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Maximum Parsimony Analysis (maximum + parsimony_analysis)
Selected AbstractsEvolution of the second orangutan: phylogeny and biogeography of hominid originsJOURNAL OF BIOGEOGRAPHY, Issue 10 2009John R. Grehan Abstract Aim, To resolve the phylogeny of humans and their fossil relatives (collectively, hominids), orangutans (Pongo) and various Miocene great apes and to present a biogeographical model for their differentiation in space and time. Location, Africa, northern Mediterranean, Asia. Methods, Maximum parsimony analysis was used to assess phylogenetic relationships among living large-bodied hominoids (= humans, chimpanzees, bonobos, gorillas, orangutans), and various related African, Asian and European ape fossils. Biogeographical characteristics were analysed for vicariant replacement, main massings and nodes. A geomorphological correlation was identified for a clade we refer to as the ,dental hominoids', and this correlation was used to reconstruct their historical geography. Results, Our analyses support the following hypotheses: (1) the living large-bodied hominoids represent a monophyletic group comprising two sister clades: humans + orangutans, and chimpanzees (including bonobos) + gorillas (collectively, the African apes); and (2) the human,orangutan clade (dental hominoids) includes fossil hominids (Homo, australopiths, Orrorin) and the Miocene-age apes Hispanopithecus, Ouranopithecus, Ankarapithecus, Sivapithecus, Lufengpithecus, Khoratpithecus and Gigantopithecus (also Plio-Pleistocene of eastern Asia). We also demonstrate that the distributions of living and fossil genera are largely vicariant, with nodes of geographical overlap or proximity between Gigantopithecus and Sivapithecus in Central Asia, and between Pongo, Gigantopithecus, Lufengpithecus and Khoratpithecus in East Asia. The main massing is represented by five genera and eight species in East Asia. The dental hominoid track is spatially correlated with the East African Rift System (EARS) and the Tethys Orogenic Collage (TOC). Main conclusions, Humans and orangutans share a common ancestor that excludes the extant African apes. Molecular analyses are compromised by phenetic procedures such as alignment and are probably based on primitive retentions. We infer that the human,orangutan common ancestor had established a widespread distribution by at least 13 Ma. Vicariant differentiation resulted in the ancestors of hominids in East Africa and various primarily Miocene apes distributed between Spain and Southeast Asia (and possibly also parts of East Africa). The geographical disjunction between early hominids and Asian Pongo is attributed to local extinctions between Europe and Central Asia. The EARS and TOC correlations suggest that these geomorphological features mediated establishment of the ancestral range. [source] Population genetic studies of Alouatta caraya (Alouattinae, Primates): inferences on geographic distribution and ecologyAMERICAN JOURNAL OF PRIMATOLOGY, Issue 10 2007Fabrícia F. Do Nascimento Abstract Cytochrome b DNA sequence data (ca. 1,140,bp) of 44 Alouatta caraya, including 42 specimens from three localities of Brazil and two from Bolivia, were used for phylogenetic reconstructions and population studies. Seventeen haplotypes were identified, eight of which were present in more than one individual. Seven of these eight haplotypes were shared by individuals from a same locality and one by individuals from two localities. We found 26 variable sites along the entire gene, consisting of 18 transitions and eight transversions; most replacements occurring at the third codon position (65.39%) in contrast to first and second positions (26.92 and 7.69%, respectively). In the sample collected at Chapada dos Guimarães (Brazil), nucleotide and haplotype diversity estimates were ,=0.002325 and h=0.8772, respectively. Maximum parsimony analysis grouped all haplotypes in two clades, separating Bolivian haplotypes from Brazilian haplotypes, the grouping of which did not show a straightforward correspondence with geographic distribution. Median-joining and TCS network pointed to haplotypes 11 or 12 as the most likely ancestral ones. Mismatch distribution and the goodness-of-fit test (SSD estimate=0.0027; P=0.6999) indicated that the population from Chapada dos Guimarães experienced a demographic expansion, in agreement with the median-joining star-like pattern, although this finding could not be confirmed by Fu's Fs test. Am. J. Primatol. 