Armando Geraldes
me

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, divergence with gene flow, sex chromosomes, domestication


Research interests

Adaptation

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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. Development of a 34K SNP array (Geraldes et al. 2013) with markers ascertained through transcriptome (Geraldes et al. 2010) and genome (Slavov et al. 2012) resequencing will be used in a large association study to find genes that are responsible for key adaptive phenotypes. In parallel, I used a landscape genomics approach, including detection of genes under diversifying selection and correlations between allele frequencies and environmental variables, to understand how genetic variability is partitioned across the landscape and hot that partitioning is a product of the interplay of neutral and adaptive processes (Geraldes et al. 2014).

Speciation

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.

tric_bals

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. I am taking two approaches to detect the genes involved in reproductive isolation and adaptation to different environments in these species. First, I am using genotyping-by-sequencing of >300 accessions collected along a North/South (from the Yukon to Southern British Columbia) transect across the hybrid zone. The resulting data will be analyzed in a cline theory framework to uncover genes involved in species differences and adaptation. I will also be using whole genome sequences of accessions from both species away from the hybrid zone to understand the genomics of species divergence.

Domestication

rabbit_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.

nyc

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. 2013) 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. We have used this data to estimate the heritability of these traits (Porth et al. 2013; Mckown et al. in press) as well as phenotypic correlations between them. The findings from these studies will provide insight into the species biology and inform poplar breeding programs.

Sex chromosome characterization and evolution

sex

In most species, sex chromosomes arise from autosomes after the acquisition of a sex-determining gene. The suppression of recombination that ensues drives this pair down a unique path that can result in highly heteromorphic sex chromosomes and, sometimes even the loss of one of these. To better understand this unique process, I work with two systems that lie at extreme opposites of the sex chromosome evolution spectrum, the European rabbit and the Black cottonwood.
Mammalian Y chromosomes are old, highly degenerated and their gene content highly variable among species. I 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, I found strong evidence that the two copies are evolving in concert through gene conversion (Geraldes et al. 2010) which could delay the degenerating process of non-recombining Y chromosomes.
Contrary to mammals, most plants are hermaphroditic, but separation of sexes in different individuals (dioecy) evolved independently in several Angiosperms. Members of the genus Populus (poplars, cottonwoods, aspens) are dioecious and dioecy is under strong genetic control. There are no clearly distinct heteromorphic sex chromosomes but previous QTL experiments have mapped gender to chromosome XIX. With collaborators, I performed a genomewide association study in P. trichocarpa and recovered hundreds of SNPs significantly associated with gender. These results were confirmed in an independent mapping association and in closely related species. We have also show that despite their young age, these regions already bear some of the hallmarks of degeneration (Geraldes et al. 2015).


Teaching

Biology 418 - Evolutionary Ecology at UBC (Winter2011/Spring2013/Winter2016).
Forestry 432 - Molecular Ecology at UBC (Winter2015)


Education

1996-2000 Universidade do Porto, Portugal. Biology degree.
2001-2006 Universidade do Porto, Portugal. PhD (advisor Nuno Ferrand)
2006-2009 University of Arizona, USA. PostDoc (advisor Michael Nachman)
2009-2011 University of British Columbia, Canada. PostDoc (advisor Quentin Cronk)


Editorial experience

News and Views editor for Molecular Ecology (2010 to present) and Molecular Ecology Resources (2014 to present).
Special Issue coordinator for Molecular Ecology and Molecular Ecology Resources (2014 to present).
Deputy Managing Editor for Molecular Ecology and Molecular Ecology Resources (2014-2015).


Publications

MEC_COVER.jpg

PubMed
Google Scholar Profile

20. Geraldes A1, Hefer CA1, Capron A, Kolosova N, Martinez-Nuñez F, Soolanayakanahally RY, Stanton B, Guy RD, Mansfield SD, Douglas CJ, Cronk QCB (2015) Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus). Molecular Ecology 24:3243-3256.
1Geraldes and Hefer contributed equally to this work.
This is a Molecular Ecology 'From the Cover' manuscript.
(News and Views in Molecular Ecology about this work: Filatov D. 2015. Homomorphic plant sex chromosomes are coming of age. Molecular Ecology, 24:3217-3219.)

19. Crutsinger GM, Rudman SM, Rodriguez-Cabal MA, McKown AD, Sato T, MacDonald AM, Heavyside J, Geraldes A, Hart EM, LeRoy CJ, El-Sabaawi RW (2014) Testing a “genes-to-ecosystems” approach to understanding aquatic-terrestrial linkages. Molecular Ecology. 23:5888-5903.

18. Geraldes A, Farzaneh N, Grassa CJ, McKown AD, Guy RD, Mansfield SD, Douglas CJ, Cronk QCB (2014) Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow and natural selection in shaping patterns of population structure. Evolution, 68(11):3260-3280.

17. McKown AD, Klápšte J, Guy RD, Geraldes A, Porth I, Hannemann J, Friedmann M, Muchero W, Tuskan, GA, Ehlting J, Cronk QCB, El-Kassaby YA, Mansfield SD and Douglas CJ (2014) Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. New Phytologist, 203(2):535-553.

16. McKown AD, Guy RD, Klápšte J, Geraldes A, Friedmann M, Cronk QCB, El-Kassaby YA, Mansfield SD and Douglas CJ. (2014) Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa. New Phytologist, 201(4):1263–1276.

15. Geraldes A, DiFazio SP, Slavov GT, Ranjan P, Muchero W, Hannemann J, Gunter LE, Wymore AM, Grassa CJ, Farzaneh N, Porth I, Mckown AD, Skyba O, Li E, Fujita M, Klapste J, Martin J, Schackwitz W, Pennacchio C, Rokhsar D, Friedmann MC, Wastenays GO, Guy RD, El-Kassaby YA, Mansfield SD, Cronk QCB, Ehlting J, Douglas CJ, Tuskan GA. 2013. 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, 13(2):306-23.

14. Porth I, Klápště J, Skyba O, Lai B, Geraldes A, Muchero W, Tuskan GA, Douglas CJ, El-Kassaby YA, Mansfield SD. 2013. Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control, and genetic correlations. New Phytologist, 197:777-90.

13. Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio L, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler T, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QCB, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA. 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 MW. 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 MW, 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 SJM, Cronk QCB, Douglas CJ. 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, Nachman, MW. 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, 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 HT, Bulatova N, Ziv Y, Nachman MW. 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 MW, 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 BA. 2009. Y not introgress? Insights into the genetics of speciation in European rabbits. Molecular Ecology, 18:23-24.)

4. Salcedo T, Geraldes A, Nachman MW. 2007. Nucleotide variation in wild and inbred mice. Genetics, 177: 2277-2291.

3. Geraldes A, Ferrand N, Nachman MW. 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, 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, Ferrand N. 2005. High levels of nucleotide diversity in the European rabbit (Oryctolagus cuniculus) SRY gene. Animal Genetics, 36: 349-351.

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