Polimorfisme nucleotídic i canvis adaptatius recents

En observar els individus d'una espècie es detecten característiques que els fan estar especialment adaptats al medi biòtic i abiòtic en què es troben. La selecció natural és la força motriu dels canvis que donen lloc a noves adaptacions (selecció positiva o adaptativa) i és també responsable del manteniment de les adaptacions ja existents (selecció negativa o purificadora). Destriar els canvis adaptatius dels no adaptatius ha estat un objectiu important dels estudis evolutius. L'anàlisi de la variabilitat nucleotídica en les poblacions actuals pot contribuir a identificar gens o regions del genoma en les quals s'hagin produït canvis adaptatius en la seva història més recent. L'increment de freqüència d'una mutació avantatjosa afecta el nivell i el patró de la variabilitat en les zones adjacents a la diana de la selecció. L'empremta produïda per l'acció recent de la selecció natural permet inferir-ne l'acció. Tanmateix, la detecció que en una regió del genoma s'ha produït recentment un canvi adaptatiu constitueix l'inici d'una cursa de llarg recorregut per entendre l'adaptació en el nivell molecular.Individuals of any species exhibit some characteristics that render them especially adapted to their biotic and abiotic environment. Natural selection is the driving force of new adaptations (positive or adaptive selection), and it is also responsible for the maintenance of existing adaptations (negative or purifying selection). Disentangling adaptive from non-adaptive changes constitutes an important and long standing question in evolutionary biology. The analysis of nucleotide variation in extant populations can contribute to the identification of genes and genomic regions that have suffered adaptive changes in their most recent evolutionary history. The fixation of an advantageous mutation affects the level and pattern of variation at sites closely linked to the target of selection. The recent action of natural selection can thus be inferred through the footprint left on linked nucleotide variation. Detecting target genes of recent positive selection constitutes the first, though very important, step toward understanding adaptation at the molecular level

Odorant Receptor (Or) genes: polymorphism and divergence in the D. melanogaster and D. pseudoobscura Lineages

Background: In insects, like in most invertebrates, olfaction is the principal sensory modality, which provides animals with essential information for survival and reproduction. Odorant receptors are involved in this response, mediating interactions between an individual and its environment, as well as between individuals of the same or different species. The adaptive importance of odorant receptors renders them good candidates for having their variation shaped by natural selection. Methodology/Principal Findings: We analyzed nucleotide variation in a subset of eight Or genes located on the 3L chromosomal arm of Drosophila melanogaster in a derived population of this species and also in a population of Drosophila pseudoobscura. Some heterogeneity in the silent polymorphism to divergence ratio was detected in the D. melanogaster/D. simulans comparison, with a single gene (Or67b) contributing ~37% to the test statistic. However, no other signals of a very recent selective event were detected at this gene. In contrast, at the speciation timescale, the MK test uncovered the footprint of positive selection driving the evolution of two of the encoded proteins in both D. melanogaster ¿OR65c and OR67a ¿and D. pseudoobscura ¿OR65b1 and OR67c. Conclusions: The powerful polymorphism/divergence approach provided evidence for adaptive evolution at a rather high proportion of the Or genes studied after relatively recent speciation events. It did not provide, however, clear evidence for very recent selective events in either D. melanogaster or D. pseudoobscura

Comment on 'The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway'

Letter to the Editor on Wang M, Wang Q, Wang Z, Zhang X, Pan Y. The molecular evolutionary patterns of the insulin/FOXO signaling pathwa

Multiple and diverse structural changes affect the breakpoint regions of polymorphic inversions across the Drosophila genus

Chromosomal polymorphism is widespread in the Drosophila genus, with extensive evidence supporting its adaptive character in diverse species. Moreover, inversions are the major contributors to the genus chromosomal evolution. The molecular characterization of a reduced number of polymorphic inversion breakpoints in Drosophila melanogaster and Drosophila subobscura supports that their inversions would have mostly originated through a mechanism that generates duplications staggered double-strand breaks and has thus the potential to contribute to their adaptive character. There is also evidence for inversion breakpoint reuse at different time scales. Here, we have characterized the breakpoints of two inversions of D. subobscura O4 and O8 involved in complex arrangements that are frequent in the warm parts of the species distribution area. The duplications detected at their breakpoints are consistent with their origin through the staggered-break mechanism, which further supports it as the prevalent mechanism in D. subobscura. The comparative analysis of inversions breakpoint regions across the Drosophila genus has revealed several genes affected by multiple disruptions due not only to inversions but also to single-gene transpositions and duplications

The molecular characterization of fixed inversions breakpoints unveils the ancestral character of the Drosophila guanche chromosomal arrangements

Cytological studies revealed that the number of chromosomes and their organization varies across species. The increasing availability of whole genome sequences of multiple species across specific phylogenies has confirmed and greatly extended these cytological observations. In the Drosophila genus, the ancestral karyotype consists of five rod-like acrocentric chromosomes (Muller elements A to E) and one dot-like chromosome (element F), each exhibiting a generally conserved gene content. Chromosomal fusions and paracentric inversions are thus the major contributors, respectively, to chromosome number variation among species and to gene order variation within chromosomal element. The subobscura cluster of Drosophila consists in three species that retain the genus ancestral karyotype and differ by a reduced number of fixed inversions. Here, we have used cytological information and the D. guanche genome sequence to identify and molecularly characterize the breakpoints of inversions that became fixed since the D. guanche-D. subobscura split. Our results have led us to propose a modified version of the D. guanche cytological map of its X chromosome, and to establish that (i) most inversions became fixed in the D. subobscura lineage and (ii) the order in which the four X chromosome overlapping inversions occurred and became fixed

