Host Genes Important to HIV Replication and Evolution.

Recent years have seen a significant increase in understanding of the host genetic and genomic determinants of susceptibility to HIV-1 infection and disease progression, driven in large part by candidate gene studies, genome-wide association studies, genome-wide transcriptome analyses, and large-scale in vitro genome screens. These studies have identified common variants in some host loci that clearly influence disease progression, characterized the scale and dynamics of gene and protein expression changes in response to infection, and provided the first comprehensive catalogs of genes and pathways involved in viral replication. Experimental models of AIDS and studies in natural hosts of primate lentiviruses have complemented and in some cases extended these findings. As the relevant technology continues to progress, the expectation is that such studies will increase in depth (e.g., to include host whole exome and whole genome sequencing) and in breadth (in particular, by integrating multiple data types).

The evolution of lncRNA repertoires and expression patterns in tetrapods.

Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that lncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for lncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.

The co-evolution of social institutions, demography, and large-scale human cooperation.

Human cooperation is typically coordinated by institutions, which determine the outcome structure of the social interactions individuals engage in. Explaining the Neolithic transition from small- to large-scale societies involves understanding how these institutions co-evolve with demography. We study this using a demographically explicit model of institution formation in a patch-structured population. Each patch supports both social and asocial niches. Social individuals create an institution, at a cost to themselves, by negotiating how much of the costly public good provided by cooperators is invested into sanctioning defectors. The remainder of their public good is invested in technology that increases carrying capacity, such as irrigation systems. We show that social individuals can invade a population of asocials, and form institutions that support high levels of cooperation. We then demonstrate conditions where the co-evolution of cooperation, institutions, and demographic carrying capacity creates a transition from small- to large-scale social groups.

Effects of long-term irrigation with treated wastewater. Part I: Evolution of soil physico-chemical properties

The long-term impact of irrigation on a Mediterranean sandy soil irrigated with Treated wastewater (TWW) since 1980 was evaluated. The main soil properties (CEC, pH, size distribution, exchangeable cations and chloride, hydraulic conductivity) as well as the organic matter and Cu, Cr and Pb speciation in an irrigated soil and a non-irrigated control soil at various soil depths were monitored and compared during a 2 years experiment. In this first part, the evolution of the physico-chemical soil properties was described. The irrigation with TWW was beneficial with regard to water and nutrient supplying. All the exchangeable cations other than K(+) were higher in the irrigated soil than in the reference one. A part of the exchangeable cations was not fixed on the exchange complex but stored as labile salts or in concentrated soil solution. Despite the very sandy soil texture, both saturated and unsaturated hydraulic conductivity exhibited a significant diminution in the irrigated soil, but remained high enough to allow water percolation during rainy periods and subsequent leaching of accumulated salts, preventing soil salinization. In the irrigated soil, exchangeable sodium percentage (ESP) exhibited high values (20% on average) and the soil organic C was lower than in the reference. No significant effect was noticed on soil mineralogical composition due to irrigation. (C) 2010 Published by Elsevier Ltd.

Evolution of the P-type II ATPase gene family in the fungi and presence of structural genomic changes among isolates of Glomus intraradices.

BACKGROUND: The P-type II ATPase gene family encodes proteins with an important role in adaptation of the cell to variation in external K+, Ca2+ and Na2+ concentrations. The presence of P-type II gene subfamilies that are specific for certain kingdoms has been reported but was sometimes contradicted by discovery of previously unknown homologous sequences in newly sequenced genomes. Members of this gene family have been sampled in all of the fungal phyla except the arbuscular mycorrhizal fungi (AMF; phylum Glomeromycota), which are known to play a key-role in terrestrial ecosystems and to be genetically highly variable within populations. Here we used highly degenerate primers on AMF genomic DNA to increase the sampling of fungal P-Type II ATPases and to test previous predictions about their evolution. In parallel, homologous sequences of the P-type II ATPases have been used to determine the nature and amount of polymorphism that is present at these loci among isolates of Glomus intraradices harvested from the same field. RESULTS: In this study, four P-type II ATPase sub-families have been isolated from three AMF species. We show that, contrary to previous predictions, P-type IIC ATPases are present in all basal fungal taxa. Additionally, P-Type IIE ATPases should no longer be considered as exclusive to the Ascomycota and the Basidiomycota, since we also demonstrate their presence in the Zygomycota. Finally, a comparison of homologous sequences encoding P-type IID ATPases showed unexpectedly that indel mutations among coding regions, as well as specific gene duplications occur among AMF individuals within the same field. CONCLUSION: On the basis of these results we suggest that the diversification of P-Type IIC and E ATPases followed the diversification of the extant fungal phyla with independent events of gene gains and losses. Consistent with recent findings on the human genome, but at a much smaller geographic scale, we provided evidence that structural genomic changes, such as exonic indel mutations and gene duplications are less rare than previously thought and that these also occur within fungal populations.

