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Laayouni H.,Institute of Evolutionary Biology UPF CSIC | Montanucci L.,Institute of Evolutionary Biology UPF CSIC | Sikora M.,Institute of Evolutionary Biology UPF CSIC | Mele M.,Institute of Evolutionary Biology UPF CSIC | And 14 more authors.
PLoS ONE | Year: 2011

Recombination varies greatly among species, as illustrated by the poor conservation of the recombination landscape between humans and chimpanzees. Thus, shorter evolutionary time frames are needed to understand the evolution of recombination. Here, we analyze its recent evolution in humans. We calculated the recombination rates between adjacent pairs of 636,933 common single-nucleotide polymorphism loci in 28 worldwide human populations and analyzed them in relation to genetic distances between populations. We found a strong and highly significant correlation between similarity in the recombination rates corrected for effective population size and genetic differentiation between populations. This correlation is observed at the genome-wide level, but also for each chromosome and when genetic distances and recombination similarities are calculated independently from different parts of the genome. Moreover, and more relevant, this relationship is robustly maintained when considering presence/absence of recombination hotspots. Simulations show that this correlation cannot be explained by biases in the inference of recombination rates caused by haplotype sharing among similar populations. This result indicates a rapid pace of evolution of recombination, within the time span of differentiation of modern humans. © 2011 Laayouni et al. Source


Ventura M.,University of Washington | Ventura M.,University of Bari | Catacchio C.R.,University of Washington | Catacchio C.R.,University of Bari | And 21 more authors.
Genome Research | Year: 2011

Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. Recent analyses have suggested that the genomes of chimpanzee and human have been particularly enriched for this form of genetic variation. Here, we set out to assess the extent of structural variation in the gorilla lineage by generating 10-fold genomic sequence coverage from a western lowland gorilla and integrating these data into a physical and cytogenetic framework of structural variation. We discovered and validated over 7665 structural changes within the gorilla lineage, including sequence resolution of inversions, deletions, duplications, and mobile element insertions. A comparison with human and other ape genomes shows that the gorilla genome has been subjected to the highest rate of segmental duplication. We show that both the gorilla and chimpanzee genomes have experienced independent yet convergent patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications, and bursts of retroviral integrations. Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human genomes. © 2011 by Cold Spring Harbor Laboratory Press. Source


Rodriguez J.A.,Institute of Evolutionary Biology UPF CSIC PRBB | Marigorta U.M.,Georgia Institute of Technology | Navarro A.,Institute of Evolutionary Biology UPF CSIC PRBB | Navarro A.,Center for Genomic Regulation | And 2 more authors.
Current Opinion in Genetics and Development | Year: 2014

The application of the principles of evolutionary biology into medicine was suggested long ago and is already providing insight into the ultimate causes of disease. However, a full systematic integration of medical genomics and evolutionary medicine is still missing. Here, we briefly review some cases where the combination of the two fields has proven profitable and highlight two of the main issues hindering the development of evolutionary genomic medicine as a mature field, namely the dissociation between fitness and health and the still considerable difficulties in predicting phenotypes from genotypes. We use publicly available data to illustrate both problems and conclude that new approaches are needed for evolutionary genomic medicine to overcome these obstacles. © 2014. Source


Camina-Tato M.,Autonomous University of Barcelona | Fernandez M.,Autonomous University of Barcelona | Morcillo-Suarez C.,University Pompeu Fabra | Morcillo-Suarez C.,National Institute for Bioinformatics INB | And 6 more authors.
Journal of Neuroimmunology | Year: 2010

We investigated caspase 8 (CASP8) as a candidate gene for multiple sclerosis (MS) susceptibility. Three SNPs (rs2037815, rs12990906 and rs1035140) were genotyped in 546 MS patients and 547 controls. For SNP rs2037815, GG homozygosity was associated with primary progressive multiple sclerosis (PPMS) when compared with relapse-onset MS and controls. We identified risk (GCA) and protective (ACT) haplotypes associated with PPMS when compared with relapse-onset MS and controls. GG homozygosity for SNP rs2037815 in PPMS patients was associated with a trend towards faster disease progression. These findings point to a role of CASP8 polymorphisms in the MS genetic risk in PPMS patients. © 2010 Elsevier B.V. Source


Navarro A.,University Pompeu Fabra | Navarro A.,National Institute for Bioinformatics INB | Navarro A.,Catalan Institution for Research and Advanced Studies | Faria R.,University Pompeu Fabra | Faria R.,University of Porto
Molecular Ecology | Year: 2014

The early period of genetics is closely associated with the study of chromosomal inversions. For almost a century, evolutionary biologists found evidence for the role of inversions in central processes such as adaptation and speciation. In spite of huge efforts, many questions remain about the evolutionary forces underlying the distribution and dynamics of inversions in natural populations. Fortunately, old problems can be solved with new tools. In this issue, Kapun et al. (2014) present a remarkable combination of resources and techniques, including publicly available data, karyotyping, statistical estimation of haplotypes, Pool-Seq data and experimental evolution, setting the ground for exciting developments in the field. © 2014 John Wiley & Sons Ltd. Source

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