http://precedings.nature.com/tags/phylogeny Recently posted documents tagged with 'phylogeny' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3386/version/1 Abstract:Biochemical analysis of the cytosol fraction isolated from the ovotestis / spermatheca glands of marine mollusc Telescopium telescopium and it’s sperm microtubular structure revealed that relatively similar biomolecules like different enzymes, hormones, minerals and structures of the sperm are also exist in humans. Moreover, antiserum of the cytosol fraction was found to cross-react with the human sperm antigen indicated presence of a common sperm surface antigenicity between these two diversified species. These findings might support and / or hypothesize about the origin and diversification of the vertebrate molecules from its ancestral form (s) from the invertebrates, and basic physiological functions of these ancestral biomolecules including some of the cellular structures plausibly remain the same regardless their structural changes even after evolution. http://precedings.nature.com/documents/3386/version/1 Wed, 01 Jul 2009 19:19:27 UTC Natural Biomolecules from Marine Snail Telescopium telescopium and structure of its sperm: A Phylogenetic Study hdl:10101/npre.2009.3386.1 2009-07-01 Uttam Datta Nature Precedings 2009-07-01T19:19:27Z Manuscript Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3150.1 Complete functional annotation of genomes is a powerful tool for researchers; however, such annotation is a time-consuming task limited by the availability of experimental data. The function of genes for which there is no experimental data can often be predicted via comparison to related, annotated sequences of known function. We describe here the Reference Genome project, an effort from the Gene Ontology (GO) Consortium to fully annotate twelve genomes to rigorous standards: human, plus eleven organisms that are important models in biomedical research, including mouse, fly, zebrafish, yeast and E. coli. To achieve this, we examine existing experimentally based annotations in a phylogenetic context in order to infer the function(s) of ancestral proteins and propagate these annotations to their descendants. This endeavor faces many difficult challenges, such as: the determination and provision of reference protein sets for each genome; the identification of gene families for curation; the application of consistent best practices for annotation; the development of methodologies for evaluating progress towards our goal; and the development of software tools to support this effort. Annotated genomes are greatly valuable to the research community and will provide the basis for using sequence similarity to annotate further genomes. An overview of the project as well as links to all resources described below can be found at http://geneontology.org/GO.refgenome.shtmlThis work is supported by NHGRI grant #HG002273 (Gene Ontology Consortium) and NIGMS #GM081084-01A1 (Phylogenetic tree building and annotation software development). Pascale Gaudet for the Reference Genome Group of the Gene Ontology Consortium. The Reference Genome project is overseen by Pascale Gaudet (dictyBase), Rex Chisholm (dictyBase) and includes these representatives from the curatorial staff: Tanya Berardini (TAIR), Emily Dimmer (GOA), Stacia R. Engel (SGD), Petra Fey (dictyBase), David P. Hill (MGI), Doug Howe (ZFIN), Jim Hu (EcoliWiki), Rachael Huntley (GOA), Varsha K. Khodiyar (UCL), Ranjana Kishore (WormBase), Donghui Li (TAIR), Ruth C. Lovering (UCL), Fiona McCarthy (AgBase), Li Ni (MGI), Victoria Petri (RGD), Deborah A. Siegel (EcoliWiki), Susan Tweedie (FlyBase), Kimberly Van Auken (WormBase), and Valerie Wood (GeneDB)—as well as the following computational staff representatives: Siddhartha Basu (dictyBase), Seth Carbon (BBOP), Mary Dolan (MGI), and Christopher J. Mungall (BBOP)—those establishing the protein families to be annotated: Kara Dolinski (PPOD), Michael S. Livstone (PPOD), and Paul Thomas (PANTHER)—and, the four PIs of the GO Consortium: Michael Ashburner (FlyBase), Judith A. Blake (MGI), J. Michael Cherry (SGD), and Suzanna E. Lewis (BBOP). http://dx.doi.org/10.1038/npre.2009.3150.1 Thu, 23 Apr 2009 17:28:39 UTC The Gene Ontology’s Reference Genome Project: *A Unified Framework for Functional Annotation across Species doi:10.1038/npre.2009.3150.1 2009-04-23 Pascale Gaudet Nature Precedings 2009-04-23T17:28:39Z Presentation Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3066.1 Cyclamen (Myrsinaceae) occupy the Mediterranean region, with highest diversity in