Morphometrics and character state recognition for cladistic analyses in theBletia reflexa complex (Orchidaceae)

Different criteria have been suggested for decisions on character state recognition for morphological characters showing continuous variation from taxon to taxon. A method proposed byMishler andDe Luna seeks to recognize as many character states as the groups of taxon means that are revealed by an analysis of variance (ANOVA) followed by multiple range tests. We apply this method as a guide in decisions of selecting taxonomic characters in species of theBletia reflexa complex. Seven species of the complex, represented by 156 individuals belonging to 54 populations, were the terminal taxa of the study. Character state codes were assigned to 20 characters. These characters together with 12 non-quantitative characters were incorporated into cladistic analyses. Results indicate that the complex is monophyletic only under one outgroup combination.     

A cladistic study of Arillastrum, Angophora and Eucalyptus (Myrtaceae)

A cladistic study of Anllastrum, Angophora and Eucalyptus (Myrtaceae). Transformed cladistic; character compatibility; branch and bound, and Farris-Wagner methods gave similar solutions in a cladistic study of Arillastrum, Angophora and Eucalyptus. These analyses, based on morphological characters, indicate that Eucalyptus is a monophyletic group and that its sister taxon is Angophora.
Within Eucalyptus , subgenera Blakella and Corymbia are sister taxa to all other groups; subgenera Monocalyptus, Idiogenes and Gaubaea form a monophyletic group with subgenus Monocalyptus sister to subgenera Idiogenes and Gaubaea ; subgenera Symphyomyrtus and Telocalyptus together also form a monophyletic group and, with Eucalyptus similis (subgenus Eudesmia group 4), are sister to the Monocalyptus group. Eucalyptus subgenus Telocalyptus (4 species), Eucalyptus subgenus Idiogenes (1 species) and Eucalyptus subgenus Gaubaea (2 species) should not be recognized as subgenera and some individual species need further examination. Eucalyptus subgenus Eudesmia is a paraphyletic group.
Some characters are identified as parallelisms, e.g. axillary inflorescences, sepaline operculum, bristle glands, and clustered anthers. A more congruent interpretation of the single operculum of Eucalyptus subgenus Monocalyptus as at least partly petaline rather than solely sepaline in origin is suggested.
The area relationships for the taxa are concordant with those derived from geological and climatological information. New Caledonia is sister area to Australia, and within Australia southwestern Australia is sister area to south-eastern and north-eastern Australia.     

THE NATURE OF CLADISTIC DATA

Abstract— Cladistic data are the characters of organisms. Character is defined as a feature that can be evaluated as a variable with two or more mutually exclusive and ordered states. Cladistic characters must be treated as multistate variables, and coded as sequential numbers or in additive binary fashion. Any other interpretation and handling of cladistic data will introduce error into analysis. Character states cannot be treated independently as present or absent, i.e., as nominal variables, because redundancy is introduced into the data and information content is sacrificed. Non-additive binary coding demonstrates that treating cladistic variables as nominal data will lead to multiple, equally parsimonious solutions. Defining characters found universally in a group of organisms, but unknown outside those organisms have no alternative state that can be designated as absent. Absence, however, is valid as a character state if it can be shown to be apomorphic. When two or more character states occur within a taxon, that taxon must be coded as having an unknown state for that character, or the taxon must be split in two or more taxa. Continuously varying quantitative data are not suitable for cladistic analysis because there is no justifiable basis for recognizing discrete states among them. Quantitative data are questionable even when they exhibit mutually exclusive states because the states can be interpreted only in reference to an archetype, i.e., as implied homologies not subject to test.     

POLYMORPHIC TAXA, MISSING VALUES AND CLADISTIC ANALYSIS

Abstract Missing values have been used in cladistic analyses when data are unavailable, inapplicable or sometimes when character states are variable within terminal taxa. The practice of scoring taxa as having "missing values" for polymorphic characters introduces errors into the calculation of cladogram lengths and consistency indices because some character change is hidden within terminals. Because these hidden character steps are not counted, the set of most parsimonious cladograms may differ from those that would be found if polymorphic taxa had been broken into monomorphic subunits. In some cases, the trees found when polymorphisms are scored as missing values may not include any of the most parsimonious trees found when the data are scored properly. Additionally, in some cases, polymorphic taxa may be found to be polyphyletic when broken into monomorphic subunits; this is undetected when polymorphisms are treated as missing. Because of these problems, terminal units in cladistic analysis should be based on unique, fixed combinations of characters. Polymorphic taxa should be subdivided into subunits that are monomorphic for each character used in the analysis. Disregarding errors in topology, the additional hidden steps in a cladogram in which polymorphisms are scored as missing can be calculated by a simple formula, based on the observation that if it is assumed that polymorphic terminals include all combinations of character states, 2 ^p − 1 additional steps are required for each taxon in which p polymorphic binary characters are scored as missing values. Thus, when several polymorphisms are scored as missing in the same taxon, very large errors can be introduced into the calculation of tree length.     

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。     

Cladistic Analysis of Human Evolution: Some Points on Character Selection

Cladistic analysis strongly depends on accurate character choice. Usually, characters include morphology or molecules, but other sources of evidence are also employed. These include stratigraphic ages of taxa and behavioural data. The inclusion of time is a controversial issue, which has no Darwinian basis. However, the cladistic treatment of stratigraphic age has the potential to resolve problematic phylogenies. Here, it is proposed that the use of stratigraphic data in phylogenetic inference should be seen as a temporary shortcut, to resolve complex phylogenies in the wait for new character and taxonomic samplings, because phylogenetic hypotheses should be based on biological evidence only. Archaeologists working on toolmaking can provide behavioural data in human prehistory. In fact, while a tool itself is not biological evidence, the movements of hands and arms needed to prepare it are biological evidence and can be compared and scored for cladistic analysis. Such an approach has been formalized in studies on functional morphology of some vertebrates. The taxonomic data set to be used in cladistic analysis should include as many taxa as possible, and also very incomplete specimens should be used. In many cases, incomplete specimens had the potential to resolve complex phylogenies by adding new character combinations that cannot be scored in molecule-based phylogenetic studies.     

Phylogeny of the Cardiidae (Mollusca, Bivalvia): Protocardiinae, Laevicardiinae, Lahilliinae, Tulongocardiinae subfam. n. and Pleuriocardiinae subfam. n.

In a preliminary cladistic analysis of the bivalve family Cardiidae (Schneider 1992), members of the subfamilies Protocardiinae, Lahilliinae, and Laevicardiinae, plus the genus Nemocardium , were found to be the least derived taxa of cardiids. A cladistic analysis is undertaken of the genera and subgenera of these cardiid taxa, plus several Mesozoic taxa which have never been assigned to any subfamily. The Late Triassic Tulongocardium , which is placed in Tulongocardiinae subfam. n., is the sister taxon to all other cardiids. Protocardiinae is restricted to the genus Protocardia. Most other Mesozoic taxa which have been placed in the Protocardiinae are found to be members of the Lahilliinae. Nemocardium is placed in the Laevicardiinae. Incacardium, Pleuriocardia , and Dochmocardia form a monophyletic group, Pleuriocardiinae subfam. n. Pleuriocardiinae, Laevicardiinae, and the remaining members of the Cardiidae (herein informally termed "cucardiids") form a monophyletic group.     

康蚖群的系统发生和生物地理学的研究(原尾目:始蚖科)(英文)

应用HENNIG86系统发生分析程序,选择出成虫的有代表性的16个共同衍征,分析了与康蚖属相关各属的各个种类,得出了该类群的相关系统树。同时对特征的演化以及其扩散途径等也进行了讨论。文中还应用Page 1993的COMPONENT程序进行了生物地理学的分析;得到种类—地区支序图。其中康蚖属表现为典型的印度—太平洋分布型,而其姐妹群新康蚖属则兼有东洋区和全北区的分布型。至于分布地区的相互关系和在这些地区的分衍替代事件的发生等问题也作了初步的假想。     

PHYLOGENY AND BIOGEOGRAPHY OF CONDEEUM GROUP (PROTURA: PROTENTOMIDAE)

Abstract  Using the Hennig 86 phylogenetic analysis program to analyse the taxa in genera related to Condeellum , the phylogenetic relationships among the species are schemed on the basis of potential synapomorphies of the adults, represented by 16 characters. The character evolution and the route of dispersal are also discussed. The cladistic biogeographic analysis is performed. The basal taxon Condeellum exhibits an Indo-Pacific distribution and the sister group Neocondeellum species exhibit a collective Oriental and Holarctic distribution. The distribution patterns and the vicariance events occurred in those areas are hypothesized.     

Ceci n'est pas une pipe: names, clades and phylogenetic nomenclature

An introduction is provided to the literature and to issues relating to phylogenetic nomenclature and the PhyloCode, together with a critique of the current Linnaean system of nomenclature. The Linnaean nomenclature fixes taxon names with types, and associates the names with ranks (genus, family, etc.). In phylogenetic nomenclature, names are instead defined with reference to cladistic relationships, and the names are not associated with ranks. We argue that taxon names under the Linnaean system are unclear in meaning and provide unstable group–name associations, notwithstanding whether or not there are agreements on relationships. Furthermore, the Linnaean rank assignments lack justification and invite unwarranted comparisons across taxa. On the contrary, the intention of taxon names in phylogenetic nomenclature is clear and stable, and the application of the names will be unambiguous under any given cladistic hypothesis. The extension of the names reflects current knowledge of relationships, and will shift as new hypotheses are forwarded. The extension of phylogenetic names is, therefore, clear but is associated to (and thus dependent upon) cladistic hypotheses. Stability in content can be maximized with carefully formulated name definitions. A phylogenetic nomenclature will shift the focus from discussions of taxon names towards the understanding of relationships. Also, we contend that species should not be recognized as taxonomic units. The term ‘species’ is ambiguous, it mixes several distinct classes of entities, and there is a large gap between most of the actual concepts and the evidence available to identify the entities. Instead, we argue that only clades should be recognized. Among these, it is useful to tag the smallest named clades, which all represent non-overlapping groups. Such taxa  – LITUs (Least Inclusive Taxonomic Units) – are distinguished from more inclusive clades by being spelled with lower-case initial letter. In contrast to species, LITUs are conceptually straightforward and are, like other clades, identified by apomorphies.     

Anatomy of a cladistic analysis

The sequential stages culminating in the publication of a morphological cladistic analysis of weevils in the Exophthalmus genus complex (Coleoptera: Curculionidae: Entiminae) are reviewed, with an emphasis on how early‐stage homology assessments were gradually evaluated and refined in light of intermittent phylogenetic insights. In all, 60 incremental versions of the evolving character matrix were congealed and analysed, starting with an assembly of 52 taxa and ten traditionally deployed diagnostic characters, and ending with 90 taxa and 143 characters that reflect significantly more narrow assessments of phylogenetic similarity and scope. Standard matrix properties and analytical tree statistics were traced throughout the analytical process, and series of incongruence length indifference tests were used to identify critical points of topology change among succeeding matrix versions. This kind of parsimony‐contingent rescoping is generally representative of the inferential process of character individuation within individual and across multiple cladistic analyses. The expected long‐term outcome is a maturing observational terminology in which precise inferences of homology are parsimony‐contingent, and the notions of homology and parsimony are inextricably linked. This contingent view of cladistic character individuation is contrasted with current approaches to developing phenotype ontologies based on homology‐neutral structural equivalence expressions. Recommendations are made to transparently embrace the parsimony‐contingent nature of cladistic homology.     

THE HOLY GRAIL OF THE PERFECT CHARACTER: THE CLADISTIC TREATMENT OF MORPHOMETRIC DATA

Abstract— Data scored for cladistic analyses may be quantitative or qualitative, continuous or discrete, and show overlapping or non-overlapping values between taxa. Quantitative and qualitative are modes of expression of data, while continuous or discrete refer to properties of the set of numbers that express the data; both these pairs of terms have been confused with overlapping and non-overlapping. The degree of overlap of values between taxa is often used to filter characters in cladistic analyses: if a minimum amount of overlap is exceeded, or a minimum amount of disjunction not reached, characters are rejected as "not cladistic". However, this rests on a confusion between features of taxa and features of individual organisms (attributes). Cladistic characters are features of taxa, and comprise frequency distributions of attribute values over individuals of a taxon. Cladistic characters logically cannot overlap, although taxa may have overlapping attribute values. Thus, a priori rejection of characters that have overlapping attribute values is non-sensical. Such data may still be rejected from consideration for cladistic analysis if it could be demonstrated that they contain little recoverable phylogenetic signal. Few published analyses have empirically tested this. An analysis of overlapping morphometric data from three series of Banksia suggests that, at least in these cases, they map phylogeny almost as accurately as more conventional, qualitative morphological data. While more such tests are required, morphometric data should not be rejected a priori from cladistic analyses.     