Social Evolution in ants

Review of the book . Social Evolution in Ants. Bourke, A. F. G. and Franks, N. R. 1995. Princeton University Press, Princeton, New Jersey, xiii + 529 pp. ISBN o-691-04427-9 (cl), O-691 -04426-o (pbk)

Evolution, société, éthique : darwinisme social versus éthique évolutionniste

L'éthique évolutionniste (EE) est une branche de la philosophie morale à la fois fascinante et génératrice de craintes, qui considère les mécanismes darwiniens et les données évolutives sur la socialité animale et humaine comme pertinents pour une réflexion éthique. Ce courant de pensée est souvent mal compris ; beaucoup de lecteurs critiques l'associent au darwinisme social et au cortège d'horreurs qu'il a servi à justifier. Il vaut cependant la peine de résister à la tentation de réduire l'EE au darwinisme social et de chercher à analyser objectivement l'intérêt d'adopter une approche évolutionnaire en éthique. L'objet de cet article est de 'dédiaboliser' l'EE tout en explorant ses limites. Je commencerai par mentionner deux manières d'intégrer un raisonnement darwinien dans le domaine des sciences politiques et sociales: le darwinisme social et ce que l'on pourrait appeler le darwinisme pro-social. Je mettrai ensuite en évidence les erreurs fondamentales sur lesquelles repose le darwinisme social afin de montrer qu'il n'est pas possible aujourd'hui pour un éthicien évolutionniste de défendre les idées propres à ce courant (à moins de faire preuve de malhonnêteté intellectuelle). Au contraire, l'EE semble s'approcher davantage de l'état d'esprit du darwinisme pro-social sans pour autant s'y assimiler car elle restreint sa réflexion au niveau de l'éthique théorique. Dans un second temps, il s'agira de présenter en quoi consiste précisément l'EE, quels sont ses domaines de réflexion, et quelle est sa pertinence au niveau des différents domaines de l'éthique. Une focale particulière sera mise sur les questions de la genèse de la moralité et du passage délicat des faits aux normes.

Artemisia (Asteraceae): Understanding its evolution using cytogenetic and molecular systematic tools, with emphasis on subgenus Dracunculus

The genus Artemisia is one of the largest of the Asteraceae family, with more than 500 species. It is widely distributed mainly across the Northern Hemisphere, being profusely represented in the Old World, with a great centre of diversification in Asia, and also reaching the New World. The evolution of this genus has been deeply studied using different approaches, and polyploidy has been found to perform an important role leading to speciation processes. Karyological, molecular cytogenetic and phylogenetic data have been compiled in the present review to provide a genomic characterization throughout some complexes within the genus.

Public Art. Timeline of the XXth Century Evolution

The concept of public art is a polysemic term, and the dispersion of its meaning is reflected in the different ways of working during the XXth Century. It cross the fields of sculpture, monument, visual arts and urban space, defined from a civic perspective. This timeline had been constructed after the publications of my PhD: http://www.tesisenred.net/handle/10803/1549

The evolution of social discounting in hierarchically clustered populations.

The expression of a social behaviour may affect the fitness of actors and recipients living in the present and in the future of the population. When there is a risk that a future reward will not be experienced in such a context, the value of that reward should be discounted; but by how much? Here, we evaluate social discount rates for delayed fitness rewards to group of recipients living at different positions in both space and time than the actor in a hierarchically clustered population. This is a population where individuals are grouped into families, families into villages, villages into clans, and so on, possibly ad infinitum. The group-wide fitness effects are assumed to either increase or decrease the fecundity or the survival of recipients and can be arbitrarily extended in space and time. We find that actions changing the survival of individuals living in the future are generally more strongly discounted than fecundity-changing actions for all future times and that the value of future rewards increases as individuals live longer. We also find that delayed fitness effects may not only be discounted by a constant factor per unit delay (exponential discounting), but that, as soon as there is localized dispersal in a population, discounting per unit delay is likely to fall rapidly for small delays and then slowly for longer delays (hyperbolic discounting). As dispersal tends to be localized in natural populations, our results suggest that evolution is likely to favour individuals that express present-biased behaviours and that may be time-inconsistent with respect to their group-wide effects.

Systematic and biogeographic relationships of the Japanese white-toothed shrew (Crocidura dsinezumi)

To assess the zoogeographic and phylogenetic relationships of C. dsinezumi, its systematic position has been investigated through electrophoretic comparisons. These comparisons comprise typical Indomalayan and Palaearctic species, including C. russula, the supposed sister taxon of the Japanese white-toothed shrew. The range of measured genetic distances that separate dsinezumi from the other shrews (Nei's D = 0.232-0.406) is typical for interspecific comparisons among Crocidura taxa. Our results reinforce morphologic considerations that suggest C. dsinezumi be treated as a valid species. Phylogenetic relationships deduced from a cladistic treatment of allozyme data refute the possibility that the western Palaearctic C. russula is the sister taxon of C. dsinezumi. Zoogeographic interpretation of the genetic results indicates that the Southeast Asian representatives constitute a clade distinct from one that includes the Palaearctic species. However, C. dsinezumi is difficult to assign to either clade due to many intermediate or plesiomorphic electrophoretic characters. Unlike the major karyologic and biochemical separation that divides Afrotropical and Palaearctic species, the subdivision between Palaearctic and Indomalayan Crocidura is not correlated with any trend in karyotypic evolution. It also is shown that the Eurasiatic species of Crocidura possessing 2n = 40 chromosomes (including C. dsinezumi) do not represent a particular clade, but probably share a plesiomorphic character. Further analysis of other Indian or Asiatic species is needed to test whether the Palaearctic versus Indomalayan separation is due to real zoogeographic barriers or whether it is the result of limited samples.