分支系统学当前的理论和方法概述及华东地区山胡椒属十二个种的分支系统学研究

本文概述了当前分支系统学研究中涉及的主要理论和方法,包括性状的选取、性状状态和极性的确定、数据矩阵的分析计算、结果分支图的处理、分支图可靠性的评价及分支图的应用。本文同时以华东地区樟科山胡椒属Linderal2个种的分支系统学研究为例,讨论了用形态性状进行分支系统学研究中可能遇到的问题,也揭示了一些分支系统学与传统的系统学在应用性状推导进化关系上的不同点。对这12个种的分支系统学研究得出了一些不同于传统系统学方法所推测的山胡椒属内的系统发育关系,如分支系统学研究显示山胡椒组和球果组很近缘。在严格一致性分支图上,杯托组的黑壳楠和江浙山胡椒分别位于最原始和最进化的分支,表明这个组是复系类群。分支图也显示山胡椒组可能是复系类群。     

The use of parsimony in testing phylogenetic hypotheses

With the advance of cladistic theory differences in principle between it and other systematic techniques are few but of fundamental importance. In the mechanics of classification they are confined to ranking and the rejection of paraphyletic taxa. In cladistic analysis, leading to cladograms, trees and phylogeny reconstruction, inconsistencies in apparent synapomorphies are said to be resolved using Popper's hypothetico-deductive method together with the principle of parsi However, not only do cladists not use Popper's methodology, which is inconsistent with parsimony, but their use of parsimony is invalid as a test of phylo The only accepted extrinsic test of a classification is that enunciated by John Stuart Mill. It has been claimed that cladistic classifications yield the best results when judged by Mill's criteria, but this is only possibly the case with analytic classifications produced by numerical techniques. No satisfactory test exists in normal (synthetic) cladism for distinguishing synapomorphy from homoplasy. The effects of this are particularly dire in cladograms and classifications involving fossils in which a Stufenreihe arrangement is adopted.     

A cladistic analysis of chloroplast DNA restriction site variation and morphology for the genera of the Juglandaceae

The phylogenetic relationships of the genera of the Juglandaceae are examined with cladistic analyses of chloroplast DNA (cpDNA) restriction site variation and morphology. Rates of evolution of the chloroplast genome are slower than in many other groups of plants, enabling the entire genome to be utilized at the intergeneric level. The trees resulting from the two independent analyses were completely congruent. The combined analysis of the two data sets produced a tree completely congruent with the cladogram from the two data sets analyzed independently. The cladogram is compared with previous classifications, cladistic analyses, and fossil history for the family. Although the topology resulting from the cladistic analyses of this study was strongly congruent with previous estimates of relationships within the family, the fossil record indicates that the basal-most lineages in the cladistic trees arose later than the more terminal lineages. This reversed order of origin indicates that perhaps the rooting of the trees is erroneous.     

Comparative biology and the importance of cladistic classification: a case study from the sensory biology of squamate reptiles

Evolutionary taxonomy has all but succumbed to cladistic methodology, but it continues to exert considerable influence in the realm of higher classification. Some systematists accept cladistic methods in phylogeny inference, but allow paraphyly in formal classifications. Most important, however, many traditional classifications based on paraphyletic groups (e.g. 'Reptilia') remain in force, deeply entrenched in the literature. Cladists have argued that such paraphyletic classifications can mislead comparative biologists into false evolutionary generalizations, but this assertion has rarely, if ever, been supported by example. This paper provides a case study, illustrating in detail the influence of a traditional paraphyletic classification of squamate reptiles on the historical development of ideas regarding the evolution of sensory modes (chemoreception vs. vision) in the group. The paraphyletic classification is shown to have led to false generalizations and incorrect conclusions stemming directly from the fact that the classification did not reflect accurately the phylogeny of Squamata, particularly the cladistic relationships of Gekkota. This study provides direct evidence that evolutionary generalization must be rooted in the branching pattern of phylogeny and not the potentially arbitrary categorical ranks of traditional taxonomies. It further supports recent calls for a truly phylogenctic taxonomy that has as its philosophical core the concept of descent.     

