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Cladistic Analysis (cladistic + analysis)
Kinds of Cladistic Analysis Selected AbstractsCladistic Analysis of A Problematic Ammonite Group: the Hamitidae (Cretaceous, Albian,turonian) and Proposals for New Cladistic TermsPALAEONTOLOGY, Issue 4 2002Neale MonksArticle first published online: 24 NOV 200 The Hamitidae are a family of mid,Cretaceous heteromorph ammonites including lineages leading to four other families. Problems are outlined in trying to describe the phylogeny of completely extinct groups such as these heteromorph ammonites using the existing cladistic terminology, which is largely concerned with extant taxa and their ancestors. To solve these problems, two new terms are proposed: ,crown groups and ,stem groups, which are equivalent to crown and stem groups in terms of the evolutionary history of a clade, but are not defined on the basis of extant taxa. Instead they are defined by the topology of the phylogenetic tree, the ,crown group being a clade defined by synapomorphies but which gave rise to no descendants. A ,stem group is a branch of a phylogenetic tree which comprises the immediate sister groups of a given ,crown group but is not itself a clade. Examples of these terms are described here with reference to the phylogeny of the Hamitidae and their descendants. The Hamitidae are paraphyletic and form ,stem groups to a number of ,crown groups, namely the Anisoceratidae, Baculitidae, Scaphitidae, and Turrilitidae. The definitions of the genera and subgenera are refined with respect to the type species and the clades within which they occur, and four new genera are described: Eohamites, Helicohamites, Sziveshamites, and Planohamites. [source] Cladistic Analysis of Human Apolipoprotein A4 Polymorphisms in Relation to Quantitative Plasma Lipid Risk Factors of Coronary Heart DiseaseANNALS OF HUMAN GENETICS, Issue 2 2003G. Q. Wang Summary Genetic variation in several genes involved in lipid metabolism is known to affect population variation in quantitative lipid risk factor profiles for coronary heart disease (CHD). The apolipoprotein A-IV gene (APOA4) is one such candidate gene. We genotyped five polymorphisms in the APOA4 gene (codon 127, codon 130, codon347, codon 360 and 3' VNTR) and investigated their impact on plasma lipid trait levels in three populations comprising 604 U.S. non-Hispanic Whites (NHWs), 408 U.S. Hispanics and 708 Nigerian Blacks. Cladistic analysis was carried out to identify 5-site haplotypes that were associated with significant phenotypic differences in each population. The distribution of APOA4 genotypes was significantly different between ethnic groups. The Africans were monomorphic for two of the five sites (codons 130 and 360), but possess a unique 12 bp insertion that was not observed in NHWs and Hispanics. Due to linkage disequilibrium between the sites, only 6 haplotypes were observed in NHWs and Hispanics, and 4 in Africans. Several gender-and ethnic-specific associations between genotypes and plasma lipid traits were observed when single sites were used. Several haplotypes were identified by cladistic analysis that may carry functional mutations that affect plasma lipid trait levels. [source] Phylogenetics and Ecology: As Many Characters as Possible Should Be Included in the Cladistic Analysis,CLADISTICS, Issue 1 2001Philippe Grandcolas As many data as possible must be included in any scientific analysis, provided that they follow the logical principles on which this analysis is based. Phylogenetic analysis is based on the basic principle of evolution, i.e., descent with modification. Consequently, ecological characters or any other nontraditional characters must be included in phylogenetic analyses, provided that they can plausibly be postulated heritable. The claim of Zrzavý (1997, Oikos 80, 186,192) or Luckow and Bruneau (1997, Cladistics 13, 145,151) that any character of interest should be included in the analysis is thus inaccurate. Many characters, broadly defined or extrinsic (such as distribution areas), cannot be considered as actually heritable. It is argued that we should better care for the precise definition and properties of characters of interest than decide a priori to include them in any case in the analysis. The symmetrical claim of de Queiroz (1996, Am. Nat. 148, 700,708) that some characters of interest should better be excluded from analyses to reconstruct their history is similarly inaccurate. If they match the logical principles of phylogenetic analysis, there is no acceptable reason to exclude them. The different statistical testing strategies of Zrzavý (1997) and de Queiroz (1996) aimed at justifying inclusion versus exclusion of characters are ill-conceived, leading respectively to Type II and Type I errors. It is argued that phylogenetic analyses should not be constrained by testing strategies that are downstream of the logical principles of phylogenetics. Excluding characters and mapping them on an independent phylogeny produces a particular and suboptimal kind of secondary homology, the use of which can be justified only for preliminary studies dealing with broadly defined characters. [source] A Cladistic Analysis of the New World Species of Lotus L. (Fabaceae, Loteae)CLADISTICS, Issue 3 2000Ana M. Arambarri The genus Lotus L. is a monophyletic group diagnosed by the possession of a standard claw with thickened infolded margin, stamens diadelphous, and the style hardened from the base. It comprises approximately 200 species distributed throughout the world. A cladistic analysis of the New World species was performed using 39 morphological and anatomical characters (29 from seed morphology and anatomy, 1 from plant habit, 1 from leaf morphology, 6 from flower morphology, and 2 from fruit morphology). Dorycnium, Edentolotus, Krokeria, and Pedrosia, of the Old World, and 28 species of the New World were considered terminal taxa. Tetragonolobus Scop. was chosen to root the cladograms and Dorycnium Mill. to reroot them. With Tetragonolobus the analysis yielded 15 equally parsimonious trees, each with a length of 74 steps, a consistency index of 0.62, and a retention index of 0.89. The 15 initial trees and the strict consensus tree defined 12 monophyletic groups. All terminal taxa form a monophyletic group diagnosed by the presence