02277nas a2200193 4500008004100000022001400041245011200055210006900167260000900236300001100245490000600256520164600262100002401908700002101932700002101953700002001974700002001994856006902014 2012 eng d a1176-934300aEvolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group.0 aEvolutionary Genomics of Genes Involved in Olfactory Behavior in c2012 a89-1040 v83 aPrevious comparative genomic studies of genes involved in olfactory behavior in Drosophila focused only on particular gene families such as odorant receptor and/or odorant binding proteins. However, olfactory behavior has a complex genetic architecture that is orchestrated by many interacting genes. In this paper, we present a comparative genomic study of olfactory behavior in Drosophila including an extended set of genes known to affect olfactory behavior. We took advantage of the recent burst of whole genome sequences and the development of powerful statistical tools to analyze genomic data and test evolutionary and functional hypotheses of olfactory genes in the six species of the Drosophila melanogaster species group for which whole genome sequences are available. Our study reveals widespread purifying selection and limited incidence of positive selection on olfactory genes. We show that the pace of evolution of olfactory genes is mostly independent of the life cycle stage, and of the number of life cycle stages, in which they participate in olfaction. However, we detected a relationship between evolutionary rates and the position that the gene products occupy in the olfactory system, genes occupying central positions tend to be more constrained than peripheral genes. Finally, we demonstrate that specialization to one host does not seem to be associated with bursts of adaptive evolution in olfactory genes in D. sechellia and D. erecta, the two specialists species analyzed, but rather different lineages have idiosyncratic evolutionary histories in which both historical and ecological factors have been involved.1 aLavagnino, Nicolás1 aSerra, François1 aArbiza, Leonardo1 aDopazo, Hernán1 aHasson, Esteban uhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273929/?tool=pubmed02098nas a2200169 4500008004100000245011500041210006900156260001600225520142700241100002501668700001701693700002101710700002401731700002001755700001901775856013401794 2011 eng d00aEvolution of the biosynthesis of di-myo-inositol phosphate, a marker of adaptation to hot marine environments.0 aEvolution of the biosynthesis of dimyoinositol phosphate a marke c2011 Oct 263 a

The synthesis of di-myo-inositol phosphate (DIP), a common compatible solute in hyperthermophiles, involves the consecutive actions of inositol-1-phosphate cytidylyltransferase (IPCT) and di-myo-inositol phosphate phosphate synthase (DIPPS). In most cases, both activities are present in a single gene product, but separate genes are also found in a few organisms. Genes for IPCT and DIPPS were found in the genomes of 33 organisms, all with thermophilic/hyperthermophilic lifestyles. Phylogeny of IPCT/DIPPS revealed an incongruent topology with 16S RNA phylogeny, thus suggesting horizontal gene transfer. The phylogenetic tree of the DIPPS domain was rooted by using phosphatidylinositol phosphate synthase sequences as out-group. The root locates at the separation of genomes with fused and split genes. We propose that the gene encoding DIPPS was recruited from the biosynthesis of phosphatidylinositol. The last DIP-synthesizing ancestor harboured separated genes for IPCT and DIPPS and this architecture was maintained in a crenarchaeal lineage, and transferred by horizontal gene transfer to hyperthermophilic marine Thermotoga species. It is plausible that the driving force for the assembly of those two genes in the early ancestor is related to the acquired advantage of DIP producers to cope with high temperature. This work corroborates the view that Archaea were the first hyperthermophilic organisms.

1 aGonçalves, Luís, G1 aBorges, Nuno1 aSerra, François1 aFernandes, Pedro, L1 aDopazo, Hernán1 aSantos, Helena uhttps://www.clinbioinfosspa.es/content/evolution-biosynthesis-di-myo-inositol-phosphate-marker-adaptation-hot-marine-environments02578nas a2200301 4500008004100000022001400041245006900055210006600124260001300190300001300203490000600216520167900222653001201901653002301913653001501936653001901951653003401970653001302004653001202017653001402029653002302043653002702066100002102093700002102114700002002135700002002155856010102175 2011 eng d a1553-735800aNatural selection on functional modules, a genome-wide analysis.0 aNatural selection on functional modules a genomewide analysis c2011 Mar ae10010930 v73 a

