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 - population genomics, adaptation, speciation with gene flow, domestication
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.
Currently I am investigating genomic patterns of divergence between black cottonwood (Populus trichocarpa) and balsam poplar (P. balsamifera) two closely related tree species in North America. These species are extremely similar phenotypically (except in flower and fruit morphology) yet have very different ecological requirements suggesting that they are diverging adaptively. This summer I will be collecting plant material in a South/North transect from Southern British Columbia to the Yukon. Genotyping By Sequence of population pools will be used and analyzed in a cline theory framework to uncover genes involved in species differences and adaptation.
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.
Back cottonwood is a tree species currently being domesticated for use as a Biofuels feedstock. Using whole genome and transcriptome polymorphism data, in collaboration with colleagues from the Bioenergy Sciences Centre (USA), I developed a 34K genotyping array (Geraldes et al. submitted) to perform whole genome association analysis (GWAs) to determine the genetic architecture of growth (yield) and wood quality (efficiency of biomass conversion to bioenergy) traits. The findings from these study will provide insight into the species biology and inform poplar breeding programs.
Sex chromosome characterization and evolution
Mammalian Y chromosomes are highly degenerated and their 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
Biology 418 - Evolutionary Ecology at UBC (Winter 2011/Spring 2013).
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
News and Views editor for Molecular Ecology (2010 to present).
Publications
PubMed
Google Scholar Profile
15. Geraldes, A., DiFazio, S.P., Slavov, G.T., Ranjan, P., Muchero, W., Hannemann, J., Gunter, L.E., Wymore, A.M., Grassa, C.J., Farzaneh, N., Porth, I., Mckown, A.D., Skyba, O., Li, E., Fujita, M., Klapste, J., Martin, J., Schackwitz, W., Pennacchio, C., Rokhsar, D., Friedmann, M.C., Wastenays, G.O., Guy, R.D., El-Kassaby, Y.A., MAnsfield, S.D., Cronk, Q.C.B., Ehlting, J., Douglas, C.J., Tuskan, G.A. (in press). A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species. Molecular Ecology Resources, doi: 10.1111/1755-0998.12056.
14. Porth, I., Klápště,J., Skyba, O., Lai, B., Geraldes, A., Muchero, W., Tuskan, G.A., Douglas, C.J., El-Kassaby, Y.A., Mansfield, S.D. 2013. Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control, and genetic correlations. New Phytologist, 197:777-90.
13. Slavov, G. T., DiFazio, S. P., Martin, J., Schackwitz, W., Muchero, W., Rodgers-Melnick, E., Lipphardt, M. F., Pennacchio, C. P., Hellsten, U., Pennacchio, L., Gunter, L. E., Ranjan, P., Vining, K., Pomraning, K. R., Wilhelm, L. J., Pellegrini, M., Mockler, T., Freitag, M., Geraldes, A., El-Kassaby, Y. A., Mansfield, S. D., Cronk, Q. C. B., Douglas, C. J., Strauss, S. H., Rokhsar, D., Tuskan, G.A. 2012. Genome Resequencing Reveals Multiscale Geographic Structure and Extensive Linkage Disequilibrium in the Forest Tree Populus trichocarpa. New Phytologist, 196:713-25.
12. Wang, Z., Hobson, N., Galindo, L., Zhu, S., Shi, D., McDill, J., Yang, L., Hawkins, S., Neutelings, G., Datla, R., Lambert, G., Galbraith, D., Grassa, C., Geraldes, A., Cronk, Q., Cullis, C., Dash, P., Kumar, P., Cloutier, S., Sharpe, A., Wong, G., Wang, J., Deyholos, M. 2012. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. The Plant Journal, 72:461-73.
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.
