Showing papers in "Molecular Phylogenetics and Evolution in 2013"

TL;DR: The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences and it is shown that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality.

TL;DR: In this article, the authors outline some of the major obstacles specific to the application of NGS to phylogeography and phylogenetics, including the focus on non-model organisms, the necessity of obtaining orthologous loci in a cost-effective manner, and the predominate use of gene trees in these fields.

TL;DR: The accuracy of phylogenetic inference may be substantially improved by selecting genes that evolve slowly across the Metazoa and applying more realistic substitution models, as well as modifying gene sampling and the taxonomic composition of the outgroup.

TL;DR: This review summarises and discusses the general aspects of mitochondrial transcription and replication with respect to control regions as well as several proposed models of gene rearrangements for metazoan mitochondrial genomes.

TL;DR: This hypothesis represents a starting point for more detailed, comprehensive phylogenetic reconstructions in the future, and highlights the synergistic interaction between modern and traditional approaches that ultimately must be exploited to provide a rich understanding of evolutionary history across the entire tree of Life.

TL;DR: The most comprehensive analysis of bilaterian relationships based on mitochondrial genome data is presented, which failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa.

TL;DR: This study is the first to include both multiple nuclear and mitochondrial genes to reconstruct a comprehensive multilocus phylogeny of gobioids encompassing most major lineages representing the overall diversity of one of the most speciose vertebrate lineages.

TL;DR: The improvements are the introduction of alternative models, including one with non-correlated rates of molecular substitution ("relaxed" model), a completely reworked fitting algorithm that considers the high-dimensionality of the optimisation problem, and the development of a new information criterion for model selection in the presence of a penalised term.

TL;DR: The Bamboo Phylogeny Group presents the most complete phylogeny estimation to date of bamboo tribes and subtribes using 6.7 kb of coding and noncoding sequence data and 37 microstructural characters from the chloroplast genome.

TL;DR: Analysis of sexual system evolution in Fragaria provides evidence that the loss of male and female function can follow polyploidization, but does not seem to be associated with loss of self-incompatibility following genome doubling.

TL;DR: A novel generic and suprageneric classification is proposed including a (re-)diagnosis of 20 haplotilapiine cichlid genera and nine tribes based on extensive morphological evidence and molecular phylogenetic evidence.

TL;DR: Both parsimony (DIVA) and likelihood (Lagrange) methods for reconstructing ancestral ranges indicate that the radiation of Sturnira is rooted in the Andes; all three basal lineages have strictly or mainly Andean distributions.

TL;DR: Ancestral area reconstructions based on the molecular phylogeny suggest that the eastern portion of the Asian continent was an important center of origin for the early diversification of all Myotis lineages, and involved relatively few subsequent transcontinental range expansions.

TL;DR: It is thought that the largely stable topology of the trees regardless of different types of analyses suggests that mitochondrial genomes show good potential to resolve the relationship within Decapoda.

TL;DR: Phylogenetic and comparative genomic analyses of the vertebrate globin gene superfamily have revealed numerous instances in which paralogous globins have convergently evolved similar expression patterns and/or similar functional specializations in different organismal lineages.

TL;DR: The large effective population sizes of spruces, and incomplete lineage sorting during speciation, mean that the interspecific relationships within each of the geographic clades require further studies, especially based on genomic information and population genetic data.

TL;DR: The results indicate that all three of the alignment strategies that were used resulted in phylogenies having similar signal levels, however, there was a slight advantage to using structural alignment for inferring family-level relationships.

TL;DR: These analyses resulted in discrepancies to the current phylogenetic hypotheses based on morphological and nuclear data, so it is highly recommend interpreting mt-genome based phylogenies with incomplete representation of major orders/taxa particularly for hexapods with cautions although the inferred relationships are highly supported.

TL;DR: Previous taxonomic and genomic sampling for Hydrophiini is extended using three mitochondrial fragments and five nuclear loci for multiple individuals of 39 species in 15 genera, and concatenated Bayesian and likelihood analyses, and a multilocus coalescent tree recovered concordant support for primary clades and several previously unresolved inter-specific groupings.

TL;DR: This study shows that molecular data derived from the symbiotic bacteria of the genus Buchnera can provide a more powerful tool than the aphid-derived sequences, and demonstrates that the symbiont-derived phylogenies support some previously questionable relationships and provide new insights into aphid phylogeny and evolution.

TL;DR: Parsimony, maximum likelihood and Bayesian analyses suggest that Pyronemataceae is paraphyletic due to the nesting of both Ascodesmidaceae and Glaziellaceae within the family, and advocate the exclusion of these four lineages in order to recognize a monophyletic Pyronmataceae.

TL;DR: A representative and dense sampling of molluscan subgroups may contribute to resolve contentious interclass relationships in the future, and is vital for exploring the evolution of especially diverse mitochondrial genomes in mollsuscs.

TL;DR: Results of analyses of ancestral area reconstructions suggest a distribution for the most recent common ancestor of Sigmodontinae in Central-South America and a South American distribution forThe most recentCommon ancestor of Oryzomyalia.

TL;DR: The number of unique taxon labels in the two databases with the number of currently recognized species for each animal phylum is contrasted, revealing an overall paucity of COI sequence data in the repositories and bear witness to the idleness towards numerous phyla, rendering current barcoding efforts either ineffective or inaccurate.

TL;DR: This study represents the first attempt to estimate the absolute timing of a complex behavioral trait in relation to a genome duplication event, and presents the first phylogenetic evidence indicating that anadromy evolved at least twice from freshwater salmonid ancestors.

TL;DR: These analyses tend to support the hypothesis that the Crinoidea group is a radiation from a small clade that passed through the Permian-Triassic extinction event rather than several lineages that survived.

TL;DR: Phylogenetic analysis of ITS/trnL-F data resulted in a monophyletic genus Crocus, probably monophyletsic sections Crocus and Nudiscapus, and inferred monophyly for eight of the 15 series of the genus.

TL;DR: Sri Lanka has one of the most phylogenetically diverse island snake faunas in the world, and more research is needed to characterize the island's biodiversity, with numerous undescribed species in multiple lineages.

TL;DR: The results clarify that some morphological characters have been overstated and others understated in previous classifications of the Urticaceae family, and provide a strong foundation for future studies on biogeography, character evolution, and circumscription of difficult genera.

TL;DR: A Bayesian approach to reconstruct ancestral states of selected morphological characters resulted in recognition of characters that support major clades within the genus and a revised interpretation of morphological evolution in Hypericum.