MODELTEST: testing the model of DNA substitution.
TL;DR: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
Abstract: Summary: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. Availability: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu.edu/zoology/crandall―lab/modeltest.html. Contact: dp47@email.byu.edu.
Citations
More filters
American Museum of Natural History1, Columbia University2, University of Hamburg3, Sao Paulo State University4, University of Richmond5, University of the Western Cape6, Natural History Museum7, University of Texas at Arlington8, Yahoo!9, Florida Fish and Wildlife Conservation Commission10, California Academy of Sciences11, University of Michigan12, National University of Colombia13, McGill University14
TL;DR: A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one, based on the largest phylogenetic analysis of living Amphibia so far accomplished, and many subsidiary taxa are demonstrated to be nonmonophyletic.
Abstract: The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit H1 (12S and 16S ribosomal RNA and tRNAValine genes, ≈ 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S (≈ 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons. The...
1,994 citations
17 Sep 2002
TL;DR: Neighbor-Net is presented, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei and can quickly produce detailed and informative networks for several hundred taxa.
Abstract: We introduce NeighborNet, a network construction and data representation method that combines aspects of the neighbor joining (NJ) and SplitsTree. Like NJ, NeighborNet uses agglomeration: taxa are combined into progressively larger and larger overlapping clusters. Like SPLITSTREE, NeighborNet constructs networks rather than trees, and so can be used to represent multiple phylogenetic hypotheses simultaneously, or to detect complex evolutionary processes like recombination, lateral transfer and hybridization. NeighborNet tends to produce networks that are substantially more resolved than those made with SPLITSTREE. The method is efficient (O(n3) time) and is well suited for the preliminary analyses of complex phylogenetic data. We report results of three case studies: one based on mitochondrial gene order data from early branching eukaryotes, another based on nuclear sequence data from New Zealand alpine buttercups (Ranunculi), and a third on poorly corrected synthetic data.
1,846 citations
Cites methods from "MODELTEST: testing the model of DNA..."
...Modeltest: testing the model of DNA substitution....
[...]
...We first estimated evolutionary distances using maximum likelihood, with parameters determined using Modeltest (Posada and Crandall 1998)....
[...]
TL;DR: The evolution of virulence is linked to bacterial sex because rates of evolution have accelerated in pathogenic lineages, culminating in highly virulent organisms whose genomic contents are altered frequently by increased rates of homologous recombination.
Abstract: Summary Pathogenic Escherichia coli cause over 160 million cases of dysentery and one million deaths per year, whereas non-pathogenic E. coli constitute part of the normal intestinal flora of healthy mammals and birds. The evolutionary pathways underlying this dichotomy in bacterial lifestyle were investigated by multilocus sequence typing of a global collection of isolates. Specific pathogen types (enterohaemorrhagic E. coli , enteropathogenic E. coli , enteroinvasive E. coli , K1 and Shigella ) have arisen independently and repeat- edly in several lineages, whereas other lineages con- tain only few pathogens. Rates of evolution have accelerated in pathogenic lineages, culminating in highly virulent organisms whose genomic contents are altered frequently by increased rates of homolo- gous recombination; thus, the evolution of virulence is linked to bacterial sex. This long-term pattern of evolution was observed in genes distributed through- out the genome, and thereby is the likely result of episodic selection for strains that can escape the host immune response.
1,773 citations
Cites methods from "MODELTEST: testing the model of DNA..."
...The best-fit model of DNA substitution and the parameter estimates used for tree reconstruction were chosen by performing hierarchical likelihood ratio tests that are implemented in PAUP* (Swofford, 2003) and MODELTEST 1.05 ( Posada and Crandall, 1998 )....
[...]
...The best-fit model of DNA substitution and the parameter estimates used for tree reconstruction were chosen by performing hierarchical likelihood ratio tests that are implemented in PAUP* (Swofford, 2003) and MODELTEST 1.05 (Posada and Crandall, 1998)....
[...]
Duke University1, Oregon State University2, Clark University3, Natural History Museum4, University of Minnesota5, Field Museum of Natural History6, Kaiserslautern University of Technology7, University of Arizona8, New York Botanical Garden9, University of Iowa10, Technische Universität Darmstadt11, University of Maine12, United States Department of Agriculture13, University of Georgia14, University of Alabama15, University of California, Berkeley16, University of Kansas17, Aberystwyth University18, West Virginia University19, Washington State University20, Harvard University21, University of North Carolina at Chapel Hill22, Centraalbureau voor Schimmelcultures23, University of Tennessee24, Okayama University25, University of Kassel26, Brandon University27, Pennsylvania State University28, Leibniz Association29, University of Hamburg30, Royal Botanic Garden Edinburgh31
TL;DR: It is indicated that there may have been at least four independent losses of the flagellum in the kingdom Fungi, and the enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.
Abstract: The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.
1,682 citations
References
More filters
TL;DR: In this article, a new estimate minimum information theoretical criterion estimate (MAICE) is introduced for the purpose of statistical identification, which is free from the ambiguities inherent in the application of conventional hypothesis testing procedure.
Abstract: The history of the development of statistical hypothesis testing in time series analysis is reviewed briefly and it is pointed out that the hypothesis testing procedure is not adequately defined as the procedure for statistical model identification. The classical maximum likelihood estimation procedure is reviewed and a new estimate minimum information theoretical criterion (AIC) estimate (MAICE) which is designed for the purpose of statistical identification is introduced. When there are several competing models the MAICE is defined by the model and the maximum likelihood estimates of the parameters which give the minimum of AIC defined by AIC = (-2)log-(maximum likelihood) + 2(number of independently adjusted parameters within the model). MAICE provides a versatile procedure for statistical model identification which is free from the ambiguities inherent in the application of conventional hypothesis testing procedure. The practical utility of MAICE in time series analysis is demonstrated with some numerical examples.
47,133 citations
TL;DR: Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
Abstract: Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or “transition” type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or “transversion” type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = — (1/2) ln {(1 — 2P — Q) }. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = — (1/2) ln (1 — 2P — Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
26,016 citations
01 Jan 1969
10,262 citations
TL;DR: A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed, and this dating may pose a problem for the widely believed hypothesis that the bipedal creatureAustralopithecus afarensis, which lived some 3.7 million years ago, was ancestral to man and evolved after the human-ape splitting.
Abstract: A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized least-squares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.3 +/- 11.7, 13.3 +/- 1.5, 10.9 +/- 1.2, 3.7 +/- 0.6, and 2.7 +/- 0.6 million years ago (where the second of each pair of numbers is the standard deviation) for the separation of mouse, gibbon, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the pipedal creature Australopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a proto-chimpanzee after the former had developed bipedalism.
8,124 citations