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Substitution Rates (substitution + rate)
Selected AbstractsDOMESTICATION OF MAIZE, SORGHUM, AND SUGARCANE DID NOT DRIVE THE DIVERGENCE OF THEIR SMUT PATHOGENSEVOLUTION, Issue 2 2007Andrew B. Munkacsi We investigated two alternative hypotheses for the origin of crop pathogen species: that human-mediated agricultural practices drove the divergence of many crop plant pathogen species or that coevolutionary processes in natural populations of the crops' ancestors drove divergence of pathogen species. We distinguished between these two hypotheses by constructing a robust multigene phylogeny and estimating the dates of divergence among four, monophyletic species of smut fungi (Ustilago maydis, U. scitaminea, Sporisorium reilianum, S. sorghi) known to specifically infect maize, sorghum, sugarcane, and their wild ancestors. Without a fossil record for smut fungi, we calibrated the pathogen species' divergence times to their plant host divergence times. Specifically, a calibration date of 10,000 years was employed to test the hypothesis that the fungal species originated at the time of domestication of their current hosts and a calibration date of 50 million years was employed to test the hypothesis that the fungal species originated on wild ancestors of their domesticated hosts. Substitution rates at five protein coding genes were calculated and rates obtained for the 10,000 year calibration date were orders of magnitude faster than those commonly reported for eukaryotes, thus rejecting the hypothesis that these smut pathogen species diverged at the time of domestication. In contrast, substitution rates obtained for the 50 million year calibration were comparable to eukaryotic substitution rates. We used the 50 million year calibration to estimate divergence times of taxa in two datasets, one comprised solely the focal species and one comprised the focal species and additional related taxa. Both datasets indicate that all taxa diverged millions of years ago, strongly supporting the hypothesis that smut species diverged before the time of domestication and modern agriculture. Thus, smut species diverged in the ecological context of natural host plant and fungal populations. [source] CALIBRATING A MOLECULAR CLOCK FROM PHYLOGEOGRAPHIC DATA: MOMENTS AND LIKELIHOOD ESTIMATORSEVOLUTION, Issue 10 2003Michael J. Hickerson Abstract We present moments and likelihood methods that estimate a DNA substitution rate from a group of closely related sister species pairs separated at an assumed time, and we test these methods with simulations. The methods also estimate ancestral population size and can test whether there is a significant difference among the ancestral population sizes of the sister species pairs. Estimates presented in the literature often ignore the ancestral coalescent prior to speciation and therefore should be biased upward. The simulations show that both methods yield accurate estimates given sample sizes of five or more species pairs and that better likelihood estimates are obtained if there is no significant difference among ancestral population sizes. The model presented here indicates that the larger than expected variation found in multitaxa datasets can be explained by variation in the ancestral coalescence and the Poisson mutation process. In this context, observed variation can often be accounted for by variation in ancestral population sizes rather than invoking variation in other parameters, such as divergence time or mutation rate. The methods are applied to data from two groups of species pairs (sea urchins and Alpheus snapping shrimp) that are thought to have separated by the rise of Panama three million years ago. [source] The influence of strain of Holstein-Friesian dairy cow and pasture-based feeding system on grazing behaviour, intake and milk productionGRASS & FORAGE SCIENCE, Issue 1 2007S. McCarthy Abstract A comparative study of grazing behaviour, herbage intake and milk production of three strains of Holstein-Friesian dairy cow was conducted using three grass-based feeding systems over two years. The three strains of Holstein-Friesian cows were: high production North American (HP), high durability North American (HD) and New Zealand (NZ). The three grass-based feeding systems were: high grass allowance (MP), high concentrate (HC) and high stocking rate (HS). In each year seventy-two pluriparous cows, divided equally between strains of Holstein-Friesian and feeding systems were used. Strain of Holstein-Friesian cow and feeding system had significant effects on grazing behaviour, dry matter (DM) intake and milk production. The NZ strain had the longest grazing time while the HD strain had the shortest. The grazing time of cows in the HC system was shorter than those in both the HS and MP systems. There was a significant strain of Holstein-Friesian cow by feeding system interaction for DM intake of grass herbage and milk production. The NZ strain had the highest substitution rate with the HP strain having the lowest. Hence, response in milk production to concentrate was much greater with the HP than the NZ strain. Reduction in milk yield as a consequence of a higher stocking rate (MP vs. HS system) was, however, greater for the HP and HD strains compared with the NZ strain. The results