Characterization of dFOXO binding sites upstream of the Insulin Receptor P2 promoter across the Drosophila phylogeny

The insulin/TOR signal transduction pathway plays a critical role in determining such important traits as body and organ size, metabolic homeostasis and life span. Although this pathway is highly conserved across the animal kingdom, the affected traits can exhibit important differences even between closely related species. Evolutionary studies of regulatory regions require the reliable identification of transcription factor binding sites. Here we have focused on the Insulin Receptor (InR) expression from its P2 promoter in the Drosophila genus, which in D. melanogaster is up-regulated by hypophosphorylated Drosophila FOXO (dFOXO). We have finely characterized this transcription factor binding sites in vitro along the 1.3 kb region upstream of the InR P2 promoter in five Drosophila species. Moreover, we have tested the effect of mutations in the characterized dFOXO sites of D. melanogaster in transgenic flies. The number of experimentally established binding sites varies across the 1.3 kb region of any particular species, and their distribution also differs among species. In D. melanogaster, InR expression from P2 is differentially affected by dFOXO binding sites at the proximal and distal halves of the species 1.3 kb fragment. The observed uneven distribution of binding sites across this fragment might underlie their differential contribution to regulate InR transcription

Inversion evolutionary rates might limit the experimental identification of inversion breakpoints in non-model species

Chromosomal inversions are structural changes that alter gene order but generally not gene content in the affected region. In Drosophila, extensive cytological studies revealed the widespread character of inversion polymorphism, with evidence for its adaptive character. In Drosophila subobscura, polymorphism affects both its four large autosomal elements and its X (A) chromosome. The characterization of eight of these autosomal inversions breakpoints revealed that most of them originated through the staggered-breaks mechanism. Here, we have performed chromosomal walks to identify the breakpoints of two X-chromosome widely distributed inversions ¿A2 and A1¿ of D. subobscura. Inversion A2 is considered a warm-adapted arrangement that exhibits parallel latitudinal clines in the species ancestral distribution area and in both American subcontinents, whereas inversion A1 is only present in the Palearctic region where it presents an east-west cline. The duplication detected at the A2 inversion breakpoints is consistent with its origin by the staggered-breaks mechanism. Inversion A1 breakpoints could not be molecularly identified even though they could be narrowly delimited. This result points to chromosome walking limitations when using as a guide the genome of other species. Limitations stem from the rate of evolution by paracentric inversions, which in Drosophila is highest for the X chromosome

The origin of chromosomal inversions as a source of segmental duplications in the Sophophora subgenus of Drosophila

Chromosomal inversions can contribute to the adaptation of organisms to their environment by capturing particular advantageous allelic combinations of a set of genes included in the inverted fragment and also by advantageous functional changes due to the inversion process itself that might affect not only the expression of flanking genes but also their dose and structure. Of the two mechanisms originating inversions ectopic recombination, and staggered double-strand breaks and subsequent repair only the latter confers the inversion the potential to have dosage effects and/or to generate advantageous chimeric genes. In Drosophila subobscura, there is ample evidence for the adaptive character of its chromosomal polymorphism, with an important contribution of some warm-climate arrangements such as E1+2+9+12. Here, we have characterized the breakpoints of inversion E12 and established that it originated through the staggered-break mechanism like four of the five inversions of D. subobscura previously studied. This mechanism that also predominates in the D. melanogaster lineage might be prevalent in the Sophophora subgenus and contribute to the adaptive character of the polymorphic and fixed inversions of its species. Finally, we have shown that the D. subobscura inversion breakpoint regions have generally been disrupted by additional structural changes occurred at different time scales

Genomes and evolution: impact on current Biology

[CAT] L’estudi dels genomes és un tema central en la biologia del segle xxi. Tenim eines perfer-ne la descripció de la seqüència que avancen ràpidament i un repte important ara mateix és la interpretació de l’allau d’informació genòmica. La comprensió dels genomes comença amb la lectura comparada: les diferències entre els genomes dels diferents individus d’una població o una espècie i les diferències entre els genomes de diferents espècies són la clau per a la reconstrucció del procés evolutiu, per entendre els canvis funcionals i per a la integració de la informació genètica en complexes xarxes d’interacció funcional. Els genomes, doncs, recullen bona part de la informació dels éssers vius, i ens permeten entendre detalladament tant l’evolució de les espècies com les implicacions de l’adquisició de noves funcions i de l’emergència de noves adaptacions que, mitjançant la selecció natural, s’han anat esdevenint durant la història, la diversificació i el desplegament de la complexitat de la vida.[EN] The study of genomes is a central theme in 21st century biology. We now have the tools that enable us to advance rapidly to obtain and describe the sequences. However, a major challenge is to interpret the avalanche of genomic information. The understanding of genomes begins with a comparative reading: the differences between the genomes of different individuals in a population or in a species, and the differences between the genomes of different species, are the key to reconstruct the evolutionary process, to understand functional changes, and for the integration of genetic information into functional complex interaction networks. The genome thus includes much of the information of living beings, and it allows us to understand in detail both the evolution of species and the implications of the acquisition of new functions and the emergence of new adaptations, which, by natural selection, have taken place along the history, the diversification and the unfolding of the complexity of life.Peer reviewe