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．     

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。     

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     

A new species of Anisopappus (Asteraceae, Inuleae) and its phylogenetic relationships within the genus

A new species of the genus Anisopappus (Asteraceae, Inuleae) from Angola, A. fruticosus , is described. The principal differences with respect to A. chinensis are discussed, and phylogenetic relationships with the other species of the genus are investigated by means of a cladistic analysis using morphological characters.     

A cladistic analysis of the nomadine bees (Hymenoptera: Apoidea)

Abstract. This study compares the results of Rozen's cladistic analysis of the larvae of fifteen genera of cleptoparasitic bees in the subfamily Nomadinae with an independent data set of adult characters for the same genera. Adult characters exhibited considerably higher levels of homoplasy and poorer resolution of cladistic relationships, with multiple equally parsimonious cladograms. However, comparison of a Nelson consensus tree based on adult characters with the cladogram based on larval characters reveals three components consistently supported in both analyses (the tribes Epeolini and Ammobatini, and Neopasites + Neolarra) , one component supported only by adult characters (Isepeolus + Protepeolus) , and one terminal component supported only by larval characters (Nomada + Ammobatini), as well as several more inclusive groupings based on larval characters that are difficult to compare with the adult consensus tree because it shows so much less resolution. When adult and larval characters are combined in a single data matrix, the resulting cladogram closely resembles the cladogram based on larval characters alone, although levels of homoplasy are considerably higher than in the larval analysis.
A preliminary analysis of adult characters for thirty-four genera in the Nomadinae also exhibited high levels of homoplasy and very large numbers of equally parsimonious cladograms. Nevertheless, certain consistent monophyletic groupings, most notably the Epeolini and Ammobatini, were also supported in this analysis. The one currently recognized tribe whose monophyly has received no support from any analysis is the Nomadini.
The relevance of these phylogenetic hypotheses to our understanding of host associations and variable features of egg morphology and oviposition behaviour in nomadine bees is briefly discussed.     

Phylogenetic analysis of the genus <Emphasis Type="Italic">Argia</Emphasis> Rambur, 1842 (Odonata: Coenagrionidae), based on morphological characters of larvae and mitochondrial DNA sequences

The study of the evolutionary interrelationships among the species encompassed in the Neotropical genus Argia (Zygoptera: Coenagrionidae) has been neglected. The goal of this study is to infer the phylogenetic relationships among 36 species of Argia Rambur, 1842, using complementary data sets (i.e., larval morphology and mitochondrial DNA). The morphological data set comprises 76% of the larvae currently described for this genus and includes 97 morphological characters. From those, 47 characters have not been previously used in taxonomic studies involving dragonflies’ larvae. This is the first cladistic study based on larvae morphology for species within the suborder Zygoptera. Data partitions were analyzed individually, as well as total evidence, using parsimony and Bayesian inference as criteria for optimal-tree selection. The results support the monophyly of the North American species of Argia. This genus can be identified by the combination of eight synapomorphies, four of which are exclusively found in Argia. According to the optimal trees, the individual data sets (i.e., morphology and DNA sequences) have a high level of homoplasy, resulting in soft polytomies and low support for several nodes. The specific relationships of the terminal units differ between the phylogenies; nonetheless, there is historical congruence among them. Within Argia, five clades were consistently recovered. Most of those clades have been identified, at least in part, in previous phylogenetic and taxonomic studies. Indubitably, the morphological characters from larvae have historical signal useful for cladistic and taxonomic inference. Therefore, it should be a priority to pay more attention to this source of characters.     

Preliminary morphological analysis of relationships between the spider wasp subfamilies (Hymenoptera: Pompilidae): revisiting an old problem

No qualitative cladistic analysis has been performed previously for the subfamily classification of Pompilidae (Hymenoptera). In 1994 Shimizu proposed six subfamilies, but their validity and relationships remain inconclusive. The objective of this study was to perform a quantitative analysis of phylogenetic relationships of the Pompilidae, with emphasis on testing the validity of proposed subfamilies. Two cladistic analyses were performed based on morphological evidence. First, a maximum-parsimony analysis of Shimizu's original morphological data matrix (72 taxa by 54 characters) was conducted, with the data subjected to a heuristic search for the first time with phylogenetic software. The resulting strict-consensus cladogram yielded a monophyletic Ceropalinae that was sister group to a large polytomy containing members of the remaining five subfamilies. In a second analysis, several of Shimizu's characters were re-examined, and new characters and more taxa were added to the data set. Terminal taxa were coded as species rather than as generic abstractions, and 20 additional morphological characters were introduced. The analysis was based on 77 morphological characters derived from the adults of 84 taxa. This second analysis suggested that Notocyphinae sensu Shimizu (1994) was nested within Pompilinae and that Epipompilinae sensu Shimizu (1994) was nested within Ctenocerinae; neither should retain their status as a separate subfamily. Lastly, Chirodamus s .s., which historically has been a member of the Pepsinae, is placed within the Pompilinae with reservations rather than erecting a new subfamily. After these allowances were made, a strict consensus tree gave the following relationships: (Ceropalinae + (Pepsinae + (Ctenocerinae + Pompilinae))).     