Classically, the functional consequences of natural selection over genomes have been analyzed as the compound effects of individual genes. The current paradigm for large-scale analysis of adaptation is based on the observed significant deviations of rates of individual genes from neutral evolutionary expectation. This approach, which assumed independence among genes, has not been able to identify biological functions significantly enriched in positively selected genes in individual species. Alternatively, pooling related species has enhanced the search for signatures of selection. However, grouping signatures does not allow testing for adaptive differences between species. Here we introduce the Gene-Set Selection Analysis (GSSA), a new genome-wide approach to test for evidences of natural selection on functional modules. GSSA is able to detect lineage specific evolutionary rate changes in a notable number of functional modules. For example, in nine mammal and Drosophilae genomes GSSA identifies hundreds of functional modules with significant associations to high and low rates of evolution. Many of the detected functional modules with high evolutionary rates have been previously identified as biological functions under positive selection. Notably, GSSA identifies conserved functional modules with many positively selected genes, which questions whether they are exclusively selected for fitting genomes to environmental changes. Our results agree with previous studies suggesting that adaptation requires positive selection, but not every mutation under positive selection contributes to the adaptive dynamical process of the evolution of species.

10aAnimals10aDatabases, Genetic10aDrosophila10aGenome, Insect10aGenome-Wide Association Study10aGenomics10aMammals10aPhylogeny10aSelection, Genetic10aSequence Analysis, DNA1 aSerra, François1 aArbiza, Leonardo1 aDopazo, Joaquin1 aDopazo, Hernán uhttps://www.clinbioinfosspa.es/content/natural-selection-functional-modules-genome-wide-analysis02025nas a2200349 4500008004100000022001400041245011700055210006900172260001300241300001100254490000700265520090400272653002501176653001301201653001301214653001401227653002301241653001301264100002101277700002101298700002301319700002001342700002101362700001701383700002401400700003301424700002401457700002001481700002001501700002001521856013401541 2011 eng d a1362-496200aPhylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.0 aPhylemon 20 a suite of webtools for molecular evolution phylogen c2011 Jul aW470-40 v393 a

Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing.

10aEvolution, Molecular10aGenomics10aInternet10aPhylogeny10aSequence Alignment10aSoftware1 aSánchez, Rubén1 aSerra, François1 aTárraga, Joaquín1 aMedina, Ignacio1 aCarbonell, José1 aPulido, Luis1 aDe Maria, Alejandro1 aCapella-Gutíerrez, Salvador1 aHuerta-Cepas, Jaime1 aGabaldón, Toni1 aDopazo, Joaquin1 aDopazo, Hernán uhttps://www.clinbioinfosspa.es/content/phylemon-20-suite-web-tools-molecular-evolution-phylogenetics-phylogenomics-and-hypotheses01461nas a2200253 4500008004100000245009300041210006900134260000900203300000700212490000700219520063100226100002300857700001500880700001900895700002300914700002800937700001500965700001700980700002100997700002401018700002001042700002001062856012501082 2011 eng d00aRecent human evolution has shaped geographical differences in susceptibility to disease.0 aRecent human evolution has shaped geographical differences in su c2011 a550 v123 a

Searching for associations between genetic variants and complex diseases has been a very active area of research for over two decades. More than 51,000 potential associations have been studied and published, a figure that keeps increasing, especially with the recent explosion of array-based Genome-Wide Association Studies. Even if the number of true associations described so far is high, many of the putative risk variants detected so far have failed to be consistently replicated and are widely considered false positives. Here, we focus on the world-wide patterns of replicability of published association studies.

1 aMarigorta, Urko, M1 aLao, Oscar1 aCasals, Ferran1 aCalafell, Francesc1 aMorcillo-Suarez, Carlos1 aFaria, Rui1 aBosch, Elena1 aSerra, François1 aBertranpetit, Jaume1 aDopazo, Hernán1 aNavarro, Arcadi uhttps://www.clinbioinfosspa.es/content/recent-human-evolution-has-shaped-geographical-differences-susceptibility-disease02327nas a2200241 4500008004100000245007500041210006900116260001300185300001100198490000700209520154000216100002401756700003301780700002101813700001901834700003501853700002001888700001801908700002701926700002001953700001701973856009501990 2011 eng d00aRole of tomato BRANCHED1-like genes in the control of shoot branching.0 aRole of tomato BRANCHED1like genes in the control of shoot branc c2011 Aug a701-140 v673 a

