Domesticació en animals i evolució

La domesticació és simplement evolució, encara que a una velocitat elevada produïda per la selecció artificial i l'adaptació de l'espècie al nou ambient en contacte amb l'home. Encara que alguns estudis tendeixen a enfocar la domesticació com una relació d'aprofitament, de parasitisme, la domesticació és sobretot simbiosi i ha produït un benefici mutu en els humans i en l'espècie domèstica. El procés de domesticació ha estat, en gairebé totes les espècies estudiades, molt més complex del que es pensava, i no solament ha ocorregut en múltiples ocasions i llocs, sinó que també ha estat un procés gradual i sovint d'anada i tornada. Com a conseqüència d'això, no sempre és fàcil interpretar els resultats experimentals sobre variabilitat genètica produïts a gran escala per les noves tècniques genòmiques. Si alguna cosa sembla certa és que la domesticació no ha fet desaparèixer la variació genètica, i sovint les races domèstiques són molt més variables del que podíem sospitar.Domestication is but evolution, only at high pace as a result of artificial selection and adaptation to the new human mediated environment. Although domestication has been considered traditionally as animal exploitation, it has benefited both human and animals, it is symbiosis rather than parasitism. The domestication process is much more complex than anticipated, it has occurred in different locations at several times, it has been a gradual process rather than a clear cut event. As a result, it is not necessarily easy to interpret results that are being produced by large scale modern genomics. One thing is undisput pered: domestication has not wiped out genetic variability, domestic breeds seem to be much more variable than expected a priori

La angustia de vivir en Comala. Entre la añoranza y el desamparo

Se expone la situación del desamparo en que se hallan los habitantes de Comala: por una parte, por la tiranía económica y psíquica de Pedro Páramo y la violencia sexual que practican tanto éste como su hijo Miguel sobre las comalenses; y, por otra parte, por la opresión que sobre ellos ejerce el padre Rentería, que les impone una religión basada en la superstición y el miedo.Here do we expose the helplessness situation in which Comala’s inhabitants are: on the one hand, because of Pedro Páramo’s economic and psichological tyranny and the sexual violence that both Pedro and his son Miguel practise on them; and, on the other, because of Priest/Father Rentería’s oppression, whose religion is imposed on them based upon superstition and fear

Sancho Panza, “entre la realidad y el deseo” (Una reflexión personal)

La figura de Sancho Panza es seguramente —a juzgar por las palabras del “Prólogo”— la creación literaria más lograda de Cervantes y tal vez la más apreciada y de la que más orgulloso y satisfecho se sentía su autor. En este trabajo intentamos analizar su rica y ambigua personalidad, una personalidad que es reflejo de la complicada y compleja existencia del ser humano, y que vive inmersa en una aventura que no es solo suya. Sancho Panza y Don Quijote viven conjuntamente la gran aventura de ser hombre. Es una aventura entretejida entre la libertad individual y el compromiso de dos seres complementarios que dialogan en busca de su propia razón de ser y de su destino, debatiéndose entre la realidad y el deseo, entre la duda y la ilusión.Sancho Panza´s figure is surely —as for the words in the “Prologue”— the best literary creation achieved by Cervantes. It is prehaps the most appreciated and the one that his writer felf mostly proud and satisfied. In this essay, we try to analyse his rich and ambiguous personality, which is the reflection of the complicated and complex existance of the human being. He lives immersed in an adventure that is not only his. Sancho Panza and Don Quixote live together the great adventure of being men. It is an adventure intertwined between the individual liberty and the commitment of two complementary beings that discuss in the search of their own reason of being and their destiny, debating themselves etween reality and desire, between doubt and illusio

Cervantes entre la realidad y la ficción de su propia obra (Una meditación personal en torno al capítulo 30 de la Segunda Parte).

Sin resumenIn this chapter of Don Quixote the union between reality and fiction achieved by Cervantes throughout the novel clearly appears. From the beginning, he takes care of the features of credibility of the fiction lived by Don Quixote and Sancho. He wants to write good literature and, with tllat purpose, the novel must comply with reality. Don Quixote asks Sansón Carrasco if it is true that a story about his 111 Miguel josé Pérez Cervantes entre la realidad y la ficción de su propia obra Julia Enciso Orellana deeds has been published; and he himself, as well as Sancho, take great care of knowing whether this printed story complies with truth. We feel as if diese characters were, simultaneously, real and fictional; that is why they reached such renown aud such fame that «there is no nation or language into which they wiU not be transíated». The deep truth depicted by Cervantes benefited the fame and good name of the Ingenioso Caballero de la Mancha

Genetical genomics: use all data

BACKGROUND: Genetical genomics is a very powerful tool to elucidate the basis of complex traits and disease susceptibility. Despite its relevance, however, statistical modeling of expression quantitative trait loci (eQTL) has not received the attention it deserves. Based on two reasonable assertions (i) a good model should consider all available variables as potential effects, and (ii) gene expressions are highly interconnected, we suggest that an eQTL model should consider the rest of expression levels as potential regressors, in addition to the markers. RESULTS: It is shown that power can be increased with this strategy. We also show, using classical statistical and support vector machines techniques in a reanalysis of public data, that the external transcripts, i.e., transcripts other than the one being analysed, explain on average much more variability than the markers themselves. The presence of eQTL hotspots is reassessed in the light of these results. CONCLUSION: Model choice is a critical yet neglected issue in genetical genomics studies. Although we are far from having a general strategy for model choice in this area, we can at least propose that any transcript level is scanned not only for the markers genotyped but also for the rest of gene expression levels. Some sort of stepwise regression strategy can be used to select the final model

