Topic
Ancestral reconstruction
About: Ancestral reconstruction is a research topic. Over the lifetime, 177 publications have been published within this topic receiving 27389 citations. The topic is also known as: character mapping & character optimization.
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TL;DR: A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available that allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests.
Abstract: The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of the estimate of the tree.
13,111 citations
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TL;DR: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
Abstract: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).
10,773 citations
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TL;DR: A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given the phylogeny and sequences of the extant species, and the new likelihood-based method was found to be superior to the parsimony method.
Abstract: A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given the phylogeny and sequences of the extant species. A model of nucleotide or amino acid substitution was employed to analyze data of the present-day sequences, and maximum likelihood estimates of parameters such as branch lengths were used to compare the posterior probabilities of assignments of character states (nucleotides or amino acids) to interior nodes of the tree; the assignment having the highest probability was the best reconstruction at the site. The lysozyme c sequences of six mammals were analyzed by using the likelihood and parsimony methods. The new likelihood-based method was found to be superior to the parsimony method. The probability that the amino acids for all interior nodes at a site reconstructed by the new method are correct was calculated to be 0.91, 0.86, and 0.73 for all, variable, and parsimony-informative sites, respectively, whereas the corresponding probabilities for the parsimony method were 0.84, 0.76, and 0.51, respectively. The probability that an amino acid in an ancestral sequence is correctly reconstructed by the likelihood analysis ranged from 91.3 to 98.7% for the four ancestral sequences.
710 citations
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Oregon State University1, Yale University2, Duke University3, University of Tennessee4, Clark University5, Kaiserslautern University of Technology6, Centraalbureau voor Schimmelcultures7, University of Copenhagen8, University of Tabriz9, Harvard University10, University of Pretoria11, ATCC12, Louisiana State University13, University of Texas at Austin14, Aberystwyth University15, United States Department of Agriculture16, Field Museum of Natural History17, Pennsylvania State University18, University of California, Berkeley19, University of North Carolina at Chapel Hill20, Stellenbosch University21, Free University of Berlin22, Washington State University23, Brandon University24, Landcare Research25, University of Helsinki26, University of Giessen27, University of Nottingham28, Swedish Museum of Natural History29, Royal Botanic Garden Edinburgh30
TL;DR: A 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi, and a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions support a terrestrial, saprobic ecology as ancestral are presented.
Abstract: We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.
592 citations
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National Institutes of Health1, Kean University2, Murdoch University3, Agricultural Research Service4, University of Graz5, Hirosaki University6, Mae Fah Luang University7, Biotec8, University of North Carolina at Chapel Hill9, Uppsala University10, Masaryk University11, DePaul University12, Oregon State University13, Illinois Natural History Survey14, University of Illinois at Chicago15, University of Chicago16, University of Minnesota17, Universidade Nova de Lisboa18, Prince of Songkla University19, University of Hong Kong20, Blaise Pascal University21, University of Illinois at Urbana–Champaign22, Technical University of Madrid23, Tuscia University24, Tottori University25, University of Pretoria26, Stellenbosch University27
TL;DR: A genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.
507 citations