41 research outputs found
Testing the relationship between morphological and molecular rates of change along phylogenies
No full textThe definitive version is available at www.blackwell-synergy.comMolecular evolution has been considered to be essentially a stochastic process, little influenced by the pace of phenotypic change. This assumption was challenged by a study that demonstrated an association between rates of morphological and molecular change estimated for "total-evidence" phylogenies, a finding that led some researchers to challenge molecular date estimates of major evolutionary radiations. Here we show that Omland's (1997) result is probably due to methodological bias, particularly phylogenetic nonindependence, rather than being indicative of an underlying evolutionary phenomenon. We apply three new methods specifically designed to overcome phylogenetic bias to 13 published phylogenetic datasets for vertebrate taxa, each of which includes both morphological characters and DNA sequence data. We find no evidence of an association between rates of molecular and morphological rates of change.Lindell Bromham, Megan Woolfit, Michael S. Y. Lee, Andrew Rambau
Parallel evolution of the make-accumulate-consume strategy in Saccharomyces and Dekkera yeasts
No full textSaccharomyces yeasts degrade sugars to two-carbon components, in particular ethanol, even in the presence of excess oxygen. This characteristic is called the Crabtree effect and is the background for the 'make-accumulate-consume' life strategy, which in natural habitats helps Saccharomyces yeasts to out-compete other microorganisms. A global promoter rewiring in the Saccharomyces cerevisiae lineage, which occurred around 100 mya, was one of the main molecular events providing the background for evolution of this strategy. Here we show that the Dekkera bruxellensis lineage, which separated from the Saccharomyces yeasts more than 200 mya, also efficiently makes, accumulates and consumes ethanol and acetic acid. Analysis of promoter sequences indicates that both lineages independently underwent a massive loss of a specific cis-regulatory element from dozens of genes associated with respiration, and we show that also in D. bruxellensis this promoter rewiring contributes to the observed Crabtree effect
Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant
No full textBackground: Invasive species pose a significant threat to global economies, agriculture and biodiversity. Despite progress towards understanding the ecological factors associated with plant invasions, limited genomic resources have made it difficult to elucidate the evolutionary and genetic factors responsible for invasiveness. This study presents the first expressed sequence tag (EST) collection for Senecio madagascariensis, a globally invasive plant species. Methods: We used pyrosequencing of one normalized and two subtractive libraries, derived from one native and one invasive population, to generate an EST collection. ESTs were assembled into contigs, annotated by BLAST comparison with the NCBI non-redundant protein database and assigned gene ontology (GO) terms from the Plant GO Slim ontologies. Key Results: Assembly of the 221 746 sequence reads resulted in 12 442 contigs. Over 50% (6183) of 12 442 contigs showed significant homology to proteins in the NCBI database, representing approx. 4800 independent transcripts. The molecular transducer GO term was significantly over-represented in the native (South African) subtractive library compared with the invasive (Australian) library. Based on NCBI BLAST hits and literature searches, 40% of the molecular transducer genes identified in the South African subtractive library are likely to be involved in response to biotic stimuli, such as fungal, bacterial and viral pathogens. Conclusions: This EST collection is the first representation of the S. madagascariensis transcriptome and provides an important resource for the discovery of candidate genes associated with plant invasiveness. The overrepresentation of molecular transducer genes associated with defence responses in the native subtractive library provides preliminary support for aspects of the enemy release and evolution of increased competitive ability hypotheses in this successful invasive. This study highlights the contribution of next-generation sequencing to better understanding the molecular mechanisms underlying ecological hypotheses that are important in successful plant invasions.Peter J. Prentis, Megan Woolfit, Skye R. Thomas-Hall, Daniel Ortiz-Barrientos, Ana Pavasovic, Andrew J. Lowe and Peer M. Schen
Explosive radiations and the reliability of molecular clocks: island endemic radiations as a test case
No full textCo-author is PhD studen
Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms
No full textCopyright: © 2015 Solà et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article.NHM Repositor
Purifying Selection in Deeply Conserved Human Enhancers Is More Consistent than in Coding Sequences
No full text(c) 2014 De Silva et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
A simple protocol to obtain highly pure Wolbachia endosymbiont DNA for genome sequencing
No full textMost genome sequencing projects using intracellular bacteria face difficulties in obtaining sufficient bacterial DNA free of host contamination. We have developed a simple and rapid protocol to isolate endosymbiont DNA virtually free from fly and mosquito host DNA. We purified DNA from six Wolbachia strains in preparation for genome sequencing using this method, and achieved up to 97% pure Wolbachia sequence, even after using frozen insects. This is a significant improvement for future Wolbachia and other endosymbiont genome projects
Median (with interquartile range) fold change in pathogen density variable hours post infection (hpi) in mosquitoes.
No full text<p>Five pairs of individuals were used for <i>E. carotovora</i> (A), <i>B. cepacia</i> (B), <i>S. typhimurium</i> (C) and <i>M. marinum</i> (D). (Mann-Whitney U-test; * P-value<0.05, ** P-value<0.01).</p
Median (with interquartile range) relative <i>Wolbachia</i> density after infection in mosquitoes.
No full text<p>Five pairs of individuals were used for <i>E. carotovora</i> (A), <i>B. cepacia</i> (B), <i>S. typhimurium</i> (C) and <i>M. marinum</i> (D). (Mann-Whitney U-test; * P-value<0.05, ** P-value<0.01).</p
