Lines of Research

1.     Human genetic variation in the context of  great ape evolution.

GreatApe_Heterozygosity

Characterizing the variation of thousand of human genomes is standard today. However, primates (our closest relatives) are the ideal set of species to study the evolution of these features from both mechanistic and adaptive points of view.

In this line of research, we use genomic approaches in primate genomes to understand the impact of variants in the evolution of every species to provide a proper perspective to the differences among species.

Publications related:

  • Prado-Martinez, Sudmant et al. Nature. 2013
  • Hormozdiari et al. Proc Natl Acad Sci U S A. 2013
  • Sudmant et al. Genome Res. 2013
  • Carbone et al. Nature 2014
  • Xue et al. Science. 2015
  • Valles-Ibáñez et al. GBE 2016

 

2. Evolution of human gene regulation

FIG1_tree_correlation.pdf

DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex disease. However, the dynamics of DNA methylation changes between human and their closest relatives is still poorly understood. In this project, we evaluate methylation patterns in recent human evolution. We identified a significant positive relationship between the rate of coding variation and alterations of methylation at the promoter level.

Publications related:

  • Hernando et al. Plos Genetics 2013
  • Heyn et al. Genome Research 2013
  • Hernando et al. NAR 2015
  • Hernando et al. Plos Genetics 2015 (Review)

 3. Canid evolution.

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        The domestic dog has been widely recognized as an important organism for studying the relationship between selection, genome variation, and phenotypic diversity. Both dogs and wolves have been extensively surveyed using mtDNA, microsatellites, SNPs  but structural variation, including variation in multicopy gene families, has not been fully characterized in canines. 

Publications related:

  • Freedman et al. Plos Genetics 2013
  • Ramirez et al. BMC genomics 2014
  • Freedman et al. Plos Genetics 2015
  • Fan et al. Genome Research 2016

4. Accelerated exon evolution in human duplicated sequences.

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Genes within segmental duplications are overlooked in most studies of selection due to the limitations of draft nonhuman genome assemblies. Using a novel approach, we detected exons with an accumulation of high-quality nucleotide differences between the human assembly and shotgun sequencing reads from single human and macaque individuals.

Publications related:

  • Lorente-Galdos et al. Genome Biol. 2013