of a radicular lobe discernible to conspicuous (character 10); rim aril thick (character 13); stipules absent (character 31); and style simple and nondilated (character 36). The New World species form a monophyletic group on the basis of the seed relationship of length to width in hilar view 1.5:1 to 2:1 (character 5); micropyle linear-deltoid to bifurcate (character 19); and keel erostrate (character 33). Identical monophyletic groups were obtained when Dorycnium was used as root. These results are discussed in the context of data on cytology and morphology. [source] Comparative anatomy and phylogenetic distribution of the mammalian cecal appendixJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 10 2009H. F. SMITH Abstract A recently improved understanding of gut immunity has merged with current thinking in biological and medical science, pointing to an apparent function of the mammalian cecal appendix as a safe-house for symbiotic gut microbes, preserving the flora during times of gastrointestinal infection in societies without modern medicine. This function is potentially a selective force for the evolution and maintenance of the appendix, and provides an impetus for reassessment of the evolution of the appendix. A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer. [source] Mitochondrial DNA sequences reveal extensive cryptic diversity within a western American springsnailMOLECULAR ECOLOGY, Issue 10 2003Hsiu-Ping Liu Abstract We analysed cytochrome c oxidase subunit I and NADH dehydrogenase subunit I sequence variation among 29 populations of a widely ranging southwestern springsnail (Pyrgulopsis micrococcus) and 18 regional congeners. Cladistic analyses of these sequences depict P. micrococcus as a polyphyletic composite of five well-supported clades. Sequence divergences among these clades and subclades imply the possible occurrence of as many as seven or eight cryptic species in addition to P. micrococcus. Our finding that P. micrococcus contains multiple, genetically distinct and geographically restricted lineages suggests that diversification within this highly speciose aquatic genus has been structured in large part by the operation of terrestrial barriers to gene flow. However, these sequence data also indicate that recent dispersal among hydrographically separated areas has occurred within one of these lineages, which we attribute to passive transport on migratory waterbirds. [source] Phylogeny of Macroptilium (Leguminosae): morphological, biochemical and molecular evidenceCLADISTICS, Issue 2 2007Shirley M. Espert Macroptilium (Benth.) Urban (Phaseoleae, Papilionoideae, Leguminosae) is an American genus of legumes, belonging to subtribe Phaseolinae along with other economically important genera, such as Vigna Savi and Phaseolus L. (the common bean genus). Cladistic analyses based on morphological, biochemical (storage seed proteins) and molecular (nuclear and plastid DNA sequences) data were performed on the 18 species currently ascribed to the genus, exploring several character weighting strategies. Equal weights, implied weighting and different transversion/transition costs were applied. The three data sets were first analyzed with separate partitions, and then combined into a single matrix. This study is the first one to analyze all the species of the genus from a cladistic point of view. In all the most parsimonious trees obtained, Macroptilium is monophyletic with excellent support values. Two monophyletic clades are recovered in almost all the analyses. Both are compound by nine species, and they constitute two sections of Macroptilium. Several interspecific relationships inside the genus are discussed. © The Willi Hennig Society 2007. [source] A new specimen of Baphetes from Ný,any, Czech Republic and the intrinsic relationships of the BaphetidaeACTA ZOOLOGICA, Issue 2009Angela C. Milner Abstract ,Loxomma'bohemicum from the Upper Carboniferous assemblage from Ný,any, Czech Republic, is a nomen dubium restricted to the type and only specimen. The new binomen Baphetes orientalis is created for a skull referred to Baphetes bohemicus by later authors. A previously undescribed baphetid specimen from Ný,any is referred to B. orientalis despite differences in skull proportions. It comprises a skull in dorsal aspect, mandibles and some associated postcranial elements. The skull possesses sclerotic ring elements within the orbital region of the dorsal fenestration of the skull, confirming the eye location. The elongate gastralia are arranged perpendicular to the interclavicle edge in contrast to the condition in temnospondyls and colosteids. Cladistic analysis of 24 characters of 11 baphetoids was carried out using Acanthostega and Crassigyrinus as outgroups. Eucritta was the most primitive baphetoid, with Spathicephalus being the sister-taxon to the remaining taxa, justifying a monotypic Spathicephalidae as a sister-taxon to the Baphetidae. The Baphetidae are divided into a subfamily Baphetinae nom.nov. containing two Baphetes species; and a subfamily Loxommatinae with Loxomma as a paraphyletic grade leading to a Megalocephalus +Kyrinion clade. The Linton taxon ,Baphetes' lintonensis is transferred to the genus Loxomma to give the new combination Loxomma lintonensis. [source] Cladistic analysis of Medusozoa and cnidarian evolutionINVERTEBRATE BIOLOGY, Issue 1 2004Antonio C. Marques Abstract. A cladistic analysis of 87 morphological and life history characters of medusozoan cnidarians, rooted with Anthozoa, results in the phylogenetic hypothesis (Anthozoa (Hydrozoa (Scyphozoa (Staurozoa, Cubozoa)))). Staurozoa is a new class of Cnidaria consisting of Stauromedusae and the fossil group Conulatae. Scyphozoa is redefined as including those medusozoans characterized by strobilation and ephyrae (Coronatae, Semaeostomeae, and Rhizostomeae). Within Hydrozoa, Limnomedusae is identified as either the earliest diverging hydrozoan lineage or as the basal group of either Trachylina (Actinulida (Trachymedusae (Narcomedusae, Laingiomedusae))) or Hydroidolina (Leptothecata (Siphonophorae, Anthoathecata)). Cladistic results are highly congruent with recently published phylogenetic analyses based on 18S molecular characters. We propose a phylogenetic classification of Medusozoa that is consistent with phylogenetic hypotheses based on our cladistic