The Phylogenetic Relationships of Eucynodontia (Amniota: Synapsida)

The phylogeny of Eucynodontia is an important topic in vertebrate paleontology and is the foundation for understanding the origin of mammals. However, consensus on the phylogeny of Eucynodontia remains elusive. To clarify their interrelationships, a cladistic analysis, based on 145 characters and 31 species, and intergrating most prior works, was performed. The monophyly of Eucynodontia is confirmed, although the results slightly differ from those of previous analyses with respect to the composition of both Cynognathia and Probainognathia. This is also the first numerical cladistic analysis to recover a monophyletic Traversodontidae. Brasilodon is the plesiomorphic sister taxon of Mammalia, although it is younger than the oldest mammals and is specialized in some characters. A monophyletic Prozostrodontia, including tritheledontids, tritylodontids, and mammals, is well supported by many characters. Pruning highly incomplete taxa generally has little effect on the inferred pattern of relationships among the more complete taxa, although exceptions sometimes occur when basal fragmentary taxa are removed. Taxon sampling of the current data matrix shows that taxon sampling was poor in some previous studies, implying that their results are not reliable. Two major unresolved questions in cynodont phylogenetics are whether tritylodontids are more closely related to mammals or to traversodontids, and whether tritylodontids or tritheledontids are closer to mammals. Analyses of possible synapomorphies support a relatively close relationship between mammals and tritylodontids, to the exclusion of traversodontids, but do not clearly indicate whether or not tritheledontids are closer to mammals than are tritylodontids.     

A CLADISTIC TEST OF THE TAXON CYCLE AND TAXON PULSE HYPOTHESES

Abstract— A species' habitat preference is intcrpretablc both as a response to present-day conditions and as a result of evolutionary response to historical conditions. The taxon cycle and taxon pulse have been proposed as hypotheses that allow prediction of patterns of habitat specialization within a lineage. Both are based on common assumptions: (1) habitat specialization is largely irreversible in a lineage, (2) ecological specializations arise in a center of origin, and (3) dispersal events leading to current distributions can be ascertained. Eight taxa of Antillean, Mexican, and Central American Carabidae, for which cladistic hypotheses of relationship have been proposed, are used to test the generality of the taxon cycle and pulse. The patterns of habitat utilization predicted by the taxon cycle and taxon pulse hypotheses are tested by comparing cladistic transformations of habitat preference to randomly generated patterns of data generated under a null hypothesis. Evolutionary changes in habitat are interpreted using Camin-Sokal coding, which assumes irreversible habitat shifts and a predetermined ecological ground state (assumptions of the taxon cycle and taxon pulse). An observed pattern is considered to demonstrate the taxon cycle or pulse when it results in an explanation of the habitat shifts that is more parsimonious than 95 % of the randomly generated patterns. Of the eight carabid groups, only one exhibits a statistically significant pattern supporting the taxon cycle and pulse. The failure of the taxon cycle and pulse as generally predictive hypotheses may be due to historical changes in climate that permit episodes of range expansion for species previously restricted to small ranges, and habitat shifts and specialization that do not progress in a linear transformation series. Habitat shifts are also analyzed using Farris optimization, resulting in the most parsimonious transformation series of habitats, subject to a predefined ordering of habitats, while allowing reversals. Significance of an observed pattern of habitat shifts under Farris optimization implies habitat constancy relative to cladogenesis, and step-wise changes in habitat preference. Two of the eight groups exhibit significant patterns of habitat utilization under Farris optimization, indicating that vicariance of areas of like habitat has been the predominant factor generating species diversity in these groups. The other groups do not exhibit habitat constancy, suggesting rapid changes in habitat preference relative to speciation.     

