Our main line of research is centered on the discovery of the extent of all kinds of genome variation within phenotypically different genomes. Specifically, we study genome variation (centered on CNVs), gene expression and epigenetic differences in the human species in the context of great ape evolution and other mammalian genomes such as canids. Our goal is to create an integrated view of genome evolution by studying changes in the composition, frequency, size and location at every major branch point of recent human evolution.
Genomic variation in ape genomes
Characterizing the variation of thousands of human genomes is standard today. However, primates (our closest relatives) are the ideal set of species for studying the evolution of these features from both mechanistic and adaptive points of view. In this line of research, we use genomic approaches in humans and primates to understand the impact of variants in the evolution of every species to provide a proper perspective to the differences among species.
Epigenetics and transcriptomics of non-human primates
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 humans 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.
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 and SNPs, but structural variation, including variation in multicopy gene families, has not been fully characterized in canines.
Lab website: Comparative Genomics Lab
Hernandez-Rodriguez, J.; Arandjelovic, M.; Lester J.; de Filippo, C.; Weihmann, A.; Meyer, M.; Angedakin, S.; Casals, F.; Navarro, A.; Vigilant, L.; Kühl, H.S.; Langergraber, K.; Boesch, C.; Hughes, D.; Marques-Bonet, T. 2018. The impact of endogenous content, replicates and pooling on genome capture from faecal samples. Molecular Ecology Resources. 18(2):319-333 doi: 10.1111/1755-0998.12728
Venkatesh, B.; Lee, A.P.; Ravi, V.; [20 authors]; Marques-Bonet, T.; [6 authors]; Wilson, R.K.; Brenner, S.; and Warren, W.C. 2014. Elephant shark genome provides unique insights into gnathostome evolution. Nature 505 (7482):174-179.
Watson, C.T.; Marques-Bonet, T.; Sharp, A.J.; and Mefford, H.C. 2014. The Genetics of Microdeletion and Microduplication Syndromes: An Update. Annual Review of Genomics and Human Genetics 15 (1):215-244.
Worley, K.C.; Warren, W.C.; Rogers, J.; Locke, D.; Muzny, D.M.; Mardis, E.R.; Marques- Bonet, T.; Lorente-Galdós, B.; et al The Marmoset Genome, SequencingAnalysis, Consortium. 2014. The common marmoset genome provides insight into primate biology and evolution. Nature Genetics 46 (8):850-857