Evolutionary relationships of euthyneuran gastropods (Mollusca): a cladistic re-evaluation of morphological characters

Morphological characters of the Euthyneura available from the literature were re-evaluated in terms of terminology and primary homology. A total of 77 characters and 75 taxa were retained in a data matrix. Several assumptions on character weights and types were tested. In the cladistic analyses, it appeared that the data matrix was highly homoplastic, and only robust nodes (those which were little modified by variations in weight and coding of characters) were retained in a concensus tree. The evolutionary histories of all characters and monophylies of higher euthyneuran taxa were discussed. The following interrelationships of the taxa were obtained in a consensus tree: the clade Heterobranchia includes paraphyletic allogastropod taxa which emerge basally, and the clade Euthyneura. The latter includes the clade Pulmonata and at least 10 opisthobranch clades of unresolved relationship (Thecosomata, Gymnosomata, Acochlidioidea, Pyramidelloidea, Runcinoidea, Cephalaspidea, Sacoglossa, Umbraculoidea, Pleurobranchoidea, Nudibranchia). The Pulmonata include basommatophoran paraphyletic taxa and the clade Geophila (Onchidiidae, Soleolifera, Stylommatophora). The position of the Sacoglossa and the monophyly of the Notaspidea are also discussed.  © 2002 The Linnean Society of London, Zoological Journal of the Linnean Society , 2002, 135 , 403–470.     

The interrelationships of the echinoderm classes: morphological and molecular evidence

The relationship between the five echinoderm classes has perplexed phylogeneticists for some time. Although each of the crinoids (C), asteroids (A), ophiuroids (O), echinoids (E) and holothuroids (H) are morphologically distinct, evidence from larval and adult morphology, molecular biology, and stratigraphy have failed to provide a single consensus solution. We have reviewed all available morphological and molecular data, added new data and reanalysed independent data sets individually and in combination, in order to resolve echinoderm class relationships. In total, we present 21 larval and 50 adult morphological characters, partial 28S-like large subunit rRNA gene data for 39 taxa and complete 18S-like small subunit rRNA gene data for 37 taxa. For a 5 taxon problem there are 105 possible rooted tree topologies, and yet we were consistently presented with three competing hypotheses when data sets were analysed both individually and in combination. The total evidence solution favoured (outgroup(C(A(O(E, H))))) although the alternative tree topology, (outgroup(C(O(A(E, H))))) was only one step longer and (outgroup(C((A, O),(E, H)))) was two steps longer. Only these three trees are serious contenders and the distribution of morphological characters suggests we should discount the solution placing ophiuroids as sister group to an asteroid+echinoid + holothurian clade. Thus we are left with (outgroup(C(A(O(E, H))))) and (outgroup(C((A, O),(E, H)))) as the two most plausible phylogenetic hypotheses. Our data showed high levels of phylogenetic signal and these trees best fit the available data.     

Systematic relationships of Nematomorpha based on molecular and morphological data

Abstract. We sequenced the 18S rRNA gene from 11 nematomorph species from 9 genera and derived hypotheses concerning the sister group of Nematomorpha and relationships within this taxon. The molecular and morphological data are consistent with the monophyly of Nematomorpha, a sister-group relationship between Nematomorpha and Nematoda, and a sister-group relationship between the marine genus Nectonema and all of the freshwater taxa, Gordiida. Hypotheses of relationships within Gordiida support the traditional taxa Gordiidae, Chordodidae, and Chordodinae but reject Parachordodinae and Spinochordodidae. The molecular results differ from those of previous morphological studies by suggesting a reduction of the two tail lobes at the posterior end of males in Chordodinae, monophyly of the genus Paragordionus , and paraphyly of the genus Chordodes .     

老鸦瓣属(百合科)的恢复: 以形态性状的分支分析为依据

老鸦瓣群(Amana群)是百合科中的一个东亚特有类群,仅分布在中国中东部、日本和朝鲜半岛。该类群在形态上与广义郁金香属Tulipa L.相似,但也具有与子房近等长的花柱以及2-3(-4)个苞片等与郁金香属不同的形态特征。有关该类群是否应置于郁金香属中或是否应独立为属的问题长期以来存在争议。为了澄清该问题,我们对产于中国的Amana群进行了广泛的标本室和野外形态观察,并采用分支系统学方法,对该类群3个种以及郁金香属的其他15种植物(包括土耳其的3个种)的28个形态性状数据进行了分支分析。结果表明广义郁金香属并非是一个单系类群。Amana群与广义郁金香属的其他4个组sect. Orithyia、sect. Eriostemones、sect. Leiostemones、sect. Tulipanum以及Lloydia属的两个种共同构成一个大支的3个分支。我们对广义郁金香属5个组共19种植物的ITS以及trnL-F分子序列综合分析的结果也表明：sect. Tulipanum、sect. Leiostemones、sect. Eriostemones和sect. Orithyia构成一大支,Amana群和猪牙花属的Erythronium sibiricum构成另一大支。因此,我们认为Amana群应从广义郁金香属中独立出来,恢复其老鸦瓣属Amana Honda作为属的分类地位。     

Phylogenetic relationships of basal hexapods among the mandibulate arthropods: a cladistic analysis based on comparative morphological characters

In this paper we propose a reappraisal of the relationships between the basal hexapod lineages (the former 'apterygote' insects) and the other major groups of mandibulate arthropods. It results from a cladistic analysis including 72 characters based on external morphology, internal anatomy and development. Detailed comments are provided on the various characters used and the scoring of their states. The 35 terminal taxa include 12 hexapods (9 of which are basal 'apterygote' representatives), 7 myriapods, 13 crustaceans, and 3 chelicerates taken as outgroups. The results of our analyses are discussed in detail for each of the taxonomic groupings, and compared with those recently obtained by other authors using different approaches based on morphological, palaeontological, developmental or molecular sequence data. Our results support the monophyly of the Mandibulata, Crustacea, Atelocerata (Tracheata) and Hexapoda, but the assemblage of Myriapoda appears poorly supported. A close relationship between Crustacea and Hexapoda, as hypothesized by several authors, is not found in any of our analyses. Within Hexapoda, the Protura and the Collembola appear as independent clades, whereas the two unresolved dipluran taxa are grouped with the monophyletic Ectognatha (Archaeognatha, Zygentoma and Pterygota).     

The evolution of Synchaetidae (Rotifera: Monogononta) with a focus on Synchaeta: An integrative approach combining molecular and morphological data

This study represents the first phylogenetic reconstruction of Synchaetidae (Rotifera, Monogononta) and combines one morphological and two molecular data sets to derive the most comprehensive database for this taxon to date. Overall, 19 species were examined both morphologically (light- and scanning electron microscopy of habitus and trophi) and genetically (COI and 18S rRNA genes), thereby delivering new morphological information as well as the first molecular data for several species. Our results strongly support the monophyly of each of the three genera within Synchaetidae, with Synchaeta being the sister taxon of Polyarthra and Ploesoma. Resolution within each genus, however, was more poorly supported, possibly because of high levels of missing data for the more poorly known species that were also not re-discovered and revised in the present study. Nevertheless, an evolutionary reconstruction based on the total evidence topology indicates that the common ancestor of Synchaetidae was a rotatorivorous and pelagic freshwater rotifer exhibiting slightly enlarged lamellar trophi that were adapted to an enhanced pumping function. These features together with several, additional key character transformations (e.g., hatching independently from benthic or periphytic habitats) probably account for the success of Synchaetidae in pelagic environments and their being one of the most widely distributed and abundant rotifer taxa.     

Evolution of metatherian and eutherian (mammalian) characters: a review based on cladistic methodology

Cladistic methodology is used to test the hypothesis that three major monophyletic groups exist among living mammals–the oviparous monotremes (Prototheria), and the viviparous marsupials (Metatheria) and placentals (Eutheria). Evaluation is made of the polarity (i.e. the direction of change in a primitive-to-derived sequence) of numerous characters which distinguish some or all of these groups, and of the usefulness of these characters in phylogenetic inference. An attempt is made to establish the state of these characters in the common Late Jurassic-Early Cretaceous therian ancestor of marsupials and placentals.
It is concluded that the most basic division of the Mammalia is the dichotomy into the subclasses Prototheria (including Monotremata, Multituberculata, Triconodonta, Docodonta) and Theria (including Metatheria, Eutheria, Pantotheria and Symmetrodonta). Two major groups exist among living viviparous mammals, the Metatheria and Eutheria; in a cladistic framework these are sister-groups. It is demonstrated that there is no special (sister-group) relationship between monotremes and marsupials, and there is no justification for placing them in a group Marsupionta.     

The phylogeny of land plants: A cladistic analysis based on male gametogenesis

A cladistic analysis was carried out to resolve phylogenetic pattern among bryophytes and other land plants. The analysis used 22 taxa of land plants and 90 characters relating to male gametogenesis.Coleochaete orChara/Nitella were the outgroups in various analyses using HENNIG86, PAUP, and MacClade, and the land plant phylogeny was unchanged regardless of outgroup utilized. The most parsimonious cladograms from HENNIG86 (7 trees) have treelengths of 243 (C.I. = 0.58, R.I. = 0.82). Bryophytes are monophyletic as are hornworts, liverworts, and mosses, with hornworts identified as the sister group of a liverwort/moss assemblage. In vascular plants, lycophytes are polyphyletic andSelaginella is close to the bryophytes.Lycopodium is the sister group of the remaining vascular plants (minusSelaginella). Longer treelengths (over 250) are required to produce tree topologies in which either lycophytes are monophyletic or to reconstruct the paraphyletic bryophyte phylogeny of recent authors. This analysis challenges existing concepts of bryophyte phylogeny based on more classical data and interpretations, and provides new insight into land plant evolution.     

Phylogenetic relationships of Microdontinae (Diptera: Syrphidae) based on molecular and morphological characters

The intrasubfamilial classification of Microdontinae Rondani (Diptera: Syrphidae) has been a challenge: until recently more than 300 out of more than 400 valid species names were classified in Microdon Meigen. We present phylogenetic analyses of molecular and morphological characters (both separate and combined) of Microdontinae. The morphological dataset contains 174 characters, scored for 189 taxa (9 outgroup), representing all 43 presently recognized genera and several subgenera and species groups. The molecular dataset, representing 90 ingroup species of 28 genera, comprises sequences of five partitions in total from the mitochondrial gene COI and the nuclear ribosomal genes 18S and 28S. We test the sister‐group relationship of Spheginobaccha with the other Microdontinae, attempt to elucidate phylogenetic relationships within the Microdontinae and discuss uncertainties in the classification of Microdontinae. Trees based on molecular characters alone are poorly resolved, but combined data are better resolved. Support for many deeper nodes is low, and placement of such nodes differs between parsimony and Bayesian analyses. However, Spheginobaccha is recovered as highly supported sister group in both. Both analyses agree on the early branching of Mixogaster, Schizoceratomyia, Afromicrodon and Paramicrodon. The taxonomical rank in relation to the other Syrphidae is discussed briefly. An additional analysis based on morphological characters only, including all 189 taxa, used implied weighting. A range of weighting strengths (k‐values) is applied, chosen such that values of character fit of the resulting trees are divided into regular intervals. Results of this analysis are used for discussing the phylogenetic relationships of genera unrepresented in the molecular dataset.     

An investigation into the cladistic relationships and monophyly of therocephalian therapsids (Amniota: Synapsida)

A comprehensive phylogenetic investigation was performed to elucidate the cladistic relationships and possible monophyly of therocephalian therapsids (Amniota: Synapsida). The phylogenetic positions of 30 therapsid taxa were examined under maximum parsimony, including 23 therocephalian genera. The analysis incorporated 110 cranial and postcranial characters in order to assess the interrelationships of basal therocephalians and eutherocephalians and their relationships to Cynodontia, representing the most complete review of therocephalian phylogeny to date. The analysis supports the hypothesis that Therocephalia represents the monophyletic sister taxon to Cynodontia, with as many as 15 morphological synapomorphies, in contrast with other recent analyses of lesser taxon sampling. The results also support the hypothesis that Scylacosauridae is more closely related to Eutherocephalia than to the basal therocephalian family Lycosuchidae, supporting a ‘Scylacosauria’ clade. The taxa suggested here to be neotenic forms (e.g. Ictidosuchoides and Ictidosuchops) are positioned near the base of a monophyletic Baurioidea. Neotenic development of the therocephalian feeding apparatus and evolutionary parallelism with cynodonts are suggested to have been important trends in the early evolution of baurioid therocephalians into the Late Permian and Early Triassic.     

Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data

The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones.     

Identification and genetic relationships among nine Albizzia species based on morphological and molecular markers

Abstract

Identifying germplasm is an important component for efficient and effective management of plant genetic resources. This investigation was undertaken for the identification and analysis of genetic variation within 9 species of Albizzia through 33 morphological parameters, and 15 Random Amplified Polymorphic DNA (RAPD) and 17 Inter Simple Sequence Repeat (ISSR) primers. The use of selected RAPD and ISSR primers generated a total of 163 and 201 amplified DNA fragments, respectively. High frequencies of polymorphism, 95.05% for RAPD and 96.02% for ISSR, were detected. Statistical approaches were employed to construct genetic relationships by RAPD, ISSR and morphological analysis. Cluster analysis by the unweighted pair-group method (UPGMA) of Nei's similarity generated dendograms with similar topology that gave a better reflection of the diversity and affinities between species. These molecular results were comparable to main morphological characteristics. The correlation matrices generated by RAPD and ISSR markers were highly correlated (r = 0.843 at p = 1.0), thereby indicating congruence between these two marker systems. Both morphometric data and molecular markers have the potential to analyse genetic variation among the nine species of Albizzia, thus providing a major input for management strategy of plant genetic resources.     

