Post-doctoral researcher - Genome BC, AGIP project: Optimized Populus feedstocks and novel enzyme systems for a British Columbia bioenergy sector (2009-2011)
Research Associate and Co-PI - Genome Canada, POPCAN project: genetic improvement of poplar trees as a Canadian bioenergy feedstock: clean energy from the poplar tree (2011-2014)
Contact - geraldes(at)mail(dot)ubc(dot)ca
Topics - genomics, adaptation, speciation with gene flow
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. Additionally, transcriptome data from several accessions of the closely related P. balsamifera will be used to detect gene flow across species boundaries.
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 (Geraldes et al. 2010) 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 centromere of the X chromosome, Geraldes et al 2006), or, are non-recombining (the Y chromosome and the mitochondria, Geraldes et al 2008). Recent studies have shown that loci near the centromere of other chromosomes also show high differentiation (Carneiro et al 2009).
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. We first contrasted patterns of gene flow between the autosomes, sex chromosomes and mitochondria and 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 (M. m. domesticus and M. m. musculus), but not between the eastern European subspecies (M. m. musculus) and the Asian subspecies (M. m. castaneus)(Geraldes et al 2008). We then focused on the autosomes and found that: i) levels of genetic differentiation among subspecies are highly heterogeneous, ii) differences in levels of genetic differentiation are highly correlated with the inferred amount of gene flow and iii) levels of gene flow are correlated with the local recombination rate (Geraldes et al 2011). These findings lend strong empirical support for the idea that regions of low recombination can be very important in the early stages of speciation even in the absence of large chromosomal rearrangements.
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. We have started by exploring the demographic history of the domestication process in rabbits (Carneiro et al 2011). Our findings support the idea that rabbits were domesticated recently in Southern France from a small pool of individuals (~1200). Despite this domestication bottleneck, domestic rabbits harbor significant amounts of nucleotide variability. Deviations from neutral expectations were found at two loci, suggesting that strong artificial selection could explain the impressive amounts of phenotypic variability observed in domestic rabbits.
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) (Geraldes et al 2005), and found that this gene is duplicated in the Y chromosome (Geraldes et al 2006). Recently, we have found strong evidence that the two copies are evolving in concert through gene conversion (Geraldes et al 2010).
Teaching
Taught Biology 418 - Evolutionary Ecology at UBC (Winter 2011).
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)
Editorial experience
As of 2010 I am, along with Dr. Nolan Kane, News and Views editor for Molecular Ecology.
Publications
11. Geraldes, A., Basset, P., Smith, K., Nachman, M. W. 2011. Higher differentiation among subspecies of the house mouse (Mus musculus) in genomic regions with low recombination. Molecular Ecology. Molecular Ecology, 20:4722-4736.
10. Carneiro, M., Afonso, S., Geraldes, A., Garreau, H., Bolet, G., Boucher, S., Tircazes, A., Queney, G., Nachman, M. W., Ferrand, N. 2011. The Genetic Structure of Domestic Rabbits. Molecular Biology and Evolution. Molecular Biology and Evolution, 28: 1785-1816.
9. Geraldes, A., Pang, J., Thiessen, N., Cezard, T., Moore, R., Zhao, Y., Tam, A., Wang, S., Friedmann, M., Birol, I., Jones, S.J.M., Cronk, Q.C.B. and Douglas, C.J. 2011. SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Molecular Ecology Resources, 11 (Suppl. 1): 81-92.
8. Geraldes, A., Rambo, T., Wing, R., Ferrand, N., and Nachman, M. W. 2010. Extensive gene conversion drives the concerted evolution of paralogous copies of the SRY gene in European rabbits. Molecular Biology and Evolution, 27: 2437-2440.
7. Geraldes, A. and Kane, N. 2010. Pushing north one bottleneck at a time: Site Frequency Spectra tell the history of Sitka spruce. News and Views perspective, Molecular Ecology, 19: 3837-3839.
6. 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.
5. 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.)
4. Salcedo, T., Geraldes, A., and Nachman, M. W. 2007. Nucleotide variation in wild and inbred mice. Genetics, 177: 2277-2291.
3. 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.
2. 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.
1. 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.