Forum – Taxonomic Stability is Ignorance

Absolute nomenclatural stability is undesirable in phylogenetic classifications because they reflect changing hypotheses of cladistic relationships. De Queiroz and Gauthier's (1990: Syst. Zool. 39, 307–322; 1992: A. Rev. Ecol. Syst. 23, 449–480; 1994: Trends Ecol. Evol. 9, 27–31) alternative to Linnaean nomenclature is concluded to provide stable names for unstable concepts. In terms of communicating either characters shared by species of a named taxon or elements (species) included in a taxon, de Queiroz and Gauthier's system is less stable than the Linnaean system. Linnaean ranks communicate limited information about inclusivity of taxa, but abandonment of ranks results in the loss of such information. As cladistic hypotheses advance, taxa named under de Queiroz and Gauthier's system can change their level of generality radically, from being part of a group to including it, without any indicative change in its spelling. The Linnaean system has been retained by taxonomists because its hierarchic ranks are logically compatible with nested sets of species, monophyletic groups, and characters. Other authors have offered conventions to increase the cladistic information content of Linnaean names or to replace them with names that convey cladistic knowledge in greater detail; de Queiroz and Gauthier sacrifice the meaning of taxon names and categorical ranks in favor of spelling stability.     

Cladistic analysis of Reduviidae (Heteroptera: Cimicomorpha) based on morphological characters

Abstract.  With more than 6600 species worldwide, Reduviidae (Insecta: Heteroptera), or assassin bugs, form the second largest and one of the most diverse groups of true bugs. The poor condition of the higher-level classification of Reduviidae is reflected by the facts that different authors recognize between 21 and 32 subfamily-level names and that Reduviidae were never subjected to a rigorous cladistic analysis using an exemplar approach. In the present study, a cladistic analysis of higher-level taxa of Reduviidae based on 162 morphological characters and 75 ingroup and outgroup species is presented. Twenty-one subfamily-level taxa of Reduviidae were examined, accounting for 28 tribes. In addition to characters previously used for diagnosis in Reduviidae, information on recently published character complexes is used in the present analysis, supplemented with new character information gathered specifically for this project. Reduviidae are supported as a monophyletic group with Pachynomidae as their sister taxon. The major results of this study are the support of a sistergroup relationship of Hammacerinae with the remaining Reduviidae, the monophyly of the Phymatine Complex, the relatively basal position of Harpactorinae within Reduviidae as well as a novel hypothesis on the relationships within this group, and the sistergroup relationship of Ectrichodiinae + Tribelocephalinae and their placement in a clade that also contains Emesinae, Saicinae, and Visayanocorinae. The analysis further supports a clade formed by paraphyletic Salyavatinae + Sphaeridopinae, renders Vesciinae non-monophyletic, and demonstrates the polyphyly of Reduviinae. Pseudocetherinae are shown to group with some Reduviinae. Triatominae are supported as a monophyletic group and are nested among additional Reduviinae and Stenopodainae.     

Macrodasyida (Gastrotricha): a cladistic analysis of morphology

Abstract. A cladistic analysis based on 33 morphological characters was performed for the 31 genera currently assigned to the order Macrodasyida (Gastrotricha). Outgroup analysis indicated that the order is monophyletic and that it is defined by the structure of the pharynx and the complex distribution of duo-gland adhesive organs. Of the 6 currently recognized families in Macrodasyida, our analysis confirmed that 4 families are monophyletic: Dactylopodolidae, Macrodasyidae, Thaumastodermatidae and Turbanellidae. Dactylopodolidae was further confirmed as the most basal family within the order based on the retention of several plesiomorphies. The other three families have well-defined autapomorphies but will require further investigation to increase inter- and intrafamilial phylogenetic resolution. Planodasyidae appeared to be a paraphyletic taxon with no obvious autapomorphies; genera clustered among members of a polyphyletic family, Lepidodasyidae. We recommend that future research on macrodasyidan phylogeny focus on issues of comparative morphology and ultrastructure in lesser-known taxa such as the Dactylopodolidae, and on the taxa Lepidodasyidae and Planodasyidae.