Greece and Turkey, with a few species endemic to islands. Cyclamen species have a phenological preference for dry summers and wet winters. A recent study developed models of the climatic niches of Cyclamen. These models were projected into future climate scenarios for 2050. The area of climatic suitability for every Cyclamen species is predicted to decrease. A limited dispersal capacity places them at high risk of extinction. Half of the species are threat ened with extinction due to their potential area loss, indicating that conservation and protection for these species has to be implemented by adding them to the red list. http://dx.doi.org/10.1038/npre.2009.3066.1 Wed, 15 Apr 2009 08:59:47 UTC Future Predictions of Cyclamen Distribution in the Mediterranean Region doi:10.1038/npre.2009.3066.1 2009-04-15 Claudia Ciotir Nature Precedings 2009-04-15T08:59:47Z Poster Ecology Plant Biology Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.2579.1 This paper describes my entry in the Elsevier Grand Challenge “Knowledge Enhancement in the Life Sciences” contest. The entry takes a collection of fulltext issues of Molecular Phylogenetics and Evolution as the starting point, then extracts citation links to both papers and data, such as Genbank sequences and specimens, together with geotagged localities, and builds a “web” of objects linked by typed relationships. Each object (such as a publication, a sequence, a specimen, a taxon name, etc.) is treated equally, so that you can take a publication and see what taxa it refers to, or take the taxon and find all the publications that refer to the taxon. Although the database has been seeded with some articles from Molecular Phylogenetics and Evolution, much of the data comes from GenBank, PubMed, and specimen databases. These are accessed through bioGUID, a tool I constructed to resolve globally unique identifiers and return associated metadata. http://dx.doi.org/10.1038/npre.2008.2579.1 Fri, 28 Nov 2008 16:52:15 UTC Visualising a scientific article doi:10.1038/npre.2008.2579.1 2008-11-28 Roderic Page Nature Precedings 2008-11-28T16:52:15Z Manuscript Ecology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.2217.1 The fact that all living organisms are related by common descent is one of the central principles of modern biology. Since the early 1990’s the amount of data available to evolutionary biologists has exploded, and Elsevier’s journal Molecular Phylogenetics and Evolution, has become the largest single publisher of evolutionary trees (phylogenies). These trees and their supporting data potentially form a tremendous resource for biologists, with applications in genomics, evolutionary biology, biodiversity, and public health. However, most published trees are not available in any public database, but instead languish as images, “locked up” in the pages of journals. A long term solution to this problem is to invert the relationship between journal and database, such that the database is the primary repository, and the journal article becomes effectively a “report” on that data, albeit a report that is citable, and thus has the same status as a scientific article. This vision is some way off being achieved. However, publishers could greatly enhance the scientific value of their digital content by expanding article metadata to include taxonomic names, shared digital identifiers, geographical coordinates, and data structures such as evolutionary trees. This metadata doesn’t require making the full text available, but could substantially improve the findability of that text. http://dx.doi.org/10.1038/npre.2008.2217.1 Fri, 22 Aug 2008 15:07:45 UTC Towards realising Darwin’s dream: setting the trees free doi:10.1038/npre.2008.2217.1 2008-08-22 Roderic Page Nature Precedings 2008-08-22T15:07:45Z Manuscript Ecology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.1597.2 The current classification of the chilean representatives of the passerine family Rhinocryptidae includes eight species. Three of them contain subspecies that don’t exhibit clear differences. Moreover, differences among two lineages of Scytalopus genera and two species of Pteroptochos are very scarce. We propose a new methodology based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds. According to our results, we postulate that there is not a cut criteria to establish differences among three sister lineages of current classification. This way the methodology developed by us does not allow to establish divergence for a given common ancestor. Our methodology allows to establish comparison among