results, as well as those derived from 18S analyses. Optimization of the characters presented in this analysis are used to discuss evolutionary scenarios. The ancestral cnidarian probably had a sessile biradial polyp as an adult form. The medusa is inferred to be a synapomorphy of Medusozoa. However, the ancestral process (metamorphosis of the apical region of the polyp or lateral budding involving an entocodon) could not be inferred unequivocally. Similarly, character states for sense organs and nervous systems could not be inferred for the ancestral medusoid of Medusozoa. [source] Geographical history of the central-western Pacific black fly subgenus Inseliellum (Diptera: Simuliidae: Simulium) based on a reconstructed phylogeny of the species, hot-spot archipelagoes and hydrological considerationsJOURNAL OF BIOGEOGRAPHY, Issue 9 2001Douglas A. Craig Aim With six new species of subgenus Inseliellum Rubtsov recently described, a revised reconstructed phylogeny based on morphology is required. Geological history of islands where Inseliellum occurs, plus a cladistic analysis and hydrological considerations, provide the basis for a reconstructed geographical history of the species. Location Inseliellum is widely distributed and occurs in Micronesia, Cook Islands and Polynesia. A single specimen is known from Tonga Islands. Methods Maximum parsimony criteria using PAUP*, plus cytological information, were used to arrive at a preferred phylogenic reconstruction. Island ages of the hot spot archipelagoes involved are well known. The phylogeny was then compared with the palaeogeology. Information on evolution of running water habitats as islands age was incorporated into the biogeography. Results Cladistic analysis of forty of the forty-eight known Inseliellum species with Simulium (Nevermannia) neornatipes Dumbleton from New Caledonia and S. (Hebridosimulium) laciniatum Edwards from Fiji as outgroups, shows basal species and clades to be on widely separated older islands. In the Society Islands basal species are widely spread. Derived species, with morphological adaptations to deal with specialized habitats, are on younger islands (e.g. Tahiti), where a major species radiation has taken place. The reconstructed phylogeny indicates dispersal back to older islands, with minor subsequent species radiation. Main conclusions Palaeogeological evidence provides a basis for postulating that Inseliellum entered the western Pacific area some 20 Ma, with the possibility that it rafted eastwards on proto-Tonga Islands to the edge of southern-central Pacific. Older Cook Islands were present at that time. Movement into the Marquesas Islands was not earlier than 6 Ma and into the Society Islands perhaps 8,10 Ma. Basal species with generalized habitat requirements would have found suitable habitats (inferred from hydrological postulates) on leaves in the original, small shaded streams. With erosion and valley development, in particular on Tahiti, species radiated into specialized habitats such as cascades. Rich seston and high velocity probably drove reduction of filtering fans in some clades. With collapse of the caldera and formation of large rivers at c. 0.9 Ma, S. exasperans Craig and S. tahitiense Edwards adapted to deep, swiftly flowing water, all indicative that specialized habitat availability drove species radiation in Inseliellum. In the Society Islands, dispersal of derived species back to the oldest western islands was not possible because erosion has removed suitable habitats. [source] The peristomatic structures of Lithobiomorpha (Myriapoda, Chilopoda): Comparative morphology and phylogenetic significanceJOURNAL OF MORPHOLOGY, Issue 2 2008Markus Koch Abstract A comparative survey of the epipharynx and hypopharynx of lithobiomorph centipedes by light and scanning electron microscopy examines 18 species that sample the major groups of both families, the Lithobiidae and Henicopidae. Cladistic analysis of 11 characters of the peristomatic structures together with 29 additional morphological characters serves as a basis for interpreting the evolution of the lithobiomorph peristomatic structures. Scutigeromorpha is used for outgroup comparison in the framework of a homology scheme for the basic components of the epi- and hypopharynx. Compared to other chilopods, the monophyly of Lithobiomorpha is supported by a row of distinctive bottle-shaped gland openings at the border between the labral and clypeal parts of the epipharynx, as well as by a distinctive shape of the hypopharynx. Paired rows of elongate spines on the clypeal part of the epipharynx are an apomorphic character of Lithobiidae. The transformation of these spine rows into a few groups of branching spines is characteristic for the Monotarsobius group sensu Verhoeff. Similar groups of branching clypeal spines characterize the Anopsobiinae within Henicopidae, whereas Henicopinae possess a dense cluster of short, simple spines instead. The recently described genus Dzhungaria is resolved closer to Henicopinae than to Anopsobiinae, a hypothesis supported by a field of grooves on the medial labral part of the epipharynx. Monophyly of Henicopidae does not receive unique support from the peristomatic structures although two homoplastic characters contribute to this node; among these, the reduction of a median spine field between clypeal and labral parts of the epipharynx to a narrow transverse band also supports a close relationship between the Ezembius group and Hessebius within Lithobiidae. An Ezembius + Hessebius clade is additionally supported by the absence of a transverse bulge between the clypeal and labral parts of the epipharynx, a character otherwise present in all lithobiomorph species studied so far. Lithobius is resolved as polyphyletic, with different species being most closely related to such genera as Australobius, Hessebius and Pleurolithobius. J. Morphol., 2008. © 2007 Wiley-Liss, Inc. [source] The Genus Chelipoda Macquart (Diptera, Empididae, Hemerodromiinae) in ChileMITTEILUNGEN AUS DEM MUSEUM FUER NATURKUNDE IN BERLIN-DEUTSCHE ENTOMOLOGISCHE ZEITSCHRIFT, Issue 1 2009Adrian R. Plant Abstract Chilean species of Chelipoda Macquart, 1823 (Diptera, Empididae, Hemerodromiinae) are reviewed and a key provided to all known species. Six new species are described; Chelipoda ceraphoron sp. n., C. deletrix sp. n., C. interfectrix sp. n., C. kolua sp. n., C. lentiginosa sp. n. and C. perditrix sp. n. Lectotypes and paralectotypes are designated for C. fimbriata Collin, 1933, C. obtusipennis Collin, 1933 and C. remissa Collin, 1933 and a lectotype is designated for C. subflava Collin, 1933. Cladistic analysis resolved two distinct clades defined largely on male genitalic characters. Habitat, biogeography and occurrence of secondary sexual characters are briefly discussed. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] ONTOGENY AND RELATIONSHIPS OF THE TRILOBITE PSEUDOPETIGURUS PRANTL AND P,IBYLPALAEONTOLOGY, Issue 3 2006YUAN WENWEI Abstract:, The ontogeny of Pseudopetigurus deprati Turvey et al., 2006 from the Ordovician Dawan Formation (Arenigian), Anhui Province, South China, is described. The presence of an anterior cranidial border in Pseudopetigurus is recognized for the first time. On account of the short (tr.), spindle-shaped anterior border, and the distinct, steeply inclined, wall-like pygidial margin, Pseudopetigurus is assigned to the family Dimeropygidae, the first genus of this family endemic to Gondwana. It has previously been regarded as a member of family Isocolidae. Cladistic analysis of species assigned to Dimeropygidae supports the monophyly of a clade including Dimeropyge, Dimeropygiella, Ischyrotoma, Pseudohystricurus and Pseudopetigurus, which may represent a subfamily Dimeropyginae. The distribution of Dimeropyginae shows a predominantly palaeotropical distribution, while the Gondwana Pseudopetigurus must have diverged from the dimeropygine common ancestor in pre-Arenigian time. [source] A TERRESTRIAL STEREOSPONDYL FROM THE LOWER TRIASSIC OF SOUTH AFRICA: THE POSTCRANIAL SKELETON OF LYDEKKERINA HUXLEYI (AMPHIBIA: TEMNOSPONDYLI)PALAEONTOLOGY, Issue 2 2005K. PAWLEY Abstract:, Description of the postcranial skeleton of the basal stereospondyl amphibian Lydekkerina huxleyi from new material shows it to be heavily ossified with large processes for muscle attachment and well-developed articulation surfaces. The structure of the postcranial skeleton implies a substantial capability for terrestrial locomotion, rather than a primarily aquatic existence as has been suggested for most other stereospondyls. The postcranial skeleton is most similar to that of Uranocentrodon and the Archegosauroidea, and is unlike that of the poorly ossified, more derived stereospondyls and Dvinosauria. The postcranial skeleton does not display any of the particular apomorphies of the fully ossified Permian terrestrial temnospondyls. Cladistic analysis using the postcranial data obtained in this study indicates that within the Stereospondyli Lydekkerina huxleyi is neither a member of the Rhinesuchidae nor the Mastodonsauroidea, rather the Lydekkerinidae are a separate taxon. [source] The Rutland Cetiosaurus: the anatomy and relationships of a Middle Jurassic British sauropod dinosaurPALAEONTOLOGY, Issue 6 2002Paul Upchurch A relatively well,preserved specimen of Cetiosaurus oxoniensis, from the Middle Jurassic (Bajocian) of Rutland, United Kingdom, is described in detail. The material includes a nearly complete cervical series, representative dorsal vertebrae, a fragment of sacrum, anterior caudals, the right femur, and numerous rib and limb fragments. Contrary to previous suggestions that this specimen possesses 14 cervical and ten dorsal vertebrae, it seems more probable that there were at most 13 cervicals and at least 12 dorsals. The vertebral column displays several autapomorphic features which supplement the generic diagnosis of Cetiosaurus, including: (1) a stout, anteriorly directed process located at the top of the neural spine of the twelfth (?) cervical vertebra; and (2) the presence of lateral pits, separated by a thin midline septum, below the transverse processes of middle dorsal vertebrae. Cladistic analysis indicates that Cetiosaurus is probably the sister,taxon to the advanced neosauropod clade. This relationship affects the distribution of particular character states that have played an important role in determining sauropod phylogeny. [source] Cladistic Analysis of Human Apolipoprotein A4 Polymorphisms in Relation to Quantitative Plasma Lipid Risk Factors of Coronary Heart DiseaseANNALS OF HUMAN GENETICS, Issue 2 2003G. Q. Wang Summary Genetic variation in several genes involved in lipid metabolism is known to affect population variation in quantitative lipid risk factor profiles for coronary heart disease (CHD). The apolipoprotein A-IV gene (APOA4) is one such candidate gene. We genotyped five polymorphisms in the APOA4 gene (codon 127, codon 130, codon347, codon 360 and 3' VNTR) and investigated their impact on plasma lipid trait levels in three populations comprising 604 U.S. non-Hispanic Whites (NHWs), 408 U.S. Hispanics and 708 Nigerian Blacks. Cladistic analysis was carried out to identify 5-site haplotypes that were associated with significant phenotypic differences in each population. The distribution of APOA4 genotypes was significantly different between ethnic groups. The Africans were monomorphic for two of the five sites (codons 130 and 360), but possess a unique 12 bp insertion that was not observed in NHWs and Hispanics. Due to linkage disequilibrium between the sites, only 6 haplotypes were observed in NHWs and Hispanics, and 4 in Africans. Several gender-and ethnic-specific associations between genotypes and plasma lipid traits were observed when single sites were used. Several haplotypes were identified by cladistic analysis that may carry functional mutations that affect plasma lipid trait levels. [source] Cladogenesis and reticulation in the Hawaiian endemic mints (Lamiaceae)CLADISTICS, Issue 6 2003Charlotte Lindqvist The Hawaiian endemic mints, which comprise 58 species of dry-fruited Haplostachys and fleshy-fruited Phyllostegia and Stenogyne, represent a major island radiation that likely originated from polyploid hybrid ancestors in the temperate North American Stachys lineage. In contrast with considerable morphological and ecological diversity among taxa, sequence variation in the nrDNA 5S non-transcribed spacer was found to be remarkably low, which when analyzed using standard parsimony resulted in a lack of phylogenetic resolution among accessions of insect-pollinated Phyllostegia and bird-pollinated Stenogyne. However, many