A phylogenetic analysis of the genus Eunice (Eunicidae, polychaete, Annelida)

Species of Eunice are distributed worldwide, inhabiting soft and hard marine bottoms. Some of these species play significant roles in coral reef communities and others are commercially important. Eunice is the largest and most poorly defined genus in Eunicidae. It has traditionally been subdivided in taxonomically informal groups based on the colour and dentition of subacicular hooks, and branchial distribution. The monophyly of Eunice and of its informal subgroups is tested here using cladistic analyses of 24 ingroup species based on morphological data. In the phylogenetic hypothesis resulting from the present analyses Eunice and its subgroups are paraphyletic; the genus may be divided in at least two monophyletic groups, Eunice s.s. and Leodice , but several species do not fall inside these two groups. Most of the traditional characters used in the taxonomy of Eunice are homoplasies; however, characters used for the first time in this study, such as certain jaw characters and characters derived from a close examination of chaetal variation along the body, are promising sources of phylogenetic signal.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 413–434.     

Meta-analysis of character utility and phylogenetic information content in cladistic studies of ammonoids

While previous workers have argued persuasively that ammonoid workers should use cladistic approaches to reconstruct phylogeny, relatively few cladistic studies have been published to date. An essential yet challenging part of cladistic analysis is the selection of characters. Are certain types of characters more likely to show homoplasy? Are certain aspects of shell anatomy more likely to contain phylogenetically informative characters? Are datasets with more characters inherently better? To answer these questions, a meta-analysis of character data from published ammonoid phylogenies was performed. I compiled 14 datasets, published between 1989 and 2007, representing parsimony-based phylogenetic analyses of ammonoids. These studies defined a combined total of 323 characters, which were grouped into categories reflecting different aspects of anatomy: shell size and shape, ornament, suture, early ontogeny, body chamber and apertural modifications. Tree searches were re-run to determine overall tree statistics, parsimony permutation tail probability (PTP) tests were calculated to assess the phylogenetic information content of the matrices, and retention and rescaled consistency indices for each character were calculated. My analyses revealed that studies with higher character/taxon ratios did not necessarily produce trees with more information content and less homoplasy, as measured by retention or rescaled consistency indices, because additional characters were often parsimony-uninformative. Rather, studies with relatively few characters could produce high-quality trees if the characters were well-chosen and character states carefully defined. Characters related to the body chamber and adult aperture typically had retention indices of either 0 or 1, rarely in between, indicating that they either worked perfectly or not at all. Suture characters tended to have higher indices than shell shape or ornament characters, suggesting more phylogenetic information and less homoplasy in the suture line than in shell traits. These results should aid in the selection of characters for future cladistic studies of ammonoids.     

中国慈姑属系统发育的研究

本文研究了中国慈姑属植物间的系统发育关系。选取了12个与该属系统发育有较重要关系的特征,将8个已知分类群与外类群刺果泽泻属进行了比较。应用数量分支分析的Farris-Wagner方法,建立了中国慈姑属系统发育分支图。讨论了各分类群间的系统发育关系、该属起源和数量分支分析方法等问题。     

Lack of congruence between morphological and molecular data in reconstructing the phylogeny of the galagonidae.

Published cladistic reconstructions of galagonid phylogeny based on morphological, behavioral, and genetic data have had few elements in common. A recent molecular study indicated that 2 of the 3 generic groupings derived from morphological data were not consistent with tree topologies constructed from the analysis of mitochondrial DNA sequences. In this study, we compiled and analyzed a data set based on craniodental morphology in 13 galagonid and 8 outgroup taxa, comprising 3 dwarf-lemur and 5 loris species, and subjected it to cladistic analysis. Our aim was not only to generate a new phylogenetic hypothesis based on these data, but also to investigate the conditions under which congruence could be achieved between these results and those obtained previously. The data set was found to be highly sensitive to the choice of outgroup, with the lorises showing high interspecific variability in cranial structure. Congruence between the craniodental and molecular trees could be achieved only if Arctocebus was used as the outgroup and two characters were preferentially weighted. Further progress in the reconstruction of galagonid phylogeny will require seeking consensus in a variety of other data sets, including postcranial morphology, behavior, and additional gene sequences. The effect of different outgroups on molecular analysis needs attention.     

