Showing papers in "Molecular Phylogenetics and Evolution in 2008"

TL;DR: This work recovered the first well resolved large phylogeny of Plasmodium and related haemosporidian parasites using sequence data for four genes from the parasites' three genomes by combining all data, correcting for variable rates of substitution by gene and site, and using both Bayesian and maximum parsimony analyses.

TL;DR: A plea for the use of vouchers in molecular phylogenetic studies is made and it is suggested that vouchers should be placed in the phylogenetic tree for the sake of clarity.

TL;DR: The results show that the mitochondrial, chloroplast and nuclear genomes of seed plant groups have different synonymous substitutions rates, that these rates are different in different seed plant group and that gymnosperms have smaller ratios than angiosperms.

TL;DR: The largest family of flowering plants Asteraceae (Compositae) is found to contain 12 major lineages rather than five as previously suggested, contradict earlier hypotheses that early divergences in the family took place on and spread from the Guayana Highlands and raise new hypotheses about how Asteraceae dispersed out of the continent of their origin.

TL;DR: A general methodology for identifying candidate single-copy NPCL from genomic databases, targeted for higher-level phylogenetics of squamate reptiles, which has developed over 25 novel NPCL, which span a variety of desirable evolutionary rates for phylogenetic analyses.

TL;DR: A fully resolved phylogenetic summary tree for the grass family at subfamily level is produced and the most likely relationships of all included tribes in the authors' analysis are indicated.

TL;DR: Bayesian molecular dating in conjunction with dispersal-vicariance analysis suggests an early Tertiaries origin in Asia for the crown group Viperidae, and rejects suggestions of a relatively recent, early to mid-Tertiary origin of the Caenophidia.

TL;DR: The results support recent taxonomic changes in finding the traditional genera Mertensiella, Euproctus, and Triturus to be non-monophyletic species assemblages and suggest that the initial diversification of extant salamandrids took place in Europe about 97 or 69Ma.

TL;DR: The concatenated data reconstruct the test phylogeny with high support in both Bayesian and parsimony analyses, indicating that combining data from multiple nuclear loci will be a fruitful approach for assembling the beetle tree of life.

TL;DR: The authors' results strongly supported monophyly of the Sahulian Old Endemic rodents and its sister relationship to the Philippine old endemics of the Chrotomys division, and support for the consensus topology increased with more (even conflicting) data.

TL;DR: The first application of two nuclear protein-coding genes, phosphoenolpyruvate carboxykinase and sodium-potassium ATPase alpha-subunit, to reconstruct the phylogeny of major infraorders within Decapoda is presented and it is proposed that nuclear Protein-Coding genes should constitute core markers for future phylogenetic studies of decapods, especially for higher systematics.

TL;DR: The findings suggest that the best phylogenetic inferences are made when all available nucleotide data from themtgenome are analyzed simultaneously, and that the mtgenome data can resolve over a wide time scale from the Permian to the Tertiary.

TL;DR: The new phylogenetic hypotheses provided here represent the currently best available tool for comparative species-level studies within Cetartiodactyla and are recommended awaiting a better supported phylogeny based on more character data to reconsider classification and taxonomy within this group.

TL;DR: The data support a traditional hypothesis of foraging behavior, in which the evolutionary transition from a one-piece type to a separate life type occurred through an intermediate behavioral form.

TL;DR: Two new genomic changes identified in the present study provide additional support of the monophyly of the IR-loss clade, and resolution of the pattern of the earliest-branching lineages in this clade.

TL;DR: Congruent lack of spatial population structure among all three species suggest that such patterns are not due to stochastic processes of DNA mutation and are most likely driven by ecological and environmental factors.

TL;DR: Phylogenetic analysis using up to 1325 base pairs of mitochondrial DNA from 179 specimens and 30 species of Chalcides, Sphenops, Eumeces, Scincopus and Scincus indicates thatSphenops arose twice independently within Chalcide, and is consequently synonymized with that genus.

TL;DR: Results support a plant-based ancestral nutritional mode for Hypocreales, which then diversified ecologically through a dynamic process of intra- and interkingdom host shifts involving fungal, higher plant and animal hosts and parallel diversification of all three insect pathogenic families during the Cretaceous, concurrent with the diversifying of insects and angiosperms.

TL;DR: Bayesian estimates of divergence and dispersal-vicariance analyses indicate that the broad-leaved and fine-leaves Loliinae likely originated in the Miocene in the panMediterranean-SW Asian region and then expanded towards C and E Asia from where they colonized the New World.

TL;DR: An 18S rRNA gene phylogeny based on 449 volvocalean sequences collected using exhaustive BLAST searches of the GenBank database revealed 21 strongly supported primary clades within phylogenetically redefined Volvocales.

TL;DR: Analysis of gene flow and divergence time estimates suggest that the endangered subspecies atlanticus (from northeastern Brazil) can be considered a full species under the general lineage species concept.

TL;DR: This work focuses on the performance of three methods of species tree inference, ESP-COAL, minimizing deep coalescence (MDC), and concatenation, when incomplete lineage sorting and gene flow jointly confound the relationship between gene and species trees.

TL;DR: For the first time, this study provides evidence of the existence of a refuge area in Eastern China on the West Tianmu Mountains and hypothesize that this evidence supports that as a long-lived dioecious plant, G. biloba displays high levels of intra-populational genetic diversity that have been maintained in most populations, regardless if they are native or reforested stands.

TL;DR: This work represents a more extensive attempt to resolve the microgastroid relationships, using seven genes (16S rRNA, cytochrome oxidase I (CO1), 28S r RNA, arginine kinase (ArgK), long wavelength rhodopsin (Ops), elongation factor 1 alpha (EF1a) and wingless) and a greater taxonomic representation.

TL;DR: A relaxed clock relying on uncorrelated rates suggests that the complicated divergent evolution of Magnolioideae began around the early Eocene (54.57mya), concordant with paleoclimatic and fossil evidence.

TL;DR: The results reject many of the underlying hypotheses about character evolution in the Cirripedia Thoracica, stimulate a variety of new thoughts on thoracican radiation, and suggest the need for a major rearrangement in Thoracican classification based on estimated phylogenetic relationships.

TL;DR: In this article, the nose-horned viper (Vipera ammodytes) was reconstructed for a total of 59 specimens using sequences from three mitochondrial regions (16S and cytochrome b genes, and control region, totalling 2308 bp).

TL;DR: An analysis of mitochondrial DNA sequence variation in 172 three-spined sticklebacks sampled across the European distribution range revealed three major evolutionary lineages occupying relatively large and separate geographic areas, suggesting a recent population expansions to the formerly glaciated marine and freshwater environments.

TL;DR: To address biogeographic questions on the origin of the genus, both New and Old World species were included in these analyses, and the results suggest that Pheidole is New World in origin with a possible single introduction into the Old World.

TL;DR: Computer simulation shows the fact that the RLNJ method can improve the possibility of recovering correct topology significantly by affording more than one topology, and the proportion of correct topologies (P(C)) will increase as the number of different topologies decreases and as theportion of "most frequent topology" increases.