within-individual nucleotide polymorphisms were observed, and under the assumption that they could contain phylogenetic information, these ambiguities were recoded as new character states. Substantially more phylogenetic structure was obtained with these data, including the resolution of most Stenogyne species into a monophyletic group with an apparent recent origin on O'ahu (3.0 My) or the Maui Nui island complex (2.2 My). Subsequent diversification appears to have involved multiple inter-island dispersal events. Intergeneric placements for a few morphotypes, seemingly misplaced within either Phyllostegia or Stenogyne, may indicate reticulation as one polymorphism-generating force. For a finer scale exploration of hybridization, preliminary AFLP fragment data were examined among putative hybrids of Stenogyne microphylla and S. rugosa from Mauna Kea, Hawai'i, that had been identified based on morphology. Cladistic analysis (corroborated by multivariate correspondence analysis) showed the morphologically intermediate individuals to group in a strongly supported monophyletic clade with S. microphylla. Therefore, reticulation could be both historic and active in Stenogyne, and perhaps a force of general importance in the evolution of the Hawaiian mints. The relatively greater extent of lineage-sorted polymorphisms in Stenogyne may indicate selective differentiation from other fleshy-fruited taxa, perhaps through the agency of highly specialized bird pollinators that restricted gene flow with other Hawaiian mint morphotypes. [source] Cladistic analysis of languages: Indo-European classification based on lexicostatistical dataCLADISTICS, Issue 2 2003ina Rexová The phylogeny of the Indo-European (IE) language family is reconstructed by application of the cladistic methodology to the lexicostatistical dataset collected by Dyen (about 200 meanings, 84 speech varieties, the Hittite language used as a functional outgroup). Three different methods of character coding provide trees that show: (a) the presence of four groups, viz., Balto-Slavonic clade, Romano-Germano-Celtic clade, Armenian-Greek group, and Indo-Iranian group (the two last groups possibly paraphyletic); (b) the unstable position of the Albanian language; (c) the unstable pattern of the basalmost IE differentiation; but (d) the probable existence of the Balto-Slavonic,Indo-Iranian ("satem") and the Romano-Germano-Celtic (+Albanian?) superclades. The results are compared with the phenetic approach to lexicostatistical data, the results of which are significantly less informative concerning the basal pattern. The results suggest a predominantly branching pattern of the basic vocabulary phylogeny and little borrowing of individual words. Different scenarios of IE differentiation based on archaeological and genetic information are discussed. [source] A Morphological Test of the Monophyly of the Cardueline Finches (Aves: Fringillidae, Carduelinae)CLADISTICS, Issue 3 2002Article first published online: 19 JUL 200, Philip C. Chu Monophyly of the cardueline finches (Aves: Fringillidae, Carduelinae), an assemblage of 119 species of seed-eating songbirds, has not yet been rigorously tested. To test the hypothesis of cardueline monophyly I examined 37 taxa, among them 1 or 2 representatives from 16 of the 19 cardueline-finch genera as well as 4 Hawaiian honeycreepers. Each taxon was scored for 225 morphological characters, 148 from the skeleton and 77 from the integument. Cladistic analysis of these data found the carduelines to be monophyletic, so long as the honeycreeper Telespiza cantans is considered to be cardueline; as for the other honeycreepers, they form a clade but do not group with either Telespiza or the carduelines. Both cardueline monophyly and the nonmonophyly of honeycreepers have comparatively strong support, with support for cardueline monophyly coming primarily from evolutionary modifications to the head skeleton. [source] Larval Case Architecture and Implications of Host-Plant Associations for North American Coleophora (Lepidoptera; Coleophoridae),CLADISTICS, Issue 1 2002Sibyl Bucheli The case-bearing moths of North America are represented by a single genus, Coleophora, which contains approximately 144 described species. All are external seed or leaf miners that inhabit portable silk cases during most of the larval stage. Architectural and ecological characters from larval cases were used in cladistic analysis to investigate existing case groups for 32 North American species of Coleophora. Cladistic analysis confirmed monophyly of certain case groups, but not of others. Host-plant preferences were also examined. The pattern of host plant use reflects more closely preference for certain plant tissues (seeds versus leaves) and growth forms (herbaceous versus woody) with exploitation of different plant taxa, rather than preference for certain plant taxa with exploitation of different plant tissues. [source] Phylogeny of the Trilobite Subgenus Acanthopyge (Lobopyge)CLADISTICS, Issue 1 2001Malte C. Ebach Cladistic analysis of the trilobite subgenus Acanthopyge (Lobopyge) has not been previously attempted, apart from an inferred phylogeny of the Lichida by Thomas and Holloway (1988, Philos. Trans. R. Soc. London B Biol. Sci. 321, 179,262). Results of two separate analyses with variable taxonomic sampling show a possible cosmopolitan affinity for Australian Devonian species of A. (Lobopyge) and corroborate the placement of A. (Lobopyge) rohri in A. (Lobopyge). Benelopyge is a junior subjective synonym of A. (Lobopyge). [source] Anatomy and systematics of the minute syrnolopsine gastropods from Lake Tanganyika (Caenogastropoda, Cerithioidea, Paludomidae)ACTA ZOOLOGICA, Issue 4 2008Ellen E. Strong Abstract The minute syrnolopsine gastropods endemic to Lake Tanganyika have been allied to a number of freshwater, marine and terrestrial groups as a consequence of superficial conchological similarity. Although early anatomical studies confirmed the cerithioid organization of this clade, their close relationship to other lake species was not consistently recognized. In several recent cladistic analyses based on molecular data, the higher taxonomic placement and sister group relationships of syrnolopsines have been unstable. The present analysis confirms that syrnolopsines possess a spermatophore-forming