Phylogeny of the subfamily Chauliodinae (Megaloptera: Corydalidae), with description of a new genus from the Oriental Realm

Abstract.  A new Oriental fishfly genus, Sinochauliodes gen.n. , is described, including four species: S. fujianensis ( Yang & Yang, 1999 ) comb.n. , S. griseus ( Yang & Yang, 1999 ) comb.n. , S. maculosus sp.n. and S. squalidus sp.n. A cladistic analysis based on adult morphological characters clarified the phylogenetic status of the new genus and allowed the reconstruction of the intergeneric relationships of the subfamily Chauliodinae. Two main clades within Chauliodinae were recognized from the cladistic analysis. The Asian fishflies, together with the two Nearctic genera, Chauliodes and Nigronia , formed a monophyletic lineage, and the new genus was assigned as the sister group to the genus Parachauliodes . The biogeography of the Asian fishflies is discussed.     

Angiosperm wood evolution and the potential contribution of paleontological data

Wood anatomy is often viewed as a source of independent data that may be used to assess evolutionary relationships among angiosperms. Comparative anatomical studies document suites of correlated characters that have been interpreted as general evolutionary trends, of which several have been asserted to be irreversible. Paleobotanical data summarized by Wheeler and Baas provide broad chronological corroboration of some wood anatomical trends, such as evolution from scalariform to simple perforation plates and long to short vessel elements. However, the focus on general evolutionary trends rather than on analyzing character distribution patterns in a cladistic phylogenetic context obscures a more detailed understanding of the evolution of wood anatomical features. Patterns of character evolution, including the assertions of irreversibility, need to be tested through cladistic analyses. In this paper selected wood anatomical features from families of Magnoliidae and “lower” Hamamelididae are summarized and mapped onto previously published cladograms as a preliminary means of testing previous hypotheses of wood evolution. The results show that many of the characters are homoplasious and have evolved both in accord with, and counter to, the hypothesized general trends in different groups of flowering plants. In general, changes that confirm generalized trends are more common than changes that are counter to those trends. Future studies should combine wood anatomical characters with other features as part of a cladistic analysis. Fossil woods have not yet contributed significantly to phylogenetic studies, but in the very few cases where they have been linked to fossil reproductive structures, the woods have provided a better understanding of wood anatomy in early members of some families. Data from fossil wood expand the diversity of anatomical structure known in some angiosperm taxa and thus provide additional evidence that might be used in phylogenetic analyses. Fossil woods have the greatest potential to affect phylogenetic analyses where they can be linked to other fossil organs. The best chance for establishing such a linkage is through the study of fossil charcoalified woods that co-occur with other dispersed mesofossils.     

龙胆属的系统发育分析

本文运用支序分类的原理和方法,对龙胆科龙胆属的属下等级进行了重新归类和系统发育分析。龙胆属是一个单系群,以3项近裔共性为归类依据。性状分析作了性状同源性分析和性状极性分析。性状极化主要以外类群比较、性状相关性及染色体资料为依据,其它方法,如生物重演律原则、地理递进原则以及孢粉形态等也被结合使用。分析结果,双蝴蝶属和蔓龙胆属被选择为外类群,71个性状被选择作为建立数据矩阵的基本资料。使用PAUP程序对矩阵进行了运算,得到4个最简约的谱系分支图,它们均具一致性系数0.637,支序长度为160步,f-比值范围为0.179～0.189,其中具最低f-比值的图被选作为类群归类和讨论亲缘关系的基础。在支序图上龙胆属归为15个组;其中5个组又划分为系,共包括23个系,其余组为单型组,故共有33个属下类群。一个严格的一致性谱系分支图总结了所有的一致点,从而支持了支序分析的结果。     

Homoplasy and the early hominid masticatory system: inferences from analyses of extant hominoids and papionins

Early hominid masticatory characters are widely considered to be more prone to homoplasy than characters from other regions of the early hominid skull and therefore less reliable for phylogenetic reconstruction. This hypothesis has important implications for current reconstructions of early hominid phylogeny, but it has never been tested. In this paper we evaluate the likely veracity of the hypothesis using craniometric data from extant primate groups for which reliable consensus molecular phylogenies are available.Datasets representing the extant large-bodied hominoid genera and the extant papionin genera were compiled from standard measurements. The data were adjusted to minimise the confounding effects of body size, and then converted into discrete character states using divergence coding. Each dataset was divided into four regional character groups: (1) palate and upper dentition, (2) mandible and lower dentition, (3) face and (4) cranial vault and base. Thereafter, the regional character groups were analysed using cladistic methods and the resulting phylogenetic hypotheses judged against the consensus molecular phylogenies for the hominoids and papionins.The analyses indicated that the regions dominated by masticatory characters-the palate and upper dentition, and the mandible and lower dentition-are no less reliable for phylogenetic reconstruction than the other regions of the skull. The four regions were equally affected by homoplasy and were, therefore, equally unreliable for phylogenetic reconstruction. This finding challenges the recent suggestion that Paranthropus is polyphyletic, which is based on the assumption that masticatory characters are especially prone to homoplasy. Our finding also suggests that, contrary to current practice, there is no a priori reason to de-emphasise the phylogenetic significance of the masticatory similarities between Homo rudolfensis and the australopiths. The corollary of this is that H. rudolfensis is unlikely to be a member of the Homo clade and should therefore be allocated to another genus.     