Cycles

Intended to support three-taxon analysis (3ta), the proposal that all character states be regarded as terminal would instead undercut that method. The same is true of the idea that cladistic methods should not account for plesiomorphies. Parsimony does not correspond to interpretation 1 for incompletely resolved cladograms. The main argument common to Nelson's (1996) and Nelson and Platnick's (1991) advocacy of three-taxon analysis rests on presupposing its conclusion. While suggesting that parsimony rests on an inferior evolutionary model, Nelson (1996) neither offered nor provided evidence for any alternative. 3ta sometimes favors reversal over parallelism, but in other cases may disregard reversed characters, so that the method seems to lack any coherent theoretical basis.     

Taxic Revisions

Parsimony analysis provides a straightforward way of assessing homology on a tree: a state shared by two terminals comprises homologous similarity if optimization attributes that state to all the stem species lying between those terminals. Three-taxon statements (3ts), although seemingly "exact" in that each either fits a tree or does not, do not provide a satisfactory assessment of homology, because that assessment can be internally contradictory and because 3ts systematically exclude homologous resemblance in reversed states. Modified 3ts analysis (m3ta), a method in which both plesiomorphic and apomorphic states of "paired homologue" (PH) characters (those other than presence/absence data) are regarded as "informative" (able to distinguish groups), can (obviously) group by symplesiomorphy and so form paraphyletic groups unless data are clocklike enough. Patterson's pattern analysis (ppa) has the same shortcoming, to which it adds the drawback that only characters fitting the tree perfectly are used, a restriction that can easily lead to discarding most of the structure in the data. Revised m3ta (rm3ta), a method in which plesiomorphic states are not taken as informative, can also form paraphyletic groups, because it cannot apply reversals as apomorphies. The idea that knowledge of phylogeny has been derived from classifications does not imply that nonevolutionary methods should be employed for classification, but instead means that systematic methods must be logically capable of phylogenetic interpretation. Neither m3ta nor rm3ta satisfies that requirement because of their contradictory assessments of homology.     

A Review of Current Theories and Methods in Cladistics and a Cladistic Study of Twelve Lindera Species in Eastern China

Cladistics has become a widely used method for phylogenetic reconstruction．Because of rapid improvement Of cladistic theories and methodologies,and application of new data,especially,molecular data,it is becoming realistic to reconstruct phylogenies of organisms,and to establish natural classifications based on these phylogenies．This paper reviews some current cladistic theories and methods in a practical way,such as choosing characters,defining character states,polarizing characters,analyzing data matrices, calculating consensus cladograms,choosing among multiple equally most parsimonious cladograms,estimating reliability of cladograms,and applying cladograms to classification, character evolution,and biogeography． Based on 36 morphological characters．a parsimony analysis of 12 species representing six sections in subgenus Lindera and an outgroup species from subgenus lteodaphne of the genus Lindera(Lauraceae)was conducted．The results suggest a close relationship between section Lindera and section Sphaerocarpae,which is different from the previous phylogenetic hypothesis within the genus．In the strict consensus cladogram,two species,L．megaphylla and L.chienii,from section Cupuliformes are in the most primitive and the most advanced clades respectively,indicating that the section is polyphyletic．The cladogram also suggests that section Lindera be a polyphyletic group．     

What do we know about chrysidoid (Hymenoptera) relationships?

The phylogeny of the superfamily Chrysidoidea is reviewed. Relationships among the families proposed by Carpenter (1986) were confirmed by Brothers & Carpenter (1993) . The status of knowledge of phylogenetic relationships within families is assessed. Cladistic analyses have been undertaken only within Plumariidae (by Roig-Alsina 1994 ; a manual analysis of genera), Chrysididae (by Kimsey & Bohart 1991 ; a manual analysis of subfamilies and tribes, and genera within subfamilies) and Bethylidae (by Sorg 1988 ; a manual analysis of subfamilies, and genus groups within three of these; and by Polaszek & Krombein 1994 ; a quantitative cladistic analysis of the genera of Bethylinae). These analyeses are critically evaluated, and the current classifications within all the families examined cladistically. Generic relationships are investigated within Scolebythidae and Embolemidae; subfamily relationships are investigated within Sclerogibbidae and Dryinidae.     