organ , a synapomorphy of the Paludomidae , corroborating their placement in this family. Consistent with the molecular data, syrnolopsine monophyly is supported by two characters that occur exclusively in this group (salivary gland ducts that bypass the nerve ring and a linear albumen gland). Several characters in Martelia tanganyicensis, the most diminutive syrnolopsine , are only evident in the smallest lake species thus far investigated (Bridouxia, Stormsia) namely reduction of ctenidial leaflets, sorting area, intestine length and number of statoconia. These features are interpreted as being correlated with reduction in size. Nevertheless, close examination reveals differences in detail that allow more refined hypotheses of homology and are consistent with their independent origin. [source] EXHAUSTION OF MORPHOLOGIC CHARACTER STATES AMONG FOSSIL TAXAEVOLUTION, Issue 2 2000Peter J. Wagner Abstract., Frequencies of new character state derivations are analyzed for 56 fossil taxa. The hypothesis that new character states are added continuously throughout clade history can be rejected for 48 of theses clades. Two alternative explanations are considered: finite states and ordered states. The former hypothesizes a limited number of states available to each character and is tested using rarefaction equations. The latter hypothesizes that there are limited possible descendant morphologies for any state, even if the character has infinite potential states. This is tested using power functions. The finite states hypothesis explains states: steps relationships significantly better than does the ordered states hypothesis in 14 cases; the converse is true for 14 other cases. Under either hypothesis, trilobite clades show appreciably more homoplasy after the same numbers of steps than do molluscs, echinoderms, or vertebrates. The prevalence of the exhaustion pattern among different taxonomic groups implies that worker biases are not to blame and instead implicates biological explanations such as intrinsic constraints or persistent selective trends. Regardless of the source of increased homoplasy, clades appear to exhaust their available character spaces. Nearly all examined taxa show significant increases in proportions of incompatible character pairs (i.e., those necessarily implying homoplasy) as progressively younger taxa are added to character matrices. Thus, a deterioration of hierarchical structure accompanies character state exhaustion. Exhaustion has several implications: (1) the basic premise of cladistic analyses (i.e., that maximum congruence reflects homology rather than homoplasy) becomes increasingly less sound as clades age; (2) sampling high proportions of taxa probably is needed for congruence to discern homoplasy from homology; (3) stratigraphic data might be necessary to discern congruent homoplasy from congruent homology; and (4) in many cases, character states appear to have evolved in ordered patterns. [source] Evolutionary-based grouping of haplotypes in association analysisGENETIC EPIDEMIOLOGY, Issue 3 2005Jung-Ying Tzeng Abstract Haplotypes incorporate more information about the underlying polymorphisms than do genotypes for individual SNPs, and are considered as a more informative format of data in association analysis. To model haplotypes requires high degrees of freedom, which could decrease power and limit a model's capacity to incorporate other complex effects, such as gene-gene interactions. Even within haplotype blocks, high degrees of freedom are still a concern unless one chooses to discard rare haplotypes. To increase the efficiency and power of haplotype analysis, we adapt the evolutionary concepts of cladistic analyses and propose a grouping algorithm to cluster rare haplotypes to the corresponding ancestral haplotypes. The algorithm determines the cluster bases by preserving common haplotypes using a criterion built on the Shannon information content. Each haplotype is then assigned to its appropriate clusters probabilistically according to the cladistic relationship. Through this algorithm, we perform association analysis based on groups of haplotypes. Simulation results indicate power increases for performing tests on the haplotype clusters when compared to tests using original haplotypes or the truncated haplotype distribution. Genet. Epidemiol. © 2005 Wiley-Liss, Inc. [source] The role of character loss in phylogenetic reconstruction as exemplified for the AnnelidaJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2007C. Bleidorn Abstract Annelid relationships are controversial, and molecular and morphological analyses provide incongruent estimates. Character loss is identified as a major confounding factor for phylogenetic analyses based on morphological data. A direct approach and an indirect approach for the identification of character loss are discussed. Character loss can frequently be found within annelids and examples of the loss of typical annelid characters, like chaetae, nuchal organs, coelomic cavities and other features, are given. A loss of segmentation is suggested for Sipuncula and Echiura; both are supported as annelid ingroups in molecular phylogenetic analyses. Moreover, character loss can be caused by some modes of heterochronic evolution (paedomorphosis) and, as shown for orbiniid and arenicolid polychaetes, paedomorphic taxa might be misplaced in phylogenies derived from morphology. Different approaches for dealing with character loss in cladistic analyses are discussed. Application of asymmetrical character state transformation costs or usage of a dynamic homology framework represents promising approaches. Identifying character loss prior to a phylogenetic analysis will help to refine morphological data matrices and improve phylogenetic analyses of annelid relationships. Zusammenfassung Die Phylogenie der Annelida wird nach wie vor kontrovers diskutiert und morphologische und molekulare Analysen liefern hierbei unterschiedliche Ergebnisse. Merkmalsverluste können phylogenetische Analysen morphologischer Daten in die Irre führen. In der vorliegenden Arbeit werden ein direkter und ein indirekter Ansatz zur Erkennung von Merkmalsverlusten vorgestellt. Es wird gezeigt, dass Merkmalsverlust innerhalb der Anneliden häufig auftritt und das hiervon auch typische Annelidenmerkmale, wie z.B Borsten, Nuchalorgane