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
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TL;DR: Four new resupinate species, Perenniporia hainaniana, P. macropora, P., russeimarginata and P. subtephropora are described as new from southern China on the basis of morphological and molecular examination.
Abstract: Four new resupinate species, Perenniporia hainaniana, P. macropora, P. russeimarginata and P. subtephropora, are described as new from southern China on the basis of morphological and molecular examination. Perenniporia hainaniana is characterized by a perennial growth habit, cream to buff pore surface, a dimitic to trimitic hyphal system with amyloid skeletal hyphae and presence of dendrohyphidia. Perenniporia macropora is distinguished by an annual growth habit, large pores (2-3 per mm), a dimitic hyphal system with branched skeletal hyphae and presence of dendrohyphidia. Perenniporia russeimarginata differs from other species in the genus by a perennial growth habit, white to cream pore surface and reddish to reddish brown sterile margin. Perenniporia subtephropora is characterized by a perennial growth habit, cream-buff to grayish buff pore surface, hymenophoral trama becoming black in KOH and a dimitic hyphal system with branched skeletal hyphae. Phylogenetic analysis inferred from the ITS and LSU-rDNA regions revealed eight clades for Perenniporia sensu lato with the four new species recognized in Perenniporia sensu stricto. The Perenniporia ochroleuca group, P. vicina group, P. martia group, P. subacida, Microporellus, Perenniporiella and Abundisporus, formed monophyletic entities respectively, and they are not related to P. medulla-panis (generic type), which belongs to Perenniporia sensu stricto. Abundisporus, Microporellus and Perenniporiella were widely applied as generic names. Other generic or clade names, Hornodermoporus, Truncospora, Vanderbylia and the P. subacida clade, have not been widely applied, but they are valid higher level taxa containing former species of Perenniporia. A key to genera and clades allied with Perennioporia sensu stricto and a key to species of Perennioporia are provided.
27 citations
Cites methods from "MODELTEST: testing the model of DNA..."
...The bestfit model of nucleotide evolution was selected by hierarchical likelihood ratio tests (hLRT) in MrModeltest 2.3 (Posada and Crandall 1998, Nylander 2004)....
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TL;DR: This study presents phylogenetic analyses using 28S-only and combined 18S, 28S rDNA and mitochondrial cytochrome c oxidase subunit I (COI) data, and presents results for a detailed morphological study of the antennae and other cephalic structures of exemplar taxa.
Abstract: A significant diversity of terrestrial oniscidean isopods was recently discovered in the subterranean ‘calcrete islands’ of Western Australia, but the species and higher-level systematic status of much of the fauna are currently uncertain. Here we focus on one group of species that was initially assigned to the genus Trichorhina (Platyarthridae), based on several shared characters, and investigate the phylogenetic relationships of these species to 21 oniscidean genera, including 13 known families, using 18S rDNA sequence data. We then present phylogenetic analyses using 28S-only and combined 18S, 28S rDNA and mitochondrial cytochrome c oxidase subunit I (COI) data for a more restricted sampling of taxa, and present results for a detailed morphological study of the antennae and other cephalic structures of exemplar taxa. Bayesian and maximum likelihood analyses of the extended 18S-only, the 28S-only and multi-gene datasets provide strong evidence for a distinct well-supported monophyletic group comprising the new Western Australian and one South American taxon. This clade is unrelated to all included members of Platyarthridae, which appears to be polyphyletic, and it forms a distinct group relative to other oniscidean families. Given these findings and the results of the morphological study, a new southern hemisphere oniscidean family, Paraplatyarthridae Javidkar & King, fam. nov. is erected based on Paraplatyarthrus subterraneus Javidkar & King, gen. & sp. nov. (type genus and species), and several undescribed taxa which occur in the arid (terrestrial and subterranean) regions of Western Australia and subtropical South America. Paraplatyarthridae is distinguishable from all other oniscidian families on a combination of character states including, among others, the presence of fan-like scale setae on the dorsal body, and the ventral second antenna with leaf-like scale setae and a furrow containing elongated hair-like capillary setae that form part of a water conducting system unique within Oniscidea. This study has important implications for the higher-level classification of oniscidean crustaceans and points to the need for a more detailed molecular phylogeny that includes a comprehensive sampling of southern hemisphere taxa.
27 citations
Cites methods from "MODELTEST: testing the model of DNA..."
...In order to estimate the best nucleotide substitution model for the presumed data partitions, MrModeltest 2.3, which is a modified version of Modeltest 3.6 (Posada and Crandall 1998), under an Akaike information criterion (AIC) (Posada and Buckley 2004) framework, was used....
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...6 (Posada and Crandall 1998), under an Akaike information criterion (AIC) (Posada and Buckley 2004) framework, was used....
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Journal Article•
TL;DR: Haplotype analysis provided evidence that the hybrid of Halodule resulted from a single hybridisation event, followed by clonal dispersal to its present localities, and allopatric differentiation into both areas may have occurred during the early stages of the evolution of the genus.
Abstract: The tropical seagrass genus, Halodule, is distributed in warm to tropical areas throughout the world. We performed separate molecular phylogenetic analyses of Halodule based on both plastid and nuclear DNA sequences, followed by haplotype analysis, focusing on plants in the western Pacific area. One western tropical Atlantic species, H. wrightii s.l., and two western Pacific species, H. pinifolia and H. uninervis, were recognised and characterised by leaf morphology. Because samples from the western tropical Atlantic and the western Pacific were nested with each other, allopatric differentiation into both areas may have occurred during the early stages of the evolution of the genus. A hybrid of Halodule was detected at two nearby localities in Okinawa, Japan, together with its co-occurring maternal and paternal species, H. uninervis and H. pinifolia, respectively. Haplotype analysis provided evidence that the hybrid resulted from a single hybridisation event, followed by clonal dispersal to its present localities.
27 citations
Cites methods from "MODELTEST: testing the model of DNA..."
...Parameter values were estimated by a hierarchical likelihood ratio test in the program Modeltest 3.7 (Posada & Crandall 1998)....
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TL;DR: The possible origin of apomictic lineages as a result of independent transition episodes to apomixis from different sexual ancestors is discussed and time of divergence reflected the genetic differentiation within and among multiple ancestors and different possible routes to parthenogenesis.
27 citations
References
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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