Fossil flowers and fruits of the Actinidiaceae from the Campanian (Late Cretaceous) of Georgia

A new genus and species of Actinidiaceae (Parasaurauia allonensis gen. et sp. nov.) are established for fossil flowers and fruits from the early Campanian (Late Cretaceous) Buffalo Creek Member of the Gaillard Formation in central Georgia, USA. The fossil flowers, which are exquisitely preserved as charcoal, have five imbricate, quincuncially arranged sepals and petals. The androecium consists of ten stamens with anthers that are deeply sagittate proximally. The gynoecium is tricarpellate, syncarpous, and has three free styles that emerge from an apical depression in the ovary. The fruit is trilocular and contains numerous ovules on intruded axile placentae. The structure of mature fruits is unknown. Comparisons with extant taxa clearly demonstrate that the affinities of Parasaurauia allonensis are with the Ericales, and particularly with the Actinidiaceae, which have been placed among the Ericales in recent cladistic analyses. Because Parasaurauia allonensis is not identical to any one genus of Actinidiaceae, or other member of the Ericales, phylogenetic relationships of the fossil were evaluated through a cladistic analysis using morphological and anatomical characters. Results of this analysis place Parasaurauia allonensis within the Actinidiaceae as sister to the extant genera Saurauia and Actinidia. Parasaurauia allonensis differs from extant Saurauia only in having ten rather than numerous stamens.     

Cladistic analysis of the Neotropical butterfly genus Adelpha (Lepidoptera: Nymphalidae), with comments on the subtribal classification of Limenitidini

Abstract.  A two-stage cladistic analysis of 114 characters from adult and immature stage morphology provided phylogenetic hypotheses for the diverse Neotropical nymphalid butterfly genus Adelpha Hübner. Higher-level cladistic relationships were inferred for thirty Adelpha species and twenty other species of Limenitidini, confirming the monophyly of Adelpha as currently conceived and indicating several montane Asian species as potential sister taxa for the genus. Cladistic relationships between all eighty-five Adelpha species were then inferred using three outgroup combinations. Basal and terminal nodes were reasonably resolved and supported, but a low proportion of non-wing pattern characters resulted in weak resolution and support in the middle of the tree. The most basal members of Adelpha feed on the temperate or montane plant family Caprifoliaceae, suggesting that a switch from this family early in the evolutionary history was important in subsequent diversification into tropical lowland habitats. The cladograms confirm suspicions of earlier authors that dorsal mimetic wing patterns have convergently evolved a number of times in Adelpha . The subtribal classification of Limenitidini is discussed and both Lebadea (from Parthenina) and Neptina are transferred to Limenitidina, whereas Cymothoe , Bhagadatta and Pseudoneptis (all formerly Limenitidina) are regarded as incertae sedis .     

The Phylogeny of the Lophopidae and the Impact of Sexual Selection and Coevolutionary Sexual Conflict

A cladistic analysis of Lophopidae was performed, using 73 observed morphological characters and 41 taxa. This analysis involved 36 genera belonging to the Lophopidae family and 5 outgroups. For a better understanding of the selected characters some illustrations are provided. The most parsimonious cladograms obtained show that the Lophopidae cannot be considered as a monophyletic lineage unless two genera are withdrawn from this family: Hesticus Walker, 1862, and Silvanana Metcalf, 1947. The systematic position of these two genera remains uncertain. They cannot yet be included in another family of Fulgoromorpha. A cladistic analysis of each of the 19 remaining Fulgoromorphan families must be performed first. A new family could be created for these two genera, but not before we are sure that these two genera are in no way members of an existing family. The outgroup problem is discussed. The monophyletic lineage represented by the Lophopidae can be divided into four natural groups: Carriona⁺, Makota⁺, Sarebasa⁺, and Bisma⁺. When a cladistic analysis is completed using a data matrix without characters linked to females, the cladogram obtained presents a disrupted basal resolution. Female characters appear to bring a phylogenetic signal important basally in the evolution of the Lophopidae but also apically, directly between the relationships of some genera. A similar analysis, using a matrix without characters linked to males, provides a phylogeny disrupted between the groups that form the Lophopidae and in the basal resolution in these groups. The respective impacts of the genitalic characters are discussed in relation to sexual selection conflict.