oder Coelomräume betroffen seien können. Molekularphylogenetische Analysen unterstützen eine Stellung der Echiura und Sipuncula innerhalb der Anneliden und somit ist für diese Taxa ein Verlust der Segmentierung anzunehmen. Es wird demonstriert, dass Merkmalsverlust durch herterochrone Evolution verursacht werden kann. Am Beispiel von Orbiniiden und Arenicoliden wird gezeigt, wie paedomorphe Taxa in kladistischen Analysen morphologischer Daten falsch platziert werden. Verschiedene Ansätze zum Umgang mit Merkmalsverlust in morphologischen Datensätzen werden präsentiert und diskutiert. Hierbei stellen die Verwendung asymmetrischer Merkmalstransformationskosten oder die Verwendung dynamischer Homologiehypothesen aussichtsreiche Ansätze dar. Jedoch werden für alle Ansätze Phylogeniehypothesen benötigt, die in einer Analyse unabhängiger Daten (bspw. Moleküle) erstellt wurden, um Merkmalsverluste sicher zu identifizieren. [source] On the evolution and morphology of the rotiferan trophi, with a cladistic analysis of RotiferaJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2002M. V. SØrensen Abstract The phylogeny of Rotifera was examined in different computer-generated cladistic analyses, including Seisonidea, Bdelloidea, Flosculariacea, Collothecacea and all ploimids treated on family level. The analyses were based on a character matrix solely dealing with morphological characters, primarily based on the trophi morphology. Limnognathia maerski (Micrognathozoa), Rastrognathia macrostoma and Gnathostomula paradoxa (Gnathostomulida) were used as outgroups. The cladistic analysis performed by paup produced 288 most parsimonious trees. peewee analyses produced between 140 and 432 trees, depending on the concavity value. The monophyly of Eurotatoria, Monogononta and Ploima was confirmed in all obtained trees. All analyses suggested a division of Ploima into major clades. One clade corresponded to Transversiramida while the other contained all other ploimid taxa and recognized Antrorsiramida as a monophylum. Based on the obtained results a scenario for the trophi evolution is proposed. The analyses suggested that the presence of an incus is synapomorphic for Gnathifera while mallei are synapomorphic for Micrognathozoa and Rotifera. The ancestral rotifer trophi probably resembled those in Harringia (Asplanchnidae). Zusammenfassung Die Phylogenie der Rotatorien wurde mit verschiedenen kladistischen Computeranalysen, unter Einbezug der Seisonidea, Bdelloidea, Flosculariacea, Collothecacea und aller Taxa von Ploima auf Familienebene, untersucht. Die Analyse basierte auf einer Mekmalsmatrix, die nur morphologische Merkmale, vorwiegend aus der Morphologie der Kiefer, enthielt. Limnognathia maerski (Micrognathozoa), Rastrognathia macrostoma und Gnathostomula paradoxa (Gnathostomulida) wurden als Außengruppe benutzt. Die mit paup durchgeführte Analyse ergab 288 ,,sparsamste'' Kladogramme. PeeWee Analysen produzierten in Abhängigkeit vom Konkavitäts-Wert 140 bzw. 432 Bäume. Die Monophylie der Eurotatoria, Monogononta und Ploima wurde in allen Kladogrammen bestätigt. Alle Analysen schlugen auch eine Teilung von Ploima in zwei große Kladen vor. Eine der Kladen entspricht den Transversiramida, die andere enthält alle anderen Ploima-Taxa und weist Antrorsiramida als Monophylum aus. Gestützt auf die gefundenen Ergebnisse wird ein Szenarium für die Evolution der Kiefer vorgeschlagen. Die Analysen lassen vermuten, daß der Besitz eines Incus eine Synapomorphie der Gnathifera ist, während der eines Malleus eine Synapomorphie der Mikrognathozoa und derRotifera darstellt. Die ursprünglichen Kiefer waren vermutlich dem von Harringia (Asplanchnidae) ähnlich. [source] Structures in the fundamental plane of early-type galaxiesMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2010D. Fraix-Burnet ABSTRACT The fundamental plane of early-type galaxies is a rather tight three-parameter correlation discovered more than 20 yr ago. It has resisted both a global and precise physical interpretation despite a consequent number of works, observational, theoretical or using numerical simulations. It appears that its precise properties depend on the population of galaxies in study. Instead of selecting a priori these populations, we propose to objectively construct homologous populations from multivariate analyses. We have undertaken multivariate cluster and cladistic analyses of a sample of 56 low-redshift galaxy clusters containing 699 early-type galaxies, using four parameters: effective radius, velocity dispersion, surface brightness averaged over effective radius and Mg2 index. All our analyses are consistent with seven groups that define separate regions on the global fundamental plane, not across its thickness. In fact, each group shows its own fundamental plane, which is more loosely defined for less diversified groups. We conclude that the global fundamental plane is not a bent surface, but made of a collection of several groups characterizing several fundamental planes with different thicknesses and orientations in the parameter space. Our diversification scenario probably indicates that the level of diversity is linked to the number and the nature of transforming events and that the fundamental plane is the result of several transforming events. We also show that our classification, not the fundamental planes, is universal within our redshift range (0.007,0.053). We find that the three groups with the thinnest fundamental planes presumably formed through dissipative (wet) mergers. In one of them, this(ese) merger(s) must have been quite ancient because of the relatively low metallicity of its galaxies, Two of these groups have subsequently undergone dry mergers to increase their masses. In the k-space, the third one clearly occupies the region where bulges (of lenticular or spiral galaxies) lie and might also have formed through minor mergers and accretions. The two least diversified groups probably did not form by major mergers and must have been strongly affected by interactions, some of the gas in the objects of one of these groups having possibly been swept out. The interpretation, based on specific assembly histories of galaxies of our seven groups, shows that they are truly homologous. They were obtained directly from several observables, thus independently of any a priori