suggest that differences in grazing behaviour are important in influencing DM intake and milk production. [source] Analysis of a Japanese Black Cattle-rearing system utilizing a bahiagrass (Paspalum notatum Flügge) pasture: 3.GRASSLAND SCIENCE, Issue 3 2006Intake from pasture Abstract A Japanese Black Cattle-rearing system utilizing a bahiagrass (Paspalum notatum Flügge) pasture in coastal Miyazaki, southern Japan, was analyzed in terms of intake from pasture. In a field approach, herbage intake by grazing cattle was measured for nine periods (1,5 days) during a grazing season (May,October) along with some other variables (e.g. air temperature, herbage mass, digestibility of grazed herbage), under varying levels of supplementary feeding. The intake from the pasture was most closely related to the intake of supplement, showing a negative linear response at a substitution rate of 0.736,0.750. The intake under no supplementation, i.e. a maximum intake from the pasture, was lower than the voluntary intake predicted with feeding standards. In a modeling approach, a semi-mechanistic model for predicting grazing intake was developed using information from the literature as well as the field data. The performance of the model was acceptable. The model showed similar substitution rates (0.64,0.69), and considerable intake restriction (nearly 30%) that is not attributable to limitations by herbage mass, herbage allowance, diet digestibility or air temperature. The results indicate that a low maximal intake by the animals due to low grazing motivation is a major characteristic of the system where supplementation is a usual management practice. [source] Heterotachy and Functional Shift in Protein EvolutionIUBMB LIFE, Issue 4-5 2003Hervé Philippe Abstract Study of structure/function relationships constitutes an important field of research, especially for modification of protein function and drug design. However, the fact that rational design (i.e. the modification of amino acid sequences by means of directed mutagenesis, based on knowledge of the three-dimensional structure) appears to be much less efficient than irrational design (i.e. random mutagenesis followed by in vitro selection) clearly indicates that we understand little about the relationships between primary sequence, three-dimensional structure and function. The use of evolutionary approaches and concepts will bring insights to this difficult question. The increasing availability of multigene family sequences that has resulted from genome projects has inspired the creation of novel in silico evolutionary methods to predict details of protein function in duplicated (paralogous) proteins. The underlying principle of all such approaches is to compare the evolutionary properties of homologous sequence positions in paralogs. It has been proposed that the positions that show switches in substitution rate over time--i.e., 'heterotachous sites'--are good indicators of functional divergence. However, it appears that heterotachy is a much more general process, since most variable sites of homologous proteins with no evidence of functional shift are heterotachous. Similarly, it appears that switches in substitution rate are as frequent when paralogous sequences are compared as when orthologous sequences are compared. Heterotachy, instead of being indicative of functional shift, may more generally reflect a less specific process related to the many intra- and inter-molecular interactions compatible with a range of more or less equally viable protein conformations. These interactions will lead to different constraints on the nature of the primary sequences, consistently with theories suggesting the non-independence of substitutions in proteins. However, a specific type of amino acid variation might constitute a good indicator of functional divergence: substitutions occurring at positions that are generally slowly evolving. Such substitutions at constrained sites are indeed much more frequent soon after gene duplication. The identification and analysis of these sites by complementing structural information with evolutionary data may represent a promising direction to future studies dealing with the functional characterization of an ever increasing number of multi-gene families identified by complete genome analysis. IUBMB Life, 55: 257-265, 2003 [source] PRIMER NOTE: Primers for amplifying the hypervariable, male-transmitted COII-COI junction region in amblemine freshwater mussels (Bivalvia: Unionoidea: Ambleminae)MOLECULAR ECOLOGY RESOURCES, Issue 3 2007JENNIFER M. WALKER Abstract Freshwater bivalves in the superfamily Unionoidea possess distinct male (M)- and female (F)-transmitted mitochondrial DNA (mtDNA). The former evolves independently of and at a significantly faster rate than the latter. Thus, population genetic and phylogenetic analyses of M sequences facilitate the generation of independent estimates of genetic variation and evolutionary relationships which are often more robust than those provided by analyses of F sequences alone. However, M mtDNA's rapid substitution rate often renders polymerase chain reaction (PCR) amplification difficult with ,universal' primers. Herein, we report on three pairs of PCR primers that consistently amplify the hypervariable M COII-COI gene junction region in 25 