Phylogenetic analysis of higher taxa of Brachiopoda

Inferred phylogenetic relationships within the Brachiopoda have long been accepted as demonstrating repeated transitions from a phosphatic shell chemistry to a calcareous composition. This interpretation is reflected in the major subdivision of the phylum into the classes Inarticulata and Articulata. Cladistic analysis suggests, however, that the phosphatic-shelled and the calcareous-shelled Brachiopoda are sister groups that have had consistently separated shell chemistries from early in phylogenetic history. This separation is recognized in the class-rank divisions Lingulata and Calciata, the former of which includes the new Subclass Lingulatea, whilst the latter includes the new Subclass Craniformea together with the 'articulates' of previous classifications. □Brachiopoda, cladistic analysis, Lingulata, Lingulatea, Calciata, Craniformea.     

Methods of classifying nemerteans: an assessment

Phenetic, cladistic and phyletic methods of classifying animals are discussed with particular reference to nemerteans. It is concluded that phenetic (numerical) taxonomy is particularly inapplicable to any group of invertebrates for which well defined character differences are relatively few, whilst both the phenetic and cladistic methods fail through their fundamental assumption that convergent evolution is a rare occurrence. Terrestrial and freshwater nemerteans especially demonstrate convergent evolution in many ways; cladistic classifications proposed for these animals are therefore untenable. Convergence is shown to be a common occurrence in other nemerteans also. It is concluded that because the traditional phyletic approach does not implicitly assume that resemblances between organisms are more likely to be due to common ancestry than to convergence, it is far more likely to reveal true evolutionary relationships between taxa.     

Insights into the phylogenetic relationships within Cixiidae (Hemiptera: Fulgoromorpha): cladistic analysis of a morphological dataset

Abstract.  According to the most recent classifications proposed, the planthopper family Cixiidae comprises three subfamilies, namely Borystheninae, Bothriocerinae and Cixiinae, the latter with 16 tribes. Here we examine morphological characters to present the first phylogenetic reconstructions within Cixiidae derived from a cladistic analysis. We scored 85 characters of the head, thorax, and male and female genitalia for 50 taxa representative of all cixiid subfamilies and tribes and for six outgroup taxa. Analyses were based on maximum parsimony – using both equally weighted and successive weighting procedures – and Bayesian inferences. The monophyly of most currently accepted tribes and subfamilies was investigated through Templeton statistical tests of alternative phylogenetic hypotheses. The cladistic analyses recover the monophyly of Cixiidae, the subfamily Bothriocerinae, and the tribes Pentastirini, Mnemosynini, and Eucarpiini. Successive weighting and Bayesian inference recover the monophyly of the tribe Gelastocephalini, but only Bayesian inference supports the monophyly of Semoniini. The relationships recovered support the groups [Stenophlepsini (Borystheninae + Bothriocerinae)] arising from the tribe Oecleini, and [Andini + Brixiidini + Brixiini (polyphyletic) + Bennini]. Templeton tests reject the alternative hypothesis of a monophyletic condition for the tribe Pintaliini as presently defined.     

Information obtained in cladistic analysis.

The application of elementary equations from information theory to the elements involved in cladistic analysis is formalized mathematically. An equation is derived that quantifies the amount of information obtained by constructing a cladogram from a cladistic data matrix. Given particular conditions, the amount of information obtained increases monotonically with increases of the number of taxa involved and, so, may be used directly as a comparative measure of species richness for sister groups; in general, however, the amount of information obtained is related to the distribution of character states on the cladogram(s) deduced. An example is presented in which clades representing 11 phyla in the animal kingdom are compared in terms of information yielded. The amount of information obtained is consistent for different numbers of taxa and characters used in classifications. Speculative evolutionary explanations are presented for differences of information yielded among the phyla analyzed.     

Taxic and Transformational Homology: Different Ways of Seeing

Hypotheses of taxic homology are hypotheses of taxa (groups). Hypotheses of transformational homology are hypotheses of transformations between character states within the context of an explicit model of character evolution. Taxic and transformational homology are discussed with respect to secondary loss and reversal in the context of three-taxon statement analysis and standard cladistic analysis. We argue that it is important to distinguish complement relation homologies from those that we term paired homologues. This distinction means that the implementation of three-taxon statement analysis needs modification if all data are to be considered potentially informative. Modified three-taxon statement analysis and standard cladistic analysis yield different results for the example of character reversal provided by Kluge (1994) for both complement relation data and paired homologues. We argue that these different results reflect the different approaches of standard cladistic analysis and modified t.t.s. analysis. In the standard cladistic approach, absence, as secondary loss, can provide evidence for a group. This is because the standard cladistic approach implements a transformational view of homology. In the t.t.s approach discussed in this paper, absence can only be interpreted as secondary loss by congruence with other data; absence alone can never provide evidence for a group. In this respect, the modified t.t.s. approach is compatible with a taxic view of homology.     

Incorporating single-locus tests into haplotype cladistic analysis in case-control studies

In case-control studies, genetic associations for complex diseases may be probed either with single-locus tests or with haplotype-based tests. Although there are different views on the relative merits and preferences of the two test strategies, haplotype-based analyses are generally believed to be more powerful to detect genes with modest effects. However, a main drawback of haplotype-based association tests is the large number of distinct haplotypes, which increases the degrees of freedom for corresponding test statistics and thus reduces the statistical power. To decrease the degrees of freedom and enhance the efficiency and power of haplotype analysis, we propose an improved haplotype clustering method that is based on the haplotype cladistic analysis developed by Durrant et al. In our method, we attempt to combine the strengths of single-locus analysis and haplotype-based analysis into one single test framework. Novel in our method is that we develop a more informative haplotype similarity measurement by using p-values obtained from single-locus association tests to construct a measure of weight, which to some extent incorporates the information of disease outcomes. The weights are then used in computation of similarity measures to construct distance metrics between haplotype pairs in haplotype cladistic analysis. To assess our proposed new method, we performed simulation analyses to compare the relative performances of (1) conventional haplotype-based analysis using original haplotype, (2) single-locus allele-based analysis, (3) original haplotype cladistic analysis (CLADHC) by Durrant et al., and (4) our weighted haplotype cladistic analysis method, under different scenarios. Our weighted cladistic analysis method shows an increased statistical power and robustness, compared with the methods of haplotype cladistic analysis, single-locus test, and the traditional haplotype-based analyses. The real data analyses also show that our proposed method has practical significance in the human genetics field.     

Rooting the Dodo Raphus cucullatus Linnaeus 1758 and the Solitaire Pezophaps solitaria Gmelin 1789 within the Ornithurae: a cladistic reappraisal

Janoo, A. 2000. Rooting the Dodo Raphus cucullatus Linnaeus 1758 and the Solitaire Pezophaps solitaria Gmelin 1789 within the Omithurae: a cladistic reappraisal. Ostrich 71 (1 & 2): 323–329.

The phylogenetic positions of the dodo and the solitaire are studied in a cladistic framework, taking into consideration the columbiform assemblage and using outgroup comparison taxa from Gruiformes, Charadriiformes, Ciconiiformes and the Ardeidae. This preliminary analysis is based upon osteological characters retrieved from Verheyen's study of the Columbiformes, and from a detailed study of dodo and solitaire skeletons. The dodo and the solitaire are monophyletic corroborating the status of Raphidae. The Pteroclididae come out as a basal group to the strict columbiforms. A hierarchical arrangement of the columbids is proposed, but complete resolution was not obtained, suggesting the need for more detailed character study of the columbiform clade.     

Nomenclature in the dock. Overclassification leads to instability: a case study in the horticulturally important genus Cyclamen (Myrsinaceae)

Nine different classifications have been produced in the last 70 years for the horticulturally valuable genus Cyclamen , a small genus with fewer than 30 species. These classifications, generated by intuitive methods and cladistic analyses, incorporated a total of four infrageneric ranks above that of species and were based on data from morphology, cytology and DNA sequencing. Our results, based on cladistic analyses of three independent data sources − nrDNA ITS, cpDNA trn L intron and morphological data − reveal good resolution only in nrDNA sequence data. However, when these three data sources are combined they provide stronger resolution and support for three major clades, only one of which, subgenus Psilanthum , has been consistently supported in previous classifications. The differing infrageneric classifications produced in Cyclamen result from varying taxon sampling, differing interpretation of morphological data, changes in the sources and analysis of data, and inconsistent application of names. Extensive subdivision of small genera in the absence of adequate data that could provide evidence for consistent patterns of relationship is premature and leads to a proliferation of names.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 146 , 339–349.     

木兰科的分支分析

主要以形态学、解剖学、细胞学为依据,以德坚木属为外类群,用分支分析的方法探讨了木兰科属间的系统发育关系。有２３个分支单位,选取３２个性状,根据外类群比较原则和化石地层学资料,确定了性状的祖征和衍征。对数据矩阵的分支分析使用ＰＡＵＰ３．１．１和Ｈｅｎｎｉｇ ８６ ｖ．１．５分别在Ｍａｃｉｎｔｏｓｈ和ＩＢＭ机上运行,前者以启发法,后者以ＢＢ命令运算,经严格一致化处理,得到一致化分支图。结果表明：１）木     

Towards an inclusive philosophy for phylogenetic inference

We defend and expand on our earlier proposal for an inclusive philosophical framework for phylogenetics, based on an interpretation of Popperian corroboration that is decoupled from the popular falsificationist interpretation of Popperian philosophy. Any phylogenetic inference method can provide Popperian "evidence" or "test statements" based on the method's goodness-of-fit values for different tree hypotheses. Corroboration, or the severity of that test, requires that the evidence is improbable without the hypothesis, given only background knowledge that includes elements of chance. This framework contrasts with attempted Popperian justifications for cladistic parsimony--in which evidence is the data, background knowledge is restricted to descent with modification, and "corroboration," as a by-product of nonfalsification, is to be measured by cladistic parsimony. Recognition that cladistic "corroboration" reflects only goodness-of-fit, not corroboration/severity, makes it clear that standard cladistic prohibitions, such as restrictions on the evolutionary models to be included in "background knowledge," have no philosophical status. The capacity to assess Popperian corroboration neither justifies nor excludes any phylogenetic method, but it does provide a framework in phylogenetics for learning from errors--cases where apparent good evidence is probable even without the hypothesis. We explore these issues in the context of corroboration assessments applied to likelihood methods and to a new form of parsimony. These different forms of evidence and corroboration assessment point also to a new way to combine evidence--not at the level of overall fit, but at the level of overall corroboration/severity. We conclude that progress in an inclusive phylogenetics will be well served by the rejection of cladistic philosophy.     

Phylogeny and jaw evolution in Gnathostomulida, with a cladistic analysis of the genera

Sørensen, M. V. (2002). Phylogeny and jaw evolution in Gnathostomulida, with a cladistic analysis of the genera. — Zoologica Scripta, 31, 461–480.
The relationships between the genera in Gnathostomulida were investigated in a computerized cladistic analysis. The data matrix comprised 55 morphological characters of sensory structures, the reproductive systems, and the hard mouthparts. The cladistic analysis produced four almost identical most parsimonious trees. The four trees differed by having different topologies within the family Gnathostomulidae. Based on the obtained trees, the following was concluded: (1) Filospermoidea and Bursovaginoidea are both monophyletic; (2) Scleroperalia is paraphyletic; (3) all known families except Onychognathiidae (Sterrer 1972) are monophyletic; (4) Onychognathiidae emend. comprises the genera Nanognathia, Onychognathia, Rastrognathia, Valvognathia and Vampyrognathia ; (5) Paucidentulidae and Onychognathiidae emend. branch off in the lower part of Bursovaginoidea; (6) the following two clades are monophyletic and appear as sister groups: Problognathiidae−Gnathostomulidae−Austrognathiidae and Gnathostomariidae− Goannagnathia −Mesognathariidae−Clausognathiidae−Agnathiellidae. Based on the character optimization it was suggested that the gnathostomulid jaw evolved from a relatively simple ancestral jaw belonging to the compact type or the open lamellar type. The fused lamellar type evolved from the open lamellar type. The ancestral dentarium resembled the arc type and evolved along two different evolutionary paths into the basket type and the row type.     

Preliminary cladistic analysis of genera of the cestode order Trypanorhyncha Diesing, 1863

A preliminary cladistic analysis was carried out on the 49 currently recognised genera of the order Trypanorhyncha. Forty-four characters were analysed; a functional outgroup was used for scolex and strobilar characters, while Nybelinia was utilised to polarise characters related to the rhyncheal system. Eight well-resolved clades were evident in the resultant cladogram, which is compared with existing phenetic classifications. An analysis of families resulted in a similar clustering of taxa to that observed in the case of the genera. The results suggest that two key characters used in existing classifications, namely the presence of sensory fossettes on the bothridia and the development of atypical heteroacanth and poeciloacanth armatures from typical heteroacanth armatures, have occurred on several occasions. Some clades provide support for the arrangements used in current classifications. Suggestions are made for future avenues of research which might provide more robust phylogenetic data for the Trypanorhyncha.