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Parsimony Methods (parsimony + methods)

Distribution by Scientific Domains

Life Sciences	75%

Selected Abstracts

Phylogenetic trends in the abundance and distribution of pit organs of elasmobranchs

ACTA ZOOLOGICA, Issue 4 2004
M. B. Peach
Abstract Pit organs (free neuromasts of the mechanosensory lateral line system) are distributed over the skin of elasmobranchs. To investigate phylogenetic trends in the distribution and abundance of pit organs, 12 relevant morphological characters were added to an existing matrix of morphological data (plus two additional end terminals), which was then re-analysed using cladistic parsimony methods (paup* 4.0b10). Character transformations were traced onto the most parsimonious phylogenetic trees. The results suggest the following interpretations. First, the distinctive overlapping denticles covering the pit organs in many sharks are a derived feature; plesiomorphic elasmobranchs have pit organs in open slits, with widely spaced accessory denticles. Second, the number of pit organs on the ventral surface of rays has been reduced during evolution, and third, spiracular pit organs have changed position or have been lost on several occasions in elasmobranch evolution. The concentrated-changes test in macclade (version 4.05) was used to investigate the association between a pelagic lifestyle and loss of spiracular pit organs (the only character transformation that occurred more than once within pelagic taxa). Depending on the choice of tree, the association was either nonsignificant at P = 0.06 or significant at P < 0.05. Future studies, using species within more restricted elasmobranch clades, are needed to resolve this issue. [source]

Molecular phylogeny of Turkish Trachurus species (Perciformes: Carangidae) inferred from mitochondrial DNA analyses

JOURNAL OF FISH BIOLOGY, Issue 5 2008
Y. Bektas
Genetic variation among three species of Trachurus (T. trachurus, T. mediterraneus and T. picturatus) from Turkey was investigated by phylogenetic analysis of the entire mtDNA control region (CR) (862 bp, n = 182) and partial cytochrome (cyt) b (239 bp, n = 174) sequences. Individuals were collected at nine stations in four geographic locations: North-eastern Mediterranean Sea, Aegean Sea, Sea of Marmara and Black Sea. Polymerase chain reaction-direct sequencing of the CR and the partial cyt b genes produced 28 and 131 distinct haplotypes, respectively. Maximum likelihood, neighbour-joining and maximum parsimony methods produced similar tree topologies. The results of both CR and cyt b sequence analyses revealed the existence of several species-specific nucleotide sites that can be used to discriminate between the three species. Genetic distances indicated that T. mediterraneus and T. picturatus are more closely related to each other than either is to T. trachurus. Inter-nucleotide and intra-nucleotide diversities of T. picturatus were larger than those of T. mediterraneus and T. trachurus. There was no evidence of a geographical difference in haplotype frequencies of these two mtDNA regions to be clustered. [source]

PHYLOGENY OF AULACOSEIRA (BACILLARIOPHYTA) BASED ON MOLECULES AND MORPHOLOGY,

JOURNAL OF PHYCOLOGY, Issue 4 2004
Stacy M. Edgar
The phylogeny of 67 populations representing 45 species of Aulacoseira Thwaites was estimated by maximum parsimony methods using a combination of nucleotide sequence data and qualitative and quantitative morphological characteristics of the silica cell wall gathered primarily from original observation by LM and SEM. A new type of character using continuous quantitative variables that describe the ontogenetic-allometric trajectories of cell wall characteristics over the life cycle (size range) of diatoms is introduced. In addition to the 45 Aulacoseira species, the phylogeny also incorporated one Miosira Krammer, Lange-Bertalot, and Schiller species and two outgroup species (Melosira varians Agardh and Stephanopyxis nipponica Gran & Yendo). Fifteen species, represented by 24 populations, also contained molecular data from the nuclear genome (18S rDNA), and 11 of these species (18 populations) contained data from the chloroplast genome (rbcL) as well, which were sequenced or downloaded from GenBank. The phylogeny of Aulacoseira is composed of five major clades: 1) an A. crenulata (Ehrenburg) Thwaites and A. italica (Ehrenburg) Simonsen clade, which is the most basal; 2) an A. granulata (Ehrenburg) Simonsen complex clade; 3) an A. ambigua (Grunow) Simonsen clade; 4) an A. subarctica (O. Müller) Haworth and A. distans (Ehrenburg) Simonsen clade; and 5) an A. islandica (O. Müller) Simonsen clade that also contained endemic species from Lake Baikal, Siberia and many extinct Aulacoseira taxa. Monophyly of Aulacoseira can only be achieved if Miosira is no longer given separate generic status. [source]

Phylogeny, biogeography and classification of the snake superfamily Elapoidea: a rapid radiation in the late Eocene

CLADISTICS, Issue 1 2009
Christopher M. R. Kelly
The snake superfamily Elapoidea presents one of the most intransigent problems in systematics of the Caenophidia. Its monophyly is undisputed and several cohesive constituent lineages have been identified (including the diverse and clinically important family Elapidae), but its basal phylogenetic structure is obscure. We investigate phylogenetic relationships and spatial and temporal history of the Elapoidea using 94 caenophidian species and approximately 2300,4300 bases of DNA sequence from one nuclear and four mitochondrial genes. Phylogenetic reconstruction was conducted in a parametric framework using complex models of sequence evolution. We employed Bayesian relaxed clocks and Penalized Likelihood with rate smoothing to date the phylogeny, in conjunction with seven fossil calibration constraints. Elapoid biogeography was investigated using maximum likelihood and maximum parsimony methods. Resolution was poor for early relationships in the Elapoidea and in Elapidae and our results imply rapid basal diversification in both clades, in the late Eocene of Africa (Elapoidea) and the mid-Oligocene of the Oriental region (Elapidae). We identify the major elapoid and elapid lineages, present a phylogenetic classification system for the superfamily (excluding Elapidae), and combine our phylogenetic, temporal and biogeographic results to provide an account of elapoid evolution in light of current palaeontological data and palaeogeographic models. © The Willi Hennig Society 2009. [source]