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DE CARA Angeles

  • Agrigenomics, Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Universidade de Porto, Vairão, Portugal
  • Adaptation, Evolutionary Applications, Evolutionary Theory, Population Genetics / Genomics, Quantitative Genetics, Speciation

Recommendations:  0

Review:  1

Areas of expertise
I am a population geneticist with a focus on evolutionary and conservation biology. I apply computational and analytical methods to make hypothesis which I test in silico and with data from a wide range of organisms. I obtained my PhD in Physics analysing the Minority Game, where individuals have strategies to take decisions. I applied this framework to understand the dynamics of colonial breeding, collaborating with behavioural ecologists who worked with raptors. I first learnt population genetics during a stay abroad in my PhD and decided to move into that field, where I could apply my quantitative knowledge into biological questions with identifiable units. I thus obtained a position at the University of Edinburgh, where I worked on a debated topic, whether speciation can occur with of gene flow. I tackled that problem using a mathematical formalism which gave me deep insight into fundamental population and quantitative genetics. This led to two major contributions on the role of how small associations (linkage disequilibria) can slowly build up in the genome, leading to barriers to introgression between emerging species. After a break to look after my children, I obtained a postdoctoral position at the department of animal breeding at INIA (Spain), where I evaluated if marker arrays were better to maintain diversity in conservation programmes. There my programming skills and evolutionary knowledge were crucial and resulted in several key studies. Firstly, I established that using high density markers maintained most diversity compared with using genealogies. The precise density was established in a later study. Secondly, I studied how by maintaining the most diversity, deleterious variants could increase in frequency in the population, with negative long-term effects on their viability. Lastly, by using regions of the genome instead of single markers, I established how to reach a compromise between maintaining diversity and viability. I then moved to France, where I combined simulations and mathematical approximations with whole-genome data analyses. I analysed which method is best to understand adaptation at the genomic level, while I also studied demography and selection in Heliconius numata. During that period, I hosted three researchers and collaborated with people from previous departments and elsewhere. I analysