Post-doctoral researcher - Genome BC Applied Genomics Innovation Program (AGIP) project: Optimized Populus feedstocks and novel enzyme systems for a British Columbia bioenergy sector.
Contact - geraldes(at)interchange(dot)ubc(dot)ca
Topics - SNP discovery, adaptation, genotype-phenotype association
Project outline - This is a large multidisciplinary project that will use genomic and metabolomic approaches to characterize the phenotypic and genetic diversity of Populus trichocarpa (black cottonwood, or poplar) accessions relevant to potential future uses of poplars as lignocellulosic feedstocks for biofuel production. As part of the project I will be analyzing transcriptome massive parallel resequencing data from several trees from British Columbia. The variation found will be parsed and candidate markers will be used to: (i) characterize the genetic variation within the species, (ii) detect signatures of positive selection and, (iii) perform a large association study in a common garden to detect genes involved in traits related to biomass, growth and cell wall composition.
Research interests
Adaptation
Finding the genes involved in adaptation of a species to its habitat is a major endeavor of evolutionary biology. Populus trichocarpa occurs naturally from Alaska to California. It can be found from sea level up to more than 2100 m. It grows on a variety of soils: from moist silts, gravels and sands to rich humus, loams and, occasionally, clays. As so, opportunities for detecting adaptation of different populations to their specific habitat are numerous. In this project we will use the nucleotide variability found through resequencing of multiple accessions to identify genes bearing signatures of positive selection. Additionally, SNP markers at a large number of candidate genes will be used in a large association study to find genes that are responsible for key adaptive phenotypes.
Speciation
I am interested in understanding the evolution of reproductive barriers among closely related populations.
For my PhD thesis I used Oryctolagus cuniculus (the European rabbit) as a model. We found that, overall, levels of gene flow among rabbit subspecies in the Iberian Peninsula are high. Despite high levels of gene flow, a few regions of the genome remain highly differentiated and they all are located in regions that likely have low recombination rates (the centromeres of the X chromosome and chromosome 7), or, are non-recombining (the Y chromosome and the mitochondria).
For my Post-Doctoral research at the University of Arizona, I focused on the three subspecies of Mus musculus (house mice). We found that there is gene flow among all subspecies, but that levels of gene flow are highly heterogeneous across the genome. Namely, we inferred that gene flow is reduced on the X chromosome relative to the autosomes, as is gene flow on the Y chromosome between the two European subspecies, but not between the eastern European subspecies (M. m. musculus) and the Asian subspecies (M. m. castaneus). Currently I am investigating the extent of this variability across autosomal loci and the potential forces driving it.
Domestication
Domestication is one of the most important technological innovations in human history. It is achieved by strong selection for traits deemed important by the domesticating species. I am interested in understanding the genomic signatures left by this strong and recurrent selection. The recent availability of the sequence of the rabbit genome, the fact that rabbit domestication likely started during the last millennium, and the availability of both the domesticated form and the population that gave rise to it, makes it a unique mammalian model to study this process.
Sex chromosome characterization and evolution
Mammalian Y chromosomes are highly degenerated and it's gene content highly variable among species. I am interested in exploring the processes that shape Y chromosome evolution and I am using the European rabbit as a model to do so. In a first step we have characterized the complete sequence of the sex determining gene (SRY), and found that this gene is likely duplicated in the Y chromosome. Moreover we have found strong evidence that the two copies are evolving in concert through gene conversion.
Education
1996-2000 Universidade do Porto, Portugal. Biology degree.
2001-2006 Universidade do Porto, Portugal. PhD (advisor Nuno Ferrand)
2006-2008 University of Arizona, USA. PostDoc (advisor Michael Nachman)
Publications
Geraldes, A., Basset, P., Gibson, B., Smith, K., Harr, B., Yu, H. T., Bulatova, N., Ziv, Y., and Nachman, M. W. 2008. Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes. Molecular Ecology 17: 5349-5363.
Geraldes, A., Carneiro, M., Delibes-Mateos, M., Villafuerte, R., Nachman, M. W., and Ferrand, N. 2008. Reduced introgression of the Y chromosome between subspecies of the European rabbit (Oryctolagus cuniculus) in the Iberian Peninsula. Molecular Ecology 17: 4489-4499.
News and Views in Molecular Ecology about this work: Payseur, B.A. 2009. Y not introgress? Insights into the genetics of speciation in European rabbits. Molecular Ecology 18:23-24.
Salcedo, T., Geraldes, A., and Nachman, M. W. 2007. Nucleotide variation in wild and inbred mice. Genetics, 177: 2277-2291.
Geraldes, A., Ferrand, N. and Nachman, M. W. 2006. Contrasting patterns of introgression at X-linked loci across the hybrid zone between subspecies of the European rabbit (Oryctolagus cuniculus). Genetics, 173: 919-933.
Geraldes, A. and Ferrand, N. 2006. A 7-bp insertion in the 3' untranslated region suggests the duplication and concerted evolution of the rabbit Sry gene. Genetics Selection and Evolution, 38: 313-320.
Geraldes, A., Rogel-Gaillard, C. and Ferrand, N. 2005. High levels of nucleotide diversity in the European rabbit (Oryctolagus cuniculus) SRY gene. Animal Genetics, 36: 349-351.