The phylogenetic position of Apterosperma (Theaceae) based on morphological and karyotype characters

Classifications of Theaceae have usually placed the endangered monotypic genus Apterosperma in tribe Schimeae (x=18), whereas recent molecular phylogenetic evidence supports its transfer to tribe Theeae (x=15). Molecular data have not resolved the phylogenetic position of Apterosperma within Theeae. We investigated the chromosome number and karyotype of Apterosperma in the context of molecular and morphological phylogenetic evidence to provide further insight into the placement of Apterosperma within Theaceae. The chromosome number and karyotype was found to be 2n = 30 = 26m + 4sm, consistent with the transfer of Apterosperma to tribe Theeae. When the chromosome data were incorporated into a data set of 46 other nonmolecular characters, Apterosperma was placed as the first-diverging lineage within the clade comprising tribe Theeae. This supports its placement based on molecular data. The low intrachromosomal asymmetry (type 1A) of Apterosperma, presumably ancestral for the family, is also consistent with this placement. Character optimization strongly supports a base chromosome number of x=15 for tribe Theeae. Because of variable and sometimes conflicting chromosome count reports of species in tribes Schimeae and Stewartieae, the base chromosome number of Theaceae could be either x=15 or 17.     

Phylogenetic relationships within the tribe Janieae (Corallinales,Rhodophyta) based on molecular and morphological data: a reappraisal of Jania1

Generic boundaries among the genera Cheilosporum, Haliptilon, and Jania—currently referred to the tribe Janieae (Corallinaceae, Corallinales, Rhodophyta)—were reassessed. Phylogenetic relationships among 42 corallinoidean taxa were determined based on 26 anatomical characters and nuclear SSU rDNA sequence data for 11 species (with two duplicate plants) referred to the tribe Corallineae and 15 species referred to the tribe Janieae (two species of Cheilosporum, seven of Haliptilon, and six of Jania, with five duplicate plants). Results from our approach were consistent with the hypothesis that the tribe Janieae is monophyletic. Our data indicate, however, that Jania and Haliptilon as currently delimited are not monophyletic, and that Cheilosporum should not be recognized as an independent genus within the Janieae. Our data resolved two well‐supported biogeographic clades for the included Janieae, an Indian‐Pacific clade and a temperate North Atlantic clade. Among anatomical characters, reproductive structures reflected the evolution of the Janieae. Based on our results, three genera, Cheilosporum, Haliptilon, and Jania, should be merged into a single genus, with Jania having nomenclatural priority. We therefore propose new combinations where necessary of some species previously included in Cheilosporum and Haliptilon.     

The distribution and systematic relevance of the androecial character oligomery

Localization of the stamens can be approached by a preliminary distinction between two characters, oligomery and polymery, occurring in two different groups of taxa, respectively the oligomerous complex and the polymerous complex. Oligomery is described by four character states standing in a close semophyletic relationship: diplostemony, obdiplostemony, haplostemony and obhaplostemony. Each character state is analysed for its distribution and systematic value. Diplostemony is the synapomorphic character state for the oligomerous line and has arisen once from a polymerous ancestor or in parallel in different lines. Obdiplostemony arises ontogenetically in three different ways. Loss of one whorl leads either to obhaplostemony, or haplostemony; both character states are believed to represent evolutionary steps of no-return. Secondary increases and reductions of the stamens within a whorl are seen as expressions of the intrinsic variability of the character states and should not be homologized with them. Stamen numbers can be increased by the building-up of complex primordia or by secondary receptacular growth. Reductions of stamens affect one or two whorls of stamens and are caused by lack of space, interactions with the gynoecium and zygomorphy. The distribution of the different character states of oligomery is presented on Dahlgrenograms and the androecia of a number of families and their relationships are discussed. The interactions between oligomery and polymery are analysed as guidelines for a global phylogeny of the Magnoliatae.     

