La Biología Evolutiva suele entrar en conflicto con un punto de vista muy arraigado de entender a los seres vivos, denominado esencialismo. Esta idea, cuyo origen se encuentra en Aristóteles y Platón, consideraba que los seres vivos poseen algunas características esenciales que no pueden ser cambiadas. Veamos un ejemplo. Si pintamos a una cebra de [...]

Coevolutionary conflict among imprinted genes that influence traits such as offspring growth may arise when maternal and paternal genomes have different evolutionary optima. This conflict is expected in outcrossing taxa with multiple paternity, but not self-fertilizing taxa. MEDEA (MEA) is an imprinted plant gene that influences seed growth. Disagreement exists regarding the type of selection acting on this gene. We present new data and analyses of sequence diversity of MEA in self-fertilizing and outcrossing Arabidopsis and its relatives, to help clarify the form of selection acting on this gene. Codon-based branch analysis among taxa (PAML) suggests that selection on the coding region is changing over time, and nonsynonymous substitution is elevated in at least one outcrossing branch. Codon-based analysis of diversity within outcrossing A. lyrata ssp. petraea (OmegaMap) suggests that diversifying selection is acting on a portion of the gene, to cause elevated nonsynonymous polymorphism. Providing further support for balancing selection in A. lyrata, HKA analysis indicates that diversity/divergence at silent sites in the MEA promoter and genic region is elevated relative to reference genes, and there are deviations from the neutral frequency spectrum. This combination of positive selection as well as balancing and diversifying selection in outcrossing lineages is consistent with other genes influence by evolutionary conflict, such as disease resistance genes. Consistent with predictions that conflict would be eliminated in self-fertilizing taxa, we found no evidence of positive, balancing or diversifying selection in A. thaliana promoter or genic region.

Sequence comparison of the medaka, Oryzias latipes, MHC class I region between two inbred strains, the HNI (derived from the Northern Population) and the Hd-rR (from the Southern Population), revealed a ~100 kb highly divergent segment encompassing two MHC class IA genes, Orla-UAA and Orla-UBA, and two immunoproteasome beta subunit genes, PSMB8 and PSMB10. To elucidate the genetic diversity of this region, we analyzed polymorphisms of the PSMB8 and PSMB10 genes using wild populations of medaka from three genetically different groups: the Northern Population, the Southern Population, and the China–West Korean Population. A total of 1245 specimens from ten localities were analyzed, and all the PSMB8 and PSMB10 alleles were classified into the N (fixed in the HNI strain) or the d (fixed in the Hd-rR strain) lineage. PCR analysis of the region from PSMB8 to PSMB10 indicated that the two allelic lineages of these genes are segregating together constituting dichotomous haplotypic lineages. Both haplotypic lineages were identified in all three groups, although the frequency of d haplotypic lineage (73–100%) was much higher than that of N haplotypic lineage (0–27%) in all analyzed populations. The two allelic lineages of the PSMB8 gene showed curious substitutions at the 31st and 53rd residues of the mature peptide, which are likely involved in formation of the S1 pocket, suggesting that these alleles have a functional difference in cleavage specificity. These results indicate that the two medaka MHC haplotypic lineages encompassing the PSMB8 and PSMB10 genes are maintained in wild populations by a balancing selection.

Assessment of the impact of DNA replication on genome architecture in Eukaryotes has long been hampered by the scarcity of experimental data. Recent work, relying on computational predictions of origins of replication, suggested that replication might be a major determinant of gene organization in human (Huvet et al., 2007). Here, we address this question by analyzing the first large-scale dataset of experimentally determined origins of replication in human: 283 origins identified in HeLa cells, in 1% of the genome covered by ENCODE regions (Cadoret et al., 2008). We show that origins of replication are not randomly distributed, as they display significant overlap with promoter regions and CpG islands. The hypothesis of a selective pressure to avoid frontal collisions between replication and transcription polymerases is not supported by experimental data, as we find no evidence for gene orientation bias in the proximity of origins of replication. The lack of a significant orientation bias remains manifest even when considering only genes expressed at a high rate, or in a wide number of tissues, and is not affected by the regional replication timing. Gene expression breadth does not appear to be correlated with the distance from the origins of replication. We conclude that the impact of DNA replication on human genome organization is considerably weaker than previously proposed.

Understanding how the variability of protein structure arises during evolution and leads to new structure-function relationships ultimately promoting evolutionary novelties is a major goal of molecular evolution and is critical for interpreting genome sequences. We addressed this issue using the ecdysone receptor, a major developmental factor which controls development and reproduction of arthropods. The functional ecdysone receptor is a heterodimer of two nuclear receptors: ECR, which binds ecdysteroids, and its obligatory partner USP which is orthologous to the retinoid X receptor (RXR) of vertebrates. Both genes underwent a dramatic increase of evolutionary rate in Mecopterida, the major insect terminal group containing Dipteras and Lepidopteras. We therefore questioned the implication of this event in terms of coevolution of their dimerisation interface.