bivalve genera (Unionoidea: Ambleminae). [source] Hidden Mediterranean biodiversity: molecular evidence for a cryptic species complex within the reef building vermetid gastropod Dendropoma petraeum (Mollusca: Caenogastropoda)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009MARTA CALVO The reef building vermetid gastropod Dendropoma petraeum inhabits the warmest waters of the Mediterranean Sea and is considered a threatened marine species. The aim of this study was to characterize its genetic structure throughout its whole distribution range using mitochondrial and nuclear sequence data. Because of its sessile adult lifestyle and lack of a pelagic larval stage, we expected a markedly subdivided population structure with limited levels of gene flow. Fragments of the mitochondrial genes cytochrome c oxidase subunit I (COI) and 16S rRNA (16S), were sequenced, along with the nuclear ribosomal cluster (internal transcribed spacer; ITS) in specimens from 18 localities. Our analyses identified four highly distinct phylogroups separated by a mean divergence of > 14% according to the COI sequence data or > 9% according to 16S, but differing only slightly in morphology. The nuclear data (ITS) indicated a lower substitution rate (divergence among groups of around 1%). These large genetic distances among the four lineages clearly point to the existence of a cryptic species complex within D. petraeum comprising at least four species. Differences in the characteristics of intracapsular larval development and protoconch were also detected among these lineages. The allopatric distribution of these cryptic species supports a predominantly vicariant-based cladogenetic pattern for the genus Dendropoma in the Mediterranean. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 898,912. [source] Synthesis and characterization of compounds LixMn1+xFe2,2xO4 with spinel structure in the quasiternary system "LiO0,5 , MnOx , FeOx"CRYSTAL RESEARCH AND TECHNOLOGY, Issue 1 2006C. Wende Abstract The thermal decomposition of freeze-dried Li-Mn(II)-Fe(III)-formate precursors was investigated by means of DTA, TG and mass spectroscopy. By the thermal treatment of the prefired precursors between 400 and 1000°C, single phase solid solutions LixMn1+xFe2,2xO4 (0 , x , 1) with cubic spinel structure were obtained. To get single phase spinels, special conditions concerning the temperature T and the oxygen partial pressure p(O2) during the synthesis are required. Because of the high reactivity of the freeze-dried precursors, in comparison with the conventional solid state reaction, the reaction temperature can be lowered by 200°C. The cation distribution and the properties of the Li-Mn-ferrites were studied by chemical analysis, X-ray powder diffraction and magnetization measurements. It was found that for high substitution rates, almost all lithium occupies the tetrahedral coordinated A-sites of the spinel lattice AB2O4, while at small x-values, lithium ions are distributed over the tetrahedral and octahedral sites. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] DOMESTICATION OF MAIZE, SORGHUM, AND SUGARCANE DID NOT DRIVE THE DIVERGENCE OF THEIR SMUT PATHOGENSEVOLUTION, Issue 2 2007Andrew B. Munkacsi We investigated two alternative hypotheses for the origin of crop pathogen species: that human-mediated agricultural practices drove the divergence of many crop plant pathogen species or that coevolutionary processes in natural populations of the crops' ancestors drove divergence of pathogen species. We distinguished between these two hypotheses by constructing a robust multigene phylogeny and estimating the dates of divergence among four, monophyletic species of smut fungi (Ustilago maydis, U. scitaminea, Sporisorium reilianum, S. sorghi) known to specifically infect maize, sorghum, sugarcane, and their wild ancestors. Without a fossil record for smut fungi, we calibrated the pathogen species' divergence times to their plant host divergence times. Specifically, a calibration date of 10,000 years was employed to test the hypothesis that the fungal species originated at the time of domestication of their current hosts and a calibration date of 50 million years was employed to test the hypothesis that the fungal species originated on wild ancestors of their domesticated hosts. Substitution rates at five protein coding genes were calculated and rates obtained for the 10,000 year calibration date were orders of magnitude faster than those commonly reported for eukaryotes, thus rejecting the hypothesis that these smut pathogen species diverged at the time of domestication. In contrast, substitution rates obtained for the 50 million year calibration were comparable to eukaryotic substitution rates. We used the 50 million year calibration to estimate divergence times of taxa in two datasets, one comprised solely the focal species and one comprised the focal species and additional related taxa. Both datasets indicate that all taxa diverged millions of years ago, strongly supporting the hypothesis that smut species diverged before the time of domestication and modern agriculture. Thus, smut species diverged in the ecological context of natural host plant and fungal populations. [source] Complete subunit sequences, structure and evolution of the 6 × 6-mer hemocyanin from the common house centipede, Scutigera coleoptrataFEBS JOURNAL, Issue 13 2003Kristina Kusche Hemocyanins are large oligomeric copper-containing proteins that serve for the transport of oxygen in many arthropod species. While studied in detail in the Chelicerata and Crustacea, hemocyanins had long been considered unnecessary in the Myriapoda. Here we report the complete molecular structure of the hemocyanin from the common house centipede Scutigera coleoptrata (Myriapoda: Chilopoda), as deduced from 2D-gel electrophoresis, MALDI-TOF mass spectrometry, protein and cDNA sequencing, and homology modeling. This is the first myriapod hemocyanin to be fully sequenced, and allows the investigation of hemocyanin structure,function relationship and evolution. S. coleoptrata hemocyanin is a 6 × 6-mer composed of four distinct subunit types that occur in an approximate 2 : 2 : 1 : 1 ratio and are 49.5,55.5% identical. The cDNA of a fifth, highly diverged, putative hemocyanin was identified that is not included in the native 6 × 6-mer hemocyanin. Phylogenetic analyses show that myriapod hemocyanins are monophyletic, but at least three distinct subunit types evolved before the separation of the Chilopoda and Diplopoda more than 420 million years ago. In contrast to the situation in the Crustacea and Chelicerata, the substitution rates among the myriapod hemocyanin subunits are highly variable. Phylogenetic analyses do not support a common clade of Myriapoda and Hexapoda, whereas there is evidence in favor of monophyletic Mandibulata. [source] Analysis of a Japanese Black Cattle-rearing system utilizing a bahiagrass (Paspalum notatum Flügge) pasture: 3.GRASSLAND SCIENCE, Issue 3 2006Intake from pasture Abstract A Japanese Black Cattle-rearing system utilizing a bahiagrass (Paspalum notatum Flügge) pasture in coastal Miyazaki, southern Japan, was analyzed in terms of intake from pasture. In a field approach, herbage intake by grazing cattle was measured for nine periods (1,5 days) during a grazing season (May,October) along with some other variables (e.g. air temperature, herbage mass, digestibility of grazed herbage), under varying levels of supplementary feeding. The intake from the pasture was most closely related to the intake of supplement, showing a negative linear response at a substitution rate of 0.736,0.750. The intake under no supplementation, i.e. a maximum intake from the pasture, was lower than the voluntary intake predicted with feeding standards. In a modeling approach, a semi-mechanistic model for predicting grazing intake was developed using information from the literature as well as the field data. The performance of the model was acceptable. The model showed similar substitution rates (0.64,0.69), and considerable intake restriction (nearly 30%) that is not attributable to limitations by herbage mass, herbage allowance, diet digestibility or air temperature. The results indicate that a low maximal intake by the animals due to low grazing motivation is a major characteristic of the system where supplementation is a usual management practice. [source] Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database,,HUMAN MUTATION, Issue 6 2007Audrey Petitjean Abstract The tumor suppressor gene TP53 is frequently mutated in human cancers. More than 75% of all mutations are missense substitutions that have been extensively analyzed in various yeast and human cell assays. The International Agency for Research on Cancer (IARC) TP53 database (www-p53.iarc.fr) compiles all genetic variations that have been reported in TP53. Here, we present recent database developments that include new annotations on the functional properties of mutant proteins, and we perform a systematic analysis of the database to determine the functional properties that contribute to the occurrence of mutational "hotspots" in different cancer types and to the phenotype of tumors. This analysis showed that loss of transactivation capacity is a key factor for the selection of missense mutations, and that difference in mutation frequencies is closely related to nucleotide substitution rates along TP53 coding sequence. An interesting new finding is that in patients with an inherited missense mutation, the age at onset of tumors was related to the functional severity of the mutation, mutations with total loss of transactivation activity being associated with earlier cancer onset compared to mutations that retain partial transactivation capacity. Furthermore, 80% of the most common mutants show a capacity to exert dominant-negative effect (DNE) over wild-type p53, compared to only 45% of the less frequent mutants studied, suggesting that DNE may play a role in shaping mutation patterns. These results provide new insights into the factors that shape mutation patterns and influence mutation phenotype, which may have clinical interest. Hum Mutat 28(6), 622,629, 2007. Published 2007 Wiley-Liss, Inc. [source] Resolution of phylogenetic relationships of the major subfamilies of the Delphacidae (Homoptera: Fulgoroidea) using the mitochondrial ribosomal DNAINSECT SCIENCE, Issue 3 2006EDDY DIJKSTRA Abstract Delphacid relationships from the genus level to the subfamily have been completely resolved (among those taxa examined) using sequence data from the 3'end of the 12S gene. Monophyly of the non-asiracine subfamilies was strongly supported and the asiracine Ugyops was placed in the most basal position of the tree. Support levels for monophyly of the Delphacini increased after weighting transversions more heavily than transitions and after removing the cixiid outgroup from the dataset. Among the Delphacini, Conomelus and Megamelus were more closely related to each other than either was to Chloriona. These results are in agreement with the tree based on morphological characters. However, in contrast to morphological data our results strongly supported a sister group relationship between the Stenocraninae and the Kelisiinae. Although the 12S gene fragment gave some information about the species relationships within Chloriona, neither this fragment nor the 5'end of the 16S gene appear to be very useful for this level. Molecular evolutionary patterns provided evidence that there has been a shift in base composition from T to A during the early evolution of the non-Asiracinae. The non-Asiracinae also had comparatively fast substitution rates and these two observations are possibly correlated. In the ,modern' delphacid Chloriona, the AT content was comparatively low in regions free of constraints but this was not the case for ,non-modern' delphacids. The tRNA for valine has been translocated elsewhere, probably before the Delphacidae and Cixiidae diverged from each other. [source] Cryptic differentiation and geographic variation in genetic diversity of Hall's Babbler Pomatostomus halliJOURNAL OF AVIAN BIOLOGY, Issue 2 2001Grant I. Miura Sequence variation was examined in domain I of the mitochondrial control region in three Queensland populations of Hall's Babbler Pomatostomus halli, a geographically restricted, monotypic songbird in eastern Australia. Surprisingly, we found that domain I sequences were strongly differentiated into two major clades differing by 3.29%. These two clades exhibited nearly complete geographic concordance with northern and southern populations, except for two haplotypes which were sampled in the north of the range but were phylogenetically allied to the southern clade. We also found a seven-fold higher level of genetic diversity in the northern than in the southern populations. Neutrality and molecular clock tests suggested that selection or differences in substitution rates were not responsible for this difference in diversity. However, a maximum likelihood analysis of gene flow between the north and south suggested that the difference in diversity could be due to both greater population size in the north and asymmetric gene flow dominated by south to north dispersal events. A likelihood ratio test rejected a model in which population sizes were equal and rates of gene flow symmetric, and came close to rejecting a model in which only population sizes were constrained to be equal. These results suggest that different population sizes and asymmetric gene flow could be a major source of differences in genetic variation between populations of Hall's Babbler, although ecological and biogeographic causes for these differences are obscure. [source] A simple covarion-based approach to analyse nucleotide substitution ratesJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2002J. Siltberg Using the ratio of nonsynonymous to synonymous nucleotide substitution rates (Ka/Ks) is a common approach for detecting positive selection. However, calculation of this ratio over a whole gene combines amino acid sites that may be under positive selection with those that are highly conserved. We introduce a new covarion-based method to sample only the sites potentially under selective pressure. Using ancestral sequence reconstruction over a phylogenetic tree coupled with calculation of Ka/Ks ratios, positive selection is better detected by this simple covarion-based approach than it is using a whole gene analysis or a windowing analysis. This is demonstrated on a synthetic dataset and is tested on primate leptin, which indicates a previously undetected round of positive selection in the branch leading to Gorilla gorilla. [source] Comparative mtDNA sequence (control region, ATPase 6 and NADH-1) divergence in Hucho taimen(Pallas) across four Siberian river basinsJOURNAL OF FISH BIOLOGY, Issue 4 2005E. Froufe Hucho taimen from eight populations spanning four drainage basins (Amur, Lena, Enisei and Khatanga) were analysed for nucleotide sequence variation across three mitochondrial genes (ATP6, NADH-1 and control region). Samples of H. hucho, Brachymystax lenok(sharp-snouted and blunt-snouted forms) and Parahucho perryi were also included for comparison. Nucleotide variation across a total of 1826 base pairs in H. taimen revealed shared haplotypes between the Amur and Lena basins, further supporting a previous hypothesis of late to post-Pleistocene hydrological exchange between these now disjunct basins. In contrast to an earlier study using the control region alone, clear phylogeographic structure was seen at a large geographic scale, reflected by two phylogroups, one corresponding to the Amur and Lena basins, and the other to the Enisei and Khatanga basins. Comparative rates of divergence revealed considerably faster and less heterogeneous substitution rates for the two coding genes, especially at interspecific levels compared to the mtDNA control region. [source] |