Data modeling as a main source of discrepancies in single and multiple marker association methods

Genome-wide association studies have successfully identified several loci underlying complex diseases in humans. The development of high density SNP maps in domestic animal species should allow the detection of QTLs for economically important traits through association studies with much higher accuracy than traditional linkage analysis. Here we report the association analysis of the dataset simulated for the XII QTL-MAS meeting (Uppsala). We used two strategies, single marker association and haplotype-based association (Blossoc) that were applied to i) the raw data, and ii) the data corrected for infinitesimal, sex and generation effects. Both methods performed similarly in detecting the most strongly associated SNPs, about ten loci in total. The most significant ones were located in chromosomes 1, 4 and 5. Overall, the largest differences were found between corrected and raw data, rather than between single and multiple marker analysis. The use of raw data increased greatly the number of significant loci, but possibly also the rate of false positives. Bootstrap model aggregation removed most of discrepancies between adjusted and raw data when SMA was employed. Model choice should be carefully considered in genome-wide association studies

Origin and Genetic Diversity of Pig Breeds

10 páginas, 5 figuras, 1 tabla.Genetic and archaeological findings suggest that pig domestication began about 9000–10 000 YBP at multiple sites across Eurasia, followed by their subsequent spread at a worldwide scale. Development of local types throughout the centuries led to the foundation, mostly during the nineteenth century, of current modern breeds with defined phenotypes and production abilities. Extensive intercrossing markedly increased the gene pool of these founder populations. For instance, it is well known that many European pig breeds carry Far Eastern haplotypes at high frequencies because of an ancient introgression with Chinese swine. Since then, artificial selection, genetic bottlenecks and inbreeding have significantly modified the allelic diversity of pig breeds. In the next future, state-of-the-art scientific advances as well as conservation programmes will be fundamental to preserve the genetic reservoir of pig breeds as well as to exploit it in the context of artificial selection schemes.Peer reviewe

HIV drug resistance prediction with weighted categorical kernel functions

Background: Antiretroviral drugs are a very effective therapy against HIV infection. However, the high mutation rate of HIV permits the emergence of variants that can be resistant to the drug treatment. Predicting drug resistance to previously unobserved variants is therefore very important for an optimum medical treatment. In this paper, we propose the use of weighted categorical kernel functions to predict drug resistance from virus sequence data. These kernel functions are very simple to implement and are able to take into account HIV data particularities, such as allele mixtures, and to weigh the different importance of each protein residue, as it is known that not all positions contribute equally to the resistance. Results: We analyzed 21 drugs of four classes: protease inhibitors (PI), integrase inhibitors (INI), nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI). We compared two categorical kernel functions, Overlap and Jaccard, against two well-known noncategorical kernel functions (Linear and RBF) and Random Forest (RF). Weighted versions of these kernels were also considered, where the weights were obtained from the RF decrease in node impurity. The Jaccard kernel was the best method, either in its weighted or unweighted form, for 20 out of the 21 drugs. Conclusions: Results show that kernels that take into account both the categorical nature of the data and the presence of mixtures consistently result in the best prediction model. The advantage of including weights depended on the protein targeted by the drug. In the case of reverse transcriptase, weights based in the relative importance of each position clearly increased the prediction performance, while the improvement in the protease was much smaller. This seems to be related to the distribution of weights, as measured by the Gini index. All methods described, together with documentation and examples, are freely available at https://bitbucket.org/elies_ramon/catkern.Peer ReviewedPostprint (published version

Impact of breed and sex on porcine endocrine transcriptome: a bayesian biometrical analysis

Background: Transcriptome variability is due to genetic and environmental causes, much like any other complex phenotype. Ascertaining the transcriptome differences between individuals is an important step to understand how selection and genetic drift may affect gene expression. To that end, extant divergent livestock breeds offer an ideal genetic material. Results: We have analyzed with microarrays five tissues from the endocrine axis (hypothalamus, adenohypophysis, thyroid gland, gonads and fat tissue) of 16 pigs from both sexes pertaining to four extreme breeds (Duroc, Large White, Iberian and a cross with SinoEuropean hybrid line). Using a Bayesian linear model approach, we observed that the largest breed variability corresponded to the male gonads, and was larger than at the remaining tissues, including ovaries. Measurement of sex hormones in peripheral blood at slaughter did not detect any breed-related differences. Not unexpectedly, the gonads were the tissue with the largest number of sex biased genes. There was a strong correlation between sex and breed bias expression, although the most breed biased genes were not the most sex biased genes. A combined analysis of connectivity and differential expression suggested three biological processes as being primarily different between breeds: spermatogenesis, muscle differentiation and several metabolic processes. Conclusion: These results suggest that differences across breeds in gene expression of the male gonads are larger than in other endocrine tissues in the pig. Nevertheless, the strong presence of breed biased genes in the male gonads cannot be explained solely by changes in spermatogenesis nor by differences in the reproductive tract development