Phylogenetic relationships of thorny catfishes (Siluriformes: Doradidae) inferred from molecular and morphological data

Doradidae is a putatively monophyletic group of South American freshwater catfishes containing 30 extant genera and 72 valid species. Only one study to date has attempted to estimate phylogenetic relationships among doradids. This morphological analysis partitioned species into two basal genera ( Wertheimeria and Francisodoras ) and a crown group of three subfamilies (Platydoradinae, Astrodoradinae and Doradinae) whose relationships were unresolved. No subsequent work has been done to resolve the subfamilial trichotomy or to assess whether postulated intergeneric relationships are accurate. We address this problem with complete sequences (2.5 kilobases, kb) of mitochondrial 12S and 16S rRNA genes and partial (1.3 kb) sequences of the nuclear elongation factor-1 alpha (EF1α) gene from representatives of 23 doradid genera (43 species) and 13 outgroups from additional siluriform families. Phylogenetic analysis of these data yields strong support for the monophyly of Doradidae and Astrodoradinae (as well as other relationships), but otherwise shows significant conflict with morphological results. A partial re-examination of published morphological data indicates that many characters may have been incorrectly polarized and many taxa have incorrect state assignments. Our results provide a framework for ongoing efforts to describe the species-level diversity of this poorly understood neotropical family.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 551–575.     

The phylogeny and taxonomy of Hippopotamidae (Mammalia: Artiodactyla): a review based on morphology and cladistic analysis

The phylogeny and taxonomy of the whole family Hippopotamidae is in need of reconsideration, the present confusion obstructing palaeoecology and palaeobiogeography studies of these Neogene mammals. The revision of the Hippopotamidae initiated here deals with the last 8 Myr of African and Asian species. The first thorough cladistic analysis of the family is presented here. The outcome of this analysis, including 37 morphological characters coded for 15 extant and fossil taxa, as well as non-coded features of mandibular morphology, was used to reconstruct broad outlines of hippo phylogeny. Distinct lineages within the paraphyletic genus Hexaprotodon are recognized and characterized. In order to harmonize taxonomy and phylogeny, two new genera are created. The genus name Choeropsis is re-validated for the extant Liberian hippo. The nomen Hexaprotodon is restricted to the fossil lineage mostly known in Asia, but also including at least one African species. The genus Hippopotamus is confirmed. These changes represent substantial advances for understanding the evolutionary history of the Hippopotamidae, and provide a new framework for future studies.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 1–26.     

A molecular systematic investigation of the Acrochaetiales (Florideophycidae,Rhodophyta) and related taxa based on nuclear small-subunit ribosomal DNA sequence data

Small-subunit ribosomal DNA (SSU) sequences for 14 members of the rhodophyte order Acrochaetiales were used to generate phylogenetic trees to determine whether the Acrochaetiales is monophyletic and to assess the relationships of acrochaetioid algae to closely related taxa. Within the Acrochaetiales, two strongly supported groups are recognized: one group that includes, in addition to three other species, the type species of the genera Acrochaetium, Audouinella and Rhodochorton; and a second group that includes an unequivocal representative of Colaconema and nine additional species. The relationships of these groups with the Batrachospermales, Palmariales and Nemaliales were not resolved and the possibility that the Acrochaetiales is polyphyletic was not eliminated. Resolution of relationships for species within these groups was strong in only a few cases, with many of the phylogenetic issues at this level remaining equivocal. Our results do not position Camontagnea in the Acrochaetiales, as has recently been suggested, but strongly ally this genus to the family Rhodothamniellaceae of the Palmariales. The phylogenetic position of Rhododraparnaldia, an alga intermediate between the Acrochaetiales and Batrachospermales, remains unresolved. These molecular results provide a foundation for assessing the taxonomic significance of phenotypic characters (e.g. anatomy, life histories, morphology, phycoerythrin type and plastid details) variously considered taxonomically significant in the Acrochaetiales.     

A multivariate and cladistic study of Vicia L. ser. Vicia (Fabaceae) based on analysis of morphological characters

 Vicia ser. Vicia, which includes the Vicia sativa aggregate, was studied by observing morphological variation. The study is an attempt to resolve the taxonomic relationships within the Vicia sativa aggregate by novel investigations along with a synthesis of the results obtained by previous researchers. The study has included some accessions and characters used previously, but has drawn accessions from a wider geographical range than has been attempted previously. Cluster analysis on the basis of 53 morphological characters justified the delimitation of four species within the series and six subspecies within the Vicia sativa aggregate. Accessions from South Asia could easily be incorporated in the classification, but some of the accessions from North Africa showed morphological differences. The morphometric data were coded using the gap weighting method of Thiele (1993) and used in a phylogenetic analysis to study the relationships between the taxa. The phylogenetic analysis, using 33 variables, showed Vicia pyrenaica closely related to Vicia sativa subsp. amphicarpa. A dichotomous key and a multi-access key to aid the identification of the taxa in the series are presented. Received January 21, 2002; accepted November 8, 2002 Published online: March 20, 2003