A structural comparison revealed a 30% larger Ligand Binding Domain (LBD) heterodimerisation surface in the Lepidoptera Heliothis when compared to basal insects, associated with a symmetrisation of the interface which is exceptional for nuclear receptors. Reconstruction of ancestral sequences and homology modelling of the ancestral Mecopterida ECR-USP reveal that this enlarged dimerisation surface is a synapomorphy for Mecopterida. Furthermore, we show that the residues implicated in the new dimerisation surface underwent specific evolutionary constraints in Mecopterida indicative of their new and conserved role in the dimerisation interface. Most of all, the novel surface originates from a 15° torsion of a subdomain of USP LBD toward its partner ECR which is a long range consequence of the peculiar position of a Mecopterida specific insertion in loop L1-3, located outside of the interaction surface, in a less crucial domain of the partner protein. These results indicate that the coevolution between ECR and USP occurred through a novel mechanism of intra-molecular epistasis which will undoubtedly be generalised for other molecules since it uses flexibility of a less constrained region of a protein to modify the structure of another, critical part of the molecule.

Its strong intergenerational bottlenecks and effectively asexual reproduction have led Buchnera aphidicola, the endocellular symbiotic bacterium of aphids, to spectacular evolutionary and genomic changes in comparison with its free-living bacterial cousins. These changes summarize into high fixation rates of mildly deleterious destabilizing mutations. This predicts a sharp decline of its fitness and the consequent early demise of this endosymbiotic bacterium. Its survival for hundreds of millions of years casts doubt on genetic drift as the sole evolutionary force and seeks further explanation. We identify in Buchnera selection to increase the robustness of proteins to misfolding translation errors. Translational robustness varies between Buchnera lineages and protein functional categories. Metabolic proteins have been under selection for translational efficiency, while evolutionary rates of proteins involved in fundamental cellular processes have been largely determined by selection for translational robustness. We detect the strongest signal of translational robustness in B. aphidicola Cinara cedri with a very similar pattern to that inferred for the most common symbiotic ancestor of Buchnera lineages. This indicates that B. aphidicola Cinara cedri lineage may have probably reached the minimum evolutionary stable gene composition for endosymbiotic lifestyle. The evolutionary patterns from the comparative genomic analyses of these endosymbionts support a paradoxically complex dynamic for apparently simple genomes.

Myelination, the ensheathment of axons by membranes of highly specialized glial cells, has been a crucial innovation during early vertebrate evolution. It enables high nerve signal conduction velocities, while maintaining nervous system size and energy requirements at moderate levels. Consequently, myelination has been conserved in all extant gnathostome vertebrates. In a genome-wide mRNA expression screen, we identified several novel neural crest and myelin-specific transcripts in the zebrafish (Danio rerio). Here, we describe the characterization of two proteins, Zwilling-A and -B, which are exclusively expressed in myelinating glia of teleosts. They are structurally homologous and are translated from a common, bicistronic transcript. No similarities to sequences or domains of other proteins were detected. Analysis of phylogeny, genomic organization, and genomic syntenies suggests that the zwi gene has appeared soon after the teleost-specific genome duplication event and evolved under conservative selective pressure. We hypothesize that Zwilling-A and -B serve important physiological functions in teleost myelin.

The McDonald-Kreitman (MK) test, which compares the ratio of polymorphism to divergence at nonsynonymous and synonymous sites, is frequently used to detect adaptive evolution in protein-coding sequences. Because the two classes of sites share a common evolutionary history, the MK test is thought to be robust to most demographic factors. However, weak selection on nonsynonymous sites can bias the MK test, especially when a species' effective population size has not been constant. Here we present an empirical analysis of the influence of demography on the MK test by comparing test results for a common set of 136 genes, including a set of sex-biased genes that shows a strong signal of adaptive evolution, in two Drosophila melanogaster populations: an ancestral population from Africa and a derived population from Europe. The latter has undergone a relatively recent bottleneck, which has reduced its effective population size. We find that the MK test has less power to detect positive selection in the European population for two reasons. First, the overall reduced level of standing variation decreases the statistical power of the test. Second, the segregation of slightly-deleterious nonsynonymous mutations biases the MK test away from detecting positive selection. The latter effect is stronger for X-linked genes, which have experienced the greatest reduction in effective population size outside of Africa, and also leads to the underestimation of rates of adaptive protein evolution by multi-locus implementations of the MK test. Interestingly, a subset of autosomal female-biased genes shows an increased signal of adaptive evolution in the European population. This is inconsistent with currently accepted demographic scenarios and may reflect female-specific changes in selective constraint following the colonization of non-African habitats.

The diversity of exon-2 (peptide binding region) of the DQB1 locus (Class II, MHC) was investigated on an extended sample of populations of three focal cetacean species (two sibling delphinid species, and another in the same family). We tested the hypothesis that dolphin populations with a world-wide distribution across different habitats and geographic regions will be under differential selective pressure by comparing DQB1 variation with variation at neutral markers, and by investigating putative functional residues within the exon-2 sequence at the population level. Variation at the DQB1 locus was not correlated to neutral differentiation (assessed by comparison with microsatellite DNA markers), and overall FST values were significantly lower for the MHC locus, consistent with expectations for balancing selection. Measures of heterozygosity and dn/ds ratios were also consistent with balancing selection. However, outliers in the FST comparisons and the analysis of putative functional residues suggested incidences of directional selection in local populations.