previously determined phylogenetic lineages. Our results show how when integrating behaviour and ecological terms as biological traits next to morphological characters of the plumage, it allows us to conclude that there is decrease of the distances among sister lineages in the cluster tree. http://dx.doi.org/10.1038/npre.2008.1597.2 Wed, 19 Mar 2008 18:01:22 UTC Speciation of chilean Rhinocryptidae (Avian) based on their behaviour doi:10.1038/npre.2008.1597.2 2008-03-19 Alejandro Correa Rueda Nature Precedings 2008-03-19T18:01:22Z Manuscript Ecology Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.1606.2 Eight species of Rhinocryptidae are recognized from Chile. Moreover, morphological, ecological and behavioral differences among two lineages of Scytalopus and two species of Pteroptochos are unclear. According to our results, there are no decisive criteria differentiating among subspecific sister taxa of Scelorchilus albicollis, S. rubecula and Pteroptochos megapodius. Here we discuss the speciation of the chilean Rhinocryptidae based in their behaviour. We propose a new methodology based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds. http://dx.doi.org/10.1038/npre.2008.1606.2 Thu, 06 Mar 2008 17:42:28 UTC Differences of morphological and ecological characters among lineages of Chilean Rhinocryptidae in relation an sister lineage of Furnariidae. doi:10.1038/npre.2008.1606.2 2008-03-06 Alejandro Correa Rueda Nature Precedings 2008-03-06T17:42:28Z Manuscript Ecology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.1606.1 Eight species of Rhinocryptidae are recognized from Chile. Moreover, morphological, ecological and behavioral differences among two lineages of Scytalopus and two species of Pteroptochos are unclear. According to our results, there are no decisive criteria differentiating among subspecific sister taxa of Scelorchilus albicollis, S. rubecula and Pteroptochos megapodius. Here we discuss the speciation of the chilean Rhinocryptidae based in their behaviour. We propose a new methodology based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds. http://dx.doi.org/10.1038/npre.2008.1606.1 Tue, 19 Feb 2008 16:47:25 UTC Differences of morphological and ecological characters among lineages of Chilean Rhinocryptidae in relation an sister lineage of Furnariidae. doi:10.1038/npre.2008.1606.1 2008-02-19 Alejandro Correa Rueda Nature Precedings 2008-02-19T16:47:25Z Manuscript Ecology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1597/version/1 The current classification of the chilean representatives of the passerine family Rhinocryptidae includes eight species. Three of them contain subspecies that don’t exhibit clear differences. Moreover, differences among two lineages of Scytalopus genera and two species of Pteroptochos are cryptic. We propose a new methodology based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds. According to our results, we postulate that there is not a cut criteria to establish differences among three sister lineages of current classification. This way the methodology developed by us does not allow to establish divergence for a given common ancestor. Our methodology allows to establish comparison among previously determined phylogenetic lineages. Our results show how when integrating behaviour and ecological terms as biological traits next to morphological characters of the plumage, it allows us to conclude that there is decrease of the distances among sister lineages in the cluster tree. http://precedings.nature.com/documents/1597/version/1 Fri, 15 Feb 2008 22:17:33 UTC Speciation of chilean Rhinocryptidae (Avian) based on their behaviour hdl:10101/npre.2008.1597.1 2008-02-15 Alejandro Correa Rueda Nature Precedings 2008-02-15T22:17:33Z Manuscript Ecology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.1028.1 This note outlines some of the key intellectual obstacles that stand in the way of creating a usable phylogenetic database. These challenges include the need to accommodate multiple taxonomic names and classifications, and the need for tools to query trees in biologically meaningful ways. Until these problems are addressed, and a taxonomically intelligent phylogenetic database created, much of our phylogenetic knowledge will languish in the pages of journals. http://dx.doi.org/10.1038/npre.2007.1028.1 Tue, 18 Sep 2007 11:42:40 UTC Towards a Taxonomically Intelligent Phylogenetic Database doi:10.1038/npre.2007.1028.1 2009-03-04 Roderic Page Nature Precedings 2007-09-18T11:42:40Z Manuscript Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/2.5/