In angiosperms, shoot branching greatly determines overall plant architecture and affects fundamental aspects of plant life. Branching patterns are determined by genetic pathways conserved widely across angiosperms. In Arabidopsis thaliana (Brassicaceae, Rosidae) BRANCHED1 (BRC1) plays a central role in this process, acting locally to arrest axillary bud growth. In tomato (Solanum lycopersicum, Solanaceae, Asteridae) we have identified two BRC1-like paralogues, SlBRC1a and SlBRC1b. These genes are expressed in arrested axillary buds and both are down-regulated upon bud activation, although SlBRC1a is transcribed at much lower levels than SlBRC1b. Alternative splicing of SlBRC1a renders two transcripts that encode two BRC1-like proteins with different C-t domains due to a 3’-terminal frameshift. The phenotype of loss-of-function lines suggests that SlBRC1b has retained the ancestral role of BRC1 in shoot branch suppression. We have isolated the BRC1a and BRC1b genes of other Solanum species and have studied their evolution rates across the lineages. These studies indicate that, after duplication of an ancestral BRC1-like gene, BRC1b genes continued to evolve under a strong purifying selection that was consistent with the conserved function of SlBRC1b in shoot branching control. In contrast, the coding sequences of Solanum BRC1a genes have evolved at a higher evolution rate. Branch-site tests indicate that this difference does not reflect relaxation but rather positive selective pressure for adaptation.

1 aMartín-Trillo, Mar1 aGrandío, Eduardo, González1 aSerra, François1 aMarcel, Fabien1 aRodríguez-Buey, María, Luisa1 aSchmitz, Gregor1 aTheres, Klaus1 aBendahmane, Abdelhafid1 aDopazo, Hernán1 aCubas, Pilar uhttps://www.clinbioinfosspa.es/content/role-tomato-branched1-genes-control-shoot-branching01980nas a2200217 4500008004100000022001400041245007200055210006900127260000900196300001100205490000600216520130500222100001601527700002001543700002101563700002901584700002001613700002501633700002501658856007901683 2011 eng d a1932-620300aSexual selection halts the relaxation of protamine 2 among rodents.0 aSexual selection halts the relaxation of protamine 2 among roden c2011 ae292470 v63 aSexual selection has been proposed as the driving force promoting the rapid evolutionary changes observed in some reproductive genes including protamines. We test this hypothesis in a group of rodents which show marked differences in the intensity of sexual selection. Levels of sperm competition were not associated with the evolutionary rates of protamine 1 but, contrary to expectations, were negatively related to the evolutionary rate of cleaved- and mature-protamine 2. Since both domains were found to be under relaxation, our findings reveal an unforeseen role of sexual selection: to halt the degree of degeneration that proteins within families may experience due to functional redundancy. The degree of relaxation of protamine 2 in this group of rodents is such that in some species it has become dysfunctional and it is not expressed in mature spermatozoa. In contrast, protamine 1 is functionally conserved but shows directed positive selection on specific sites which are functionally relevant such as DNA-anchoring domains and phosphorylation sites. We conclude that in rodents protamine 2 is under relaxation and that sexual selection removes deleterious mutations among species with high levels of sperm competition to maintain the protein functional and the spermatozoa competitive.1 aLüke, Lena1 aVicens, Alberto1 aSerra, François1 aLuque-Larena, Juan, Jose1 aDopazo, Hernán1 aRoldan, Eduardo, R S1 aGomendio, Montserrat uhttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.002924701750nas a2200181 4500008004100000022002200041245009600063210007100159260002600230300001000256520107600266100002101342700001501363700001501378700001501393700001601408856014401424 2009 eng d a978-84-92910-06-900aGenómica Comparativa y Selección Natural. Aplicaciones en el Genoma Humano. Capítulo 1.60 aGenómica Comparativa y Selección Natural Aplicaciones en el Geno aValenciabObrapropia. a51-593 a

La búsqueda de los eventos adaptativos a nivel molecular que ha diferenciado el genoma humano del de nuestro pariente vivo más cercano, el chimpancé, ha sido una de las áreas de mayor investigación en genómica comparativa. Paralelamente, la predicción funcional de variantes genéticas en nuestra especie ha sido un área de intenso desarrollo en bioinformática. En este trabajo discutiremos resultados previos y otros más recientes que dan cuenta de estos desarrollos. Veremos que en todos los casos la estimación de las presiones selectivas a nivel de los genes individuales o de los residuos de las proteínas son el denominador común para discutir ambos aspectos. Finalmente mostraremos cómo el análisis de estas presiones selectivas por grupos funcionales de genes resulta una alternativa viable y con suficiente poder estadístico para el análisis de la adaptación y de las restricciones evolutivas a nivel genómico. 

1 aSerra, François1 aArbiza, L.1 aDopazo, H.1 aDopazo, H.1 aNavarro, A. uhttps://www.clinbioinfosspa.es/content/gen%C3%B3mica-comparativa-y-selecci%C3%B3n-natural-aplicaciones-en-el-genoma-humano-cap%C3%ADtulo-16