The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Michael M Miyamoto - One of the best experts on this subject based on the ideXlab platform.
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predicting Functional Divergence in protein evolution by site specific rate shifts
Trends in Biochemical Sciences, 2002Co-Authors: Eric A Gaucher, Michael M Miyamoto, Steven A BennerAbstract:Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts Functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread Divergence of Functional behavior among proteins to generate paralogs and orthologs.
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a likelihood ratio test for evolutionary rate shifts and Functional Divergence among proteins
Proceedings of the National Academy of Sciences of the United States of America, 2001Co-Authors: Bjarne Knudsen, Michael M MiyamotoAbstract:Changes in protein function can lead to changes in the selection acting on specific residues. This can often be detected as evolutionary rate changes at the sites in question. A maximum-likelihood method for detecting evolutionary rate shifts at specific protein positions is presented. The method determines significance values of the rate differences to give a sound statistical foundation for the conclusions drawn from the analyses. A statistical test for detecting slowly evolving sites is also described. The methods are applied to a set of Myc proteins for the identification of both conserved sites and those with changing evolutionary rates. Those positions with conserved and changing rates are related to the structures and functions of their proteins. The results are compared with an earlier Bayesian method, thereby highlighting the advantages of the new likelihood ratio tests.
Kenneth H. Wolfe - One of the best experts on this subject based on the ideXlab platform.
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Functional Divergence of duplicated genes formed by polyploidy during arabidopsis evolution
The Plant Cell, 2004Co-Authors: Guillaume Blanc, Kenneth H. WolfeAbstract:To study the evolutionary effects of polyploidy on plant gene functions, we analyzed Functional genomics data for a large number of duplicated gene pairs formed by ancient polyploidy events in Arabidopsis thaliana. Genes retained in duplicate are not distributed evenly among Gene Ontology or Munich Information Center for Protein Sequences Functional categories, which indicates a nonrandom process of gene loss. Genes involved in signal transduction and transcription have been preferentially retained, and those involved in DNA repair have been preferentially lost. Although the two members of each gene pair must originally have had identical transcription profiles, less than half of the pairs formed by the most recent polyploidy event still retain significantly correlated profiles. We identified several cases where groups of duplicated gene pairs have diverged in concert, forming two parallel networks, each containing one member of each gene pair. In these cases, the expression of each gene is strongly correlated with the other nonhomologous genes in its network but poorly correlated with its paralog in the other network. We also find that the rate of protein sequence evolution has been significantly asymmetric in >20% of duplicate pairs. Together, these results suggest that Functional diversification of the surviving duplicated genes is a major feature of the long-term evolution of polyploids.
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positive selection and subFunctionalization of duplicated cct chaperonin subunits
Molecular Biology and Evolution, 2003Co-Authors: Mario A. Fares, Kenneth H. WolfeAbstract:To reach a Functional and energetically stable conformation, many proteins need molecular helpers called chaperonins. Among the group II chaperonins, CCT proteins provide crucial machinery for the stabilization and properfolding of several proteins in the cytosol of eukaryotic cells through interactions that are subunit-specific and geometry-dependent. CCT proteins are made up of eight different subunits, all with similar sequences, positioned in a precise arrangement. Each subunit has been proposed to have a specialized function during the binding and folding of the CCT protein substrate. Here, we demonstrate that Functional Divergence occurred after several CCT duplication events due to the fixation of amino acid substitutions by positive selection. Sites critical for ATP binding and substrate binding were found to have undergone positive selection and Functional Divergence predominantly in subunits that bind tubulin but not actin. Furthermore, we show clear Functional Divergence between CCT subunits that bind the C-terminal domains of actin and tubulin and those that bind the N-terminal domains. Phylogenetic analyses could not resolve the deep relationships between most subunits, except for the groups α/β/γ and δ/e, suggesting several almost simultaneous ancient duplication events. Together, the results support the idea that, in contrast to homo-oligomeric chaperonins such as GroEL, the high Divergence level between CCT subunits is the result of positive selection after each duplication event to provide a specialized role for each CCT subunit in the different steps of protein folding.
