions of these backgrounds could be recognized in recent taxonomic thought. One of them follows the scholastic tradition of elaboration of a formal and, hence, universal classificatory method ("new typology", numerical phenetics, pattern cladistics). Another one asserts dependence of classificatory approach on the judgment of the nature of taxic reality (natural philosophy, evolutionary schools of taxonomy). Some arguments are put forward in favor of significant impact of evolutionary thinking onto the theory of modern taxonomy. This impact is manifested by the correspondence principle which makes classificatory algorithms (and hence resulting classifications) depending onto initial assumptions about causes of taxic diversity. It is asserted that criteria of "quality" of both classifications proper and classificatory methods can be correctly formulated within the framework of a particular consideration aspect only. For any group of organisms, several particular classifications are rightful to exist, each corresponding to a particular consideration aspect. These classifications could not be arranged along the "better-worse" scale, as they reflect different fragments of the taxic reality. Their mutual interpretation depends on degree of compatibility of background assumptions and of the tasks being resolved. Extensionally, classifications are compatible as much as they coincide by context and hierarchical structure of included taxa. Intentionally, typological classifications are compatible if included taxa are comparable by their diagnoses, while phylogenetic classifications are compatible if the included taxa are ascribed monophyletic status. A brief consideration is given to the "new phylogenetics" (= "genophyletics") as to a classificatory approach aimed at elaboration of parsimonious phylogenetic hypotheses based on molecular biology data and employing numerical methods of cladistic analysis. This approach is shown to borrows some phenetic ideas and revives scholastic principle of unified classificatory basis. It is supposed that, in a time, biological classification would get escaping from plethora of positivistic ideas (including those being developed by nowaday cladistics) and would assimilate (revive) more actively holistic worldview.     

Molecules and Morphology,Phylogenetics and Genetics

Various explanations can be offered for the incongruence between phylogenetic hypotheses resulting from morphological and molecular data sets. Of these, the possibility that incongruence may result from the mutation of major morphogenetic genes leading to dramatic morphological divergence unaccompanied by equivalent change of the phylogenetic marker molecule(s) used is discussed in detail. As evidence for this hypothesis, several examples for such incongruence are surveyed. It seems possible that in many cases the genetic basis of the morphological characters responsible for the incongruence found may be simple, and that the genes involved may be homologous to genes known from mutant systems. It is suggested that: 1. the systematic documentation of incongruence between molecular and morphological phylogenies may help to assess the frequency of evolutionary change through the mutation of major morphogenetic genes, and that 2. the identification of major morphological characters distinguishing closely related taxa with mutant phenotypes known from mutant systems eventually may allow an experimental approach to the problem of evolutionary change resulting from major genes. Natural taxa suspected to be the result of such processes could be changed morphologically through transformation with the relevant genes.     

Phenetic and phylogenetic studies based on measurements of Plantago ser. Brasilienses

Numerical taxonomic methods for a programmable pocket calculator are proposed. Operational taxonomic units (OTU's) may be either accepted taxa or single specimens, or a mixture of both. All types of characters are employable. A calculated or estimated common standard deviation and the mean (or reading) define the normal distribution curve for each measurement variable. Similarity between two OTU's is calculated as the overlapping area below their distribution curves. Ninety specimens of Plantago ser. Brasilienses are used as examples. The clusters are finally grouped using both phenetic and several cladistic methods. Results from phylogenetic sys–tematics cannot be used directly in taxonomy because the basic principles are discordant with those in the botanical code.     

Sero‐taxonomy of skeletal macromolecules in living Terebratulid brachiopods

Antibodies prepared against macromolecules isolated from the shells of three living brachiopod genera have proved to be of considerable taxonomic significance, in that the pattern of cross‐reactivity of all three antisera consistently points to a new interpretation for the evolution of the largest extant brachiopod order, the Terebratulida. This new molecular evidence actually complements rather than contradicts the existing morphology‐based taxonomy, since detailed systematic investigation of the taxa in question has already demonstrated subtle but significant morphological differences in the major taxonomic characters which appear to reflect this new interpretation.

As fragments of skeletal macromolecules, including antigenic determinants, are known to survive for many millions of years within the protected micro‐environments provided by enclosing biominerals, these results suggest that such molecular fossils could well provide important insights on at least the high‐level taxonomic relationships of fossil organisms.     

Phylogenomics: the beginning of incongruence?

Until recently, molecular phylogenies based on a single or few orthologous genes often yielded contradictory results. Using multiple genes in a large concatenation was proposed to end these incongruences. Here we show that single-gene phylogenies often produce incongruences, albeit ones lacking statistically significant support. By contrast, the use of different tree reconstruction methods on different partitions of the concatenated supergene leads to well-resolved, but real (i.e. statistically significant) incongruences. Gathering a large amount of data is not sufficient to produce reliable trees, given the current limitation of tree reconstruction methods, especially when the quality of data is poor. We propose that selecting only data that contain minimal nonphylogenetic signals takes full advantage of phylogenomics and markedly reduces incongruence.     

杉科植物的分类学研究

本文对杉科植物的研究历史作了回顾,根据分支分类结果和表征分类结果,提出了一个新的分类系统.以形态学为依据,结合其他学科的研究成果,对杉科的分类作了订正。作者承认杉科植物共9属、12种及3变种,将杉木、厚皮杉木、德昌杉木和米德杉木归并,支持柳杉作为日本柳杉的变种、台湾杉木作为杉木的变种、秃杉和台湾杉归并的观点。