classification. The diversification scenario relating these groups does not depend on models or numerical simulations, but is objectively provided by the cladistic analysis. Consequently, our classification is more easily compared to models and numerical simulations, and our work can be readily repeated with additional observables. [source] Molecular Phylogeny of Caryophyllidae s.l. Based on MatK Sequences with Special Emphasis on Carnivorous TaxaPLANT BIOLOGY, Issue 2 2000H. Meimberg Abstract: Despite intensive morphological, chemical and cladistic studies on Caryophyllidae, the circumscription of this subclass and the interfamilial relationships are still under discussion. Using comparative sequencing of the chloroplast matK gene, hypotheses of relationships between the carnivorous Droseraceae, Nepenthaceae and Dioncophyllaceae and ten other families of the Caryophyllidae s.l. were tested and compared with previously published cladograms based on rbcL, 18S rDNA and ORF2280 sequences. Parsimony analyses indicate two well-differentiated clades. One strongly supported clade comprises the carnivorous families Droseraceae and Nepenthaceae, along with its close relatives Dioncophyllaceae and Ancistrocladaceae. The second clade is restricted to the Polygonaceae, Plumbaginaceae, Tamaricaceae and Frankeniaceae. The Simmondsiaceae are more closely related to Caryophyllales and are at the base of the remaining taxa. Results of this analysis suggest that carnivory within Caryophyllidae s.l. has a monophyletic origin and, with the exception of Triphyophyllum, this syndrome was lost in the taxa of Dioncophyllaceae and Ancistrocladaceae. The exclusion of Drosophyllum from Droseraceae suggests no close relationship with this family. Finally, the data support a sister group relationship between the Plumbaginaceae and Polygonaceae and the Frankeniaceae and Tamaricaceae. An extensive survey of the rpl2 intron via PCR amplification indicates that the intron is absent from chloroplast genomes of Droseraceae and all taxa of Caryophyllales, but is present in Drosophyllum. Consequently, there is evidence for a multiple loss of the intron and strong support that Drosophyllum has affinities outside the Droseraceae. Our sequence data corroborate many aspects of recent cladistic analyses based predominantly on rbcL sequences. This study shows that matK sequences are useful for'phylogenetic inference among closely related members of Caryophyllidae. [source] Are behavioral differences among wild chimpanzee communities genetic or cultural?AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2010An assessment using tool-use data, phylogenetic methods Abstract Over the last 30 years it has become increasingly apparent that there are many behavioral differences among wild communities of Pan troglodytes. Some researchers argue these differences are a consequence of the behaviors being socially learned, and thus may be considered cultural. Others contend that the available evidence is too weak to discount the alternative possibility that the behaviors are genetically determined. Previous phylogenetic analyses of chimpanzee behavior have not supported the predictions of the genetic hypothesis. However, the results of these studies are potentially problematic because the behavioral sample employed did not include communities from central Africa. Here, we present the results of a study designed to address this shortcoming. We carried out cladistic analyses of presence/absence data pertaining to 19 tool-use behaviors in 10 different P. troglodytes communities plus an outgroup (P. paniscus). Genetic data indicate that chimpanzee communities in West Africa are well differentiated from those in eastern and central Africa, while the latter are not reciprocally monophyletic. Thus, we predicted that if the genetic hypothesis is correct, the tool-use data should mirror the genetic data in terms of structure. The three measures of phylogenetic structure we employed (the Retention Index, the bootstrap, and the Permutation Tail Probability Test) did not support the genetic hypothesis. They were all lower when all 10 communities were included than when the three western African communities are excluded. Hence, our study refutes the genetic hypothesis and provides further evidence that patterns of behavior in chimpanzees are the product of social learning and therefore meet the main condition for culture. Am J Phys Anthropol, 2010. © 2010 Wiley-Liss, Inc. [source] Taxon combinations, parsimony analysis (PAUP*), and the taxonomy of the yellow-tailed woolly monkey, Lagothrix flavicaudaAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2008Luke J. Matthews Abstract The classifications of primates, in general, and platyrrhine primates, in particular, have been greatly revised subsequent to the rationale for taxonomic decisions shifting from one rooted in the biological species concept to one rooted solely in phylogenetic affiliations. Given the phylogenetic justification provided for revised taxonomies, the scientific validity of taxonomic distinctions can be rightly judged by the robusticity of the phylogenetic results supporting them. In this study, we empirically investigated taxonomic-sampling effects on a cladogram previously inferred from craniodental data for the woolly monkeys (Lagothrix). We conducted the study primarily through much greater sampling of species-level taxa (OTUs) after improving some character codings and under a variety of outgroup choices. The results indicate that alternative selections of species subsets from within genera produce various tree topologies. These results stand even after adjusting the character set and considering the potential role of interobserver disagreement. We conclude that specific taxon combinations, in this case, generic or species pairings, of the primary study group has a biasing effect in parsimony analysis, and that the cladistic rationale for resurrecting the Oreonax generic distinction for the yellow-tailed woolly monkey (Lagothrix flavicauda) is based on an artifact of idiosyncratic sampling within the study group below the genus level. Some recommendations to minimize the problem, which is prevalent in all cladistic analyses, are proposed. Am J Phys Anthropol, 2008. © 2008 Wiley-Liss, Inc. [source] | ||||||||||||||||||||||||||||||||||||||||