Yongping Cai - One of the best experts on this subject based on the ideXlab platform.
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Evolution and Functional Divergence of MADS-box genes in Pyrus.
Scientific reports, 2019Co-Authors: Dandan Meng, Yunpeng Cao, Tianzhe Chen, Muhammad Abdullah, Qing Jin, Honghong Fan, Yi Lin, Yongping CaiAbstract:MADS-box transcription factors widely regulate all aspects of plant growth including development and reproduction. Although the MADS-box gene family genes have been extensively characterized in many plants, they have not been studied in closely related species. In this study, 73 and 74 MADS-box genes were identified in European pear (Pyrus communis) and Chinese pear (Pyrus bretschneideri), respectively. Based on the phylogenetic relationship, these genes could be clustered into five groups (Mα, Mβ, Mr, MIKCC, MIKC*) and the MIKCC group was further categorized into 10 subfamilies. The distribution of MADS-box genes on each chromosome was significantly nonrandom. Thirty-seven orthologs, twenty-five PcpMADS (P. communis MADS-box) paralogs and nineteen PbrMADS (P. bretschneideri MADS-box) paralogs were predicted. Among these paralogous genes, two pairs arose from tandem duplications (TD), nineteen from segmental duplication (SD) events and twenty-three from whole genome duplication (WGD) events, indicating SD/WGD events led to the expansion of MADS-box gene family. The MADS-box genes expression profiles in pear fruits indicated Functional Divergence and neo-Functionalization or sub-Functionalization of some orthologous genes originated from a common ancestor. This study provided a useful reference for further analysis the mechanisms of species differentiation and biodiversity formation among closely related species.
Stephen D. Mccormick - One of the best experts on this subject based on the ideXlab platform.
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Functional Divergence of thyrotropin beta-subunit paralogs gives new insights into salmon smoltification metamorphosis
Scientific Reports, 2019Co-Authors: Mitchell S. Fleming, Gersende Maugars, Jocelyn Rancon, Romain Fontaine, Rasoul Nourizadeh-lillabadi, Elena Santidrian Yebra-pimentel, Ron Dirks, Anne-gaëlle Lafont, Finn-arne Weltzien, Stephen D. MccormickAbstract:Smoltification is a metamorphic event in salmon life history, which initiates downstream migration and pre-adapts juvenile salmon for seawater entry. While a number of reports concern thyroid hormones and smoltification, few and inconclusive studies have addressed the potential role of thyrotropin (TSH). TSH is composed of a α-subunit common to gonadotropins, and a β-subunit conferring hormone specificity. We report the presence and Functional Divergence of duplicated TSH β-subunit paralogs ( tshβa and tshβb ) in Atlantic salmon. Phylogeny and synteny analyses allowed us to infer that they originated from teleost-specific whole genome duplication. Expression profiles of both paralogs in the pituitary were measured by qPCR throughout smoltification in Atlantic salmon from the endangered Loire-Allier population raised in a conservation hatchery. This revealed a striking peak of tshβb expression in April, concomitant with downstream migration initiation, while tshβa expression remained relatively constant. In situ hybridization showed two distinct pituitary cell populations, tshβa c ells in the anterior adenohypophysis, and tshβb cells near to the pituitary stalk, a location comparable to the pars tuberalis TSH cells involved in seasonal physiology and behaviour in birds and mammals. Functional Divergence of tshβ paralogs in Atlantic salmon supports a specific role of tshβb in smoltification.
Norman W H Mason - One of the best experts on this subject based on the ideXlab platform.
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A guide for using Functional diversity indices to reveal changes in assembly processes along ecological gradients
Journal of Vegetation Science, 2013Co-Authors: Norman W H Mason, Francesco De Bello, Sandrine Pavoine, David Mouillot, Susan DrayAbstract:Question Which Functional diversity indices have the power to reveal changes in community assembly processes along abiotic stress gradients? Is their power affected by stochastic processes and variations in species richness along stress gradients? Methods We used a simple community assembly model to explore the power of Functional diversity indices across a wide range of ecological contexts. The model assumes that with declining stress the influence of niche complementarity on species fitness increases while that of environmental filtering decreases. We separately incorporated two trait-independent stochastic processes – mass and priority effects – in simulating species occurrences and abundances along a hypothetical stress gradient. We ran simulations where species richness was constant along the gradient, or increased, decreased or varied randomly with declining stress. We compared observed values for two indices of Functional richness – total Functional dendrogram length (FD) and convex hull volume (FRic) – with a matrix-swap null model (yielding indices SESFD and SESFRic) to remove any trivial effects of species richness. We also compared two indices that measure both Functional richness and Functional Divergence – Rao quadratic entropy (Rao) and Functional dispersion (FDis) – with a null model that randomizes abundances across species but within communities. This converts them to pure measures of Functional Divergence (SESRao and SESFDis). Results When mass effects operated, only SESRao and SESFDis gave reasonable power, irrespective of how species richness varied along the stress gradient. FD, FRic, Rao and FDis had low power when species richness was constant, and variation in species richness greatly influenced their power. SESFRic and SESFD were unaffected by variation in species richness. When priority effects operated, FRic, SESFRic, Rao and FDis had good power and were unaffected by variation in species richness. Variation in species richness greatly affected FD and SESFD. SESRao and SESFDis had low power in the priority effects model but were unaffected by variation in species richness. Conclusions Our results demonstrate that a reliable test for changes in assembly processes along stress gradients requires Functional diversity indices measuring either Functional richness or Functional Divergence. We recommend using SESFRic as a measure of Functional richness and either SESRao or SESFDis (which are very closely related mathematically) as a measure of Functional Divergence. Used together, these indices of Functional richness and Functional Divergence provide good power to test for increasing niche complementarity with declining stress across a broad range of ecological contexts.
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Functional diversity measures an overview of their redundancy and their ability to discriminate community assembly rules
Functional Ecology, 2010Co-Authors: Maud A Mouchet, Norman W H Mason, Sebastien Villeger, David MouillotAbstract:Summary 1. Indices quantifying the Functional aspect of biodiversity are essential in understanding relationships between biodiversity, ecosystem functioning and environmental constraints. Many indices of Functional diversity have been published but we lack consensus about what indices quantify, how redundant they are and which ones are recommended. 2. This study aims to build a typology of Functional diversity indices from artificial data sets encompassing various community structures (different assembly rules, various species richness levels) and to identify a set of independent indices able to discriminate community assembly rules. 3. Our results confirm that indices can be divided into three main categories, each of these corresponding to one aspect of Functional diversity: Functional richness, Functional evenness and Functional Divergence. Most published indices are highly correlated and quantify Functional richness while quadratic entropy (Q) represents a mix between Functional richness and Functional Divergence. Conversely, two indices (FEve and FDiv respectively quantifying Functional evenness and Functional Divergence) are rather independent to all the others. The power analysis revealed that some indices efficiently detect assembly rules while others performed poorly. 4. To accurately assess Functional diversity and establish its relationships with ecosystem functioning and environmental constraints, we recommend investigating each Functional component separately with the appropriate index. Guidelines are provided to help choosing appropriate indices given the issue being investigated. 5. This study demonstrates that Functional diversity indices have the potential to reveal the processes that structure biological communities. Combined with complementary methods (phylogenetic and taxonomic diversity), the multifaceted framework of Functional diversity will help improve our understanding of how biodiversity interacts with ecosystem processes and environmental constraints.
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Functional richness Functional evenness and Functional Divergence the primary components of Functional diversity
Oikos, 2005Co-Authors: Norman W H Mason, David Mouillot, Bastow J WilsonAbstract:Functiona] diversity is hypothesised as being beneficial for ecosystem functions, such as productivity and resistance to invasion. However, a precise definition of Functional diversity, and hence a framework for its quantification, have proved elusive. We present a definition based on the analogy of the components of species diversity - richness, evenness and Divergence. These concepts are applied to Functional characters to give three components of Functional diversity - Functional richness, Functional evenness and Functional Divergence. We demonstrate how each of these components may be calculated. It is hoped that our definition of Functional diversity and its components will aid in elucidation of the mechanisms behind diversity/ecosystem-function relationships.