69:1093,1104, 2007. © 2007 Wiley-Liss, Inc. [source] Phylogeny of Syllidae (Polychaeta) based on combined molecular analysis of nuclear and mitochondrial genesCLADISTICS, Issue 6 2007M. Teresa Aguado The phylogeny of Syllidae is assessed in a combined analysis of molecular data from nuclear 18S rDNA and mitochondrial 16S rDNA and cytochrome c oxidase subunit I. In total, 103 terminal taxa are examined: 88 syllids in the four classical subfamilies Eusyllinae, Exogoninae, Syllinae and Autolytinae, as well as 15 outgroup taxa from Phyllodocida and Eunicida. Maximum parsimony analysis of the combined data set indicates that Syllidae, as currently delineated, is monophyletic, though not with very high support values. Astreptosyllis Kudenov & Dorsey, 1982, Streptosyllis Webster & Benedict, 1884 and SyllidesÖrsted, 1845 comprise a monophyletic group well differentiated from the rest of the Syllidae. The subfamilies Autolytinae and Syllinae are monophyletic. Exogoninae is monophyletic, although not well supported, and Eusyllinae is clearly paraphyletic. Results corroborate previous studies about the evolution of reproductive modes in that epigamy is the plesiomorphic condition and schizogamy appeared independently in Autolytinae and Syllinae. © The Willi Hennig Society 2007. [source] MOLECULAR AND MORPHOLOGICAL DATA IDENTIFY A CRYPTIC SPECIES COMPLEX IN ENDOPHYTIC MEMBERS OF THE GENUS COLEOCHAETE BRÉB. (CHAROPHYTA: COLEOCHAETACEAE),JOURNAL OF PHYCOLOGY, Issue 6 2002Matthew T. Cimino The genus Coleochaete Bréb. is a relatively small group of freshwater microscopic green algae with about 15 recognized species. Although Coleochaete has long been considered to be a close relative of embryophytes, a comprehensive study of the genus has not been published since Pringsheim's 1860 monograph. As part of a systematic study of Coleochaete, we investigated four accessions of the genus that are morphologically similar to the endophytic species C. nitellarum Jost. Each of the four cultures was determined to be capable of endophytic growth in Nitella C. A. Agardh, a member of the closely related order Charales. Maximum likelihood and maximum parsimony analyses were performed on nucleotide data from the chloroplast genes atpB and rbcL that were sequenced from 16 members of the Coleochaetales and from other members of the Charophyceae, embryophytes, and outgroup taxa. These analyses indicate that the Coleochaetales are monophyletic and that the endophytic accessions are members of the scutata group of species. In addition, cell size and nucleotide data suggest that at least three different endophytic species may be represented. Herbivory, nutritional benefits, and substrate competition are three hypotheses that could explain the evolution and maintenance of the endophytic habit in Coleochaete. These data also imply that diversity in the genus may be markedly underestimated. [source] MONOPHYLY OF THE GENUS CLOSTERIUM AND THE ORDER DESMIDIALES (CHAROPHYCEAE, CHLOROPHYTA) INFERRED FROM NUCLEAR SMALL SUBUNIT rDNA DATAJOURNAL OF PHYCOLOGY, Issue 6 2001Takashi Denboh We newly sequenced the nuclear-encoded small subunit (SSU) rDNA coding region for 21 taxa of the genus Closterium. The new sequences were integrated into an alignment with 13 known sequences of conjugating green algae representing six traditional families (i.e. Zygnemataceae, Mesotaeniaceae, Gonatozygaceae, Peniaceae, Closteriaceae, and Desmidiaceae) and five known charophycean sequences as outgroups. Both maximum likelihood and maximum parsimony analyses supported with high bootstrap values one large clade containing all placoderm desmids (Desmidiales). All the Closterium taxa formed one clade with 100% bootstrap support, indicating their monophyly, but not paraphyly, as suggested earlier. As to the taxa within the genus Closterium, we found two clades of morphologically closely related taxa in both maximum likelihood and maximum parsimony trees. They corresponded to the C. calosporum species complex and the C. moniliferum-ehrenbergii species complex. It is of particular interest that the homothallic entity of C. moniliferum v. moniliferum was distinguished from and ancestral to all other entities of the C. moniliferum-ehrenbergii species complex. Superimposing all 50 charophycean sequences on the higher order SSU rRNA structure model of Closterium, we investigated degrees of nucleotide conservation at a given position in the nucleotide sequence. A characteristic "signature" structure to the genus Closterium was found as an additional helix at the tip of V1 region. In addition, eight base deletions at the tip of helix 10 were found to be characteristic of the C. calosporum species complex, C. gracile, C. incurvum, C. pleurodermatum, and C. pusillum v. maius. These taxa formed one clade with an 82% bootstrap value in maximum parsimony analysis. [source] A molecular phylogeny of the peacock-pheasants (Galliformes: Polyplectron spp.) indicates loss and reduction of ornamental traits and display behavioursBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2001REBECCA T. KIMBALL The South-east Asian pheasant genus Polyplectron is comprised of six or seven species which are characterized by ocelli (ornamental eye-spots) in all but one species, though the sizes and distribution of ocelli vary among species. All Polyplectron species have lateral displays, but species with ocelli also display frontally to females, with feathers held erect and spread to clearly display the ocelli. The two least ornamented Polyplectron species, one of which completely lacks ocelli, have been considered the primitive members of the genus, implying that ocelli are derived. We examined this hypothesis phylogenetically using complete mitochondrial cytochrome b and control region sequences, as well as sequences from intron G in the nuclear ovomucoid gene, and found that the two least ornamented species are in fact the most recently evolved. Thus, the absence and reduction of ocelli and other ornamental traits in Polyplectronare recent losses. The only variable that may correlate with the reduction in ornamentation is habitat, as the two less-ornamented species inhabit montane regions, while the ornamented species inhabit lowland regions. The implications of these findings are discussed in light of models of sexual selection. The phylogeny is not congruent with current geographical distributions, and there is little evidence that Pleistocene sea level changes promoted speciation in this genus. Maximum likelihood and maximum parsimony analyses of cytochrome b sequences suggest that the closest relatives of Polyplectron are probably the peafowl and the argus pheasants. [source] MONOPHYLY OF THE GENUS CLOSTERIUM AND THE ORDER DESMIDIALES (CHAROPHYCEAE, CHLOROPHYTA) INFERRED FROM NUCLEAR SMALL SUBUNIT rDNA DATAJOURNAL OF PHYCOLOGY, Issue 6 2001Takashi Denboh We newly sequenced the nuclear-encoded small subunit (SSU) rDNA coding region for 21 taxa of the genus Closterium. The new sequences were integrated into an alignment with 13 known sequences of conjugating green algae representing six traditional families (i.e. Zygnemataceae, Mesotaeniaceae, Gonatozygaceae, Peniaceae, Closteriaceae, and Desmidiaceae) and five known charophycean sequences as outgroups. Both maximum likelihood and maximum parsimony analyses supported with high bootstrap values one large clade containing all placoderm desmids (Desmidiales). All the Closterium taxa formed one clade with 100% bootstrap support, indicating their monophyly, but not paraphyly, as suggested earlier. As to the taxa within the genus Closterium, we found two clades of morphologically closely related taxa in both maximum likelihood and maximum parsimony trees. They corresponded to the C. calosporum species complex and the C. moniliferum-ehrenbergii species complex. It is of particular interest that the homothallic entity of C. moniliferum v. moniliferum was distinguished from and ancestral to all other entities of the C. moniliferum-ehrenbergii species complex. Superimposing all 50 charophycean sequences on the higher order SSU rRNA structure model of Closterium, we investigated degrees of nucleotide conservation at a given position in the nucleotide sequence. A characteristic "signature" structure to the genus Closterium was found as an additional helix at the tip of V1 region. In addition, eight base deletions at the tip of helix 10 were found to be characteristic of the C. calosporum species complex, C. gracile, C. incurvum, C. pleurodermatum, and C. pusillum v. maius. These taxa formed one clade with an 82% bootstrap value in maximum parsimony analysis. [source] Phylogeny of Dicranophoridae (Rotifera: Monogononta) , a maximum parsimony analysis based on morphological charactersJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 1 2009O. Riemann Abstract This study presents the first phylogenetic analysis of Dicranophoridae (Rotifera: Monogononta), a species rich rotifer family of about 230 species currently recognized. It is based on a maximum parsimony analysis including 77 selected ingroup and three outgroup taxa and a total of 59 phylogenetically informative morphological characters. Character coding is based on personal investigation of material collected by the authors and an extensive survey of the literature. Apart from covering general body organization, character coding primarily relies on scanning electron microscopic preparations of the mastax jaw elements. Our study suggests monophyly of Dicranophoridae with a clade of Dicranophorus and Dorria as the sister taxon of all other dicranophorid species. Monophyly of Encentrum, the most species rich genus within Dicranophoridae, cannot be demonstrated. Within Dicranophoridae our study identifies the monophyletic taxa Caudosubbasifenestrata, Intramalleata, Praeuncinata and Proventriculata, each based on unambiguous character transformations evolved in their stem lineages. However, resolution within Praeuncinata and Proventriculata is very limited. Although some terminal clades within Praeuncinata and Proventriculata are recognized, basal splits remain obscure. Probably, other characters such as DNA sequence data are needed to further our understanding of phylogenetic relationships within these poorly resolved taxa. Zusammenfassung Die hier vorgelegte Studie stellt die erste phylogenetische Analyse des Taxons Dicranophoridae (Rotifera: Monogononta) dar, einer artenreichen Familie der Rotiferen mit zurzeit etwa 230 validen Arten. Die resultierenden phylogenetischen Verwandtschaftsbeziehungen fußen auf einer Maximum Parsimonie Analyse mit 77 ausgewählten Vertretern der Innen, und 3 Vertretern der Außengruppe bei insgesamt 59 Parsimonie,informativen Merkmalen. Die Kodierung der Merkmale basiert einerseits auf Material, das von den Autoren selbst gesammelt und bestimmt wurde und andererseits auf einem ausgedehnten Studium der relevanten Literatur. Neben der Erfassung von Merkmalen zur allgemeinen Körperorganisation stützt sich die Merkmalskodierung vor allem auf rasterelektronenmikroskopische Präparationen der Hartelemente des Mastax. Das Ergebnis der Analyse stützt die Monophylie der Dicranophoridae. Innerhalb der Dicranophoridae stellt ein monophyletisches Taxon, das die Gattungen Dicranophorus und Dorria umfasst, die Schwestergruppe aller übrigen Dicranophoridae dar. Die bei weitem artenreichste Gattung Encentrum lässt sich nicht als Monophylum begründen. Als monophyletische Teilgruppen innerhalb der Dicranophoridae identifiziert unsere Analyse die Taxa Caudosubbasifenestrata, Intramalleata, Praeuncinata und Proventriculata, die jeweils durch mindestens eine unzweideutige Merkmalstransformation in ihren Stammlinien begründet werden. Innerhalb der Taxa Praeuncinata und Proventriculata bietet unsere Analyse nur sehr begrenzte Auflösung. Obgleich sich einzelne Teilgruppen über unzweideutige Merkmalstransformationen als Monophyla begründen lassen, fehlen Merkmale für die Auflösung der basalen Verzweigungen innerhalb der Praeuncinata und Proventriculata. Es ist zu erwarten, dass andere Merkmalssysteme, wie zum Beispiel DNA Sequenzdaten, bei der Aufklärung der Verwandtschaftsbeziehungen innerhalb dieser Teilgruppen Klärung erbringen. [source] A new root-knot nematode, Meloidogyne silvestris n. sp. (Nematoda: Meloidogynidae), parasitizing European holly in northern SpainPLANT PATHOLOGY, Issue 3 2009P. Castillo High infection rates of European holly (Ilex aquifolium) feeder roots by an unknown root-knot nematode were found in a holly forest at Arévalo de la Sierra (Soria province) in northern Spain. Holly trees infected by the root-knot nematode showed some decline and low growth. Infected feeder roots were distorted and showed numerous root galls of large (8,10 mm) to moderate (2,3 mm) size. Morphometry, esterase and malate dehydrogenase electrophoretic phenotypes and phylogenetic trees of sequences within the ribosomal DNA (rDNA) demonstrated that this nematode species differs clearly from other previously described root-knot nematodes. Studies of host-parasite relationships showed a typical susceptible reaction in naturally infected European holly plants, but did not reproduce on a number of cultivated plants, including tomato, grapevine, princess-tree and olive. The species is described here, illustrated and named as Meloidogyne silvestris n. sp. The new root-knot nematode can be morphologically distinguished from other Meloidogyne spp. by: (i) roundish perineal pattern, dorsal arch low, with fine, sinuous cuticle striae, lateral fields faintly visible; (ii) female excretory pore level with stylet knobs, or just anterior to them, EP/ST ratio about 0·8; (iii) second-stage juveniles with hemizonid located 1 to 2 annuli anterior to excretory pore and short, sub-digitate tail; and (iv) males with lateral fields composed of four incisures, with areolated outer bands. Phylogenetic trees derived from maximum parsimony analysis based on 18S, ITS1-5·8S-ITS2 and D2,D3 of 28S rDNA showed that M. silvestris n. sp. can be differentiated from all described root-knot nematode species, and it is clearly separated from other species with resemblance in morphology, such as M. ardenensis, M. dunensis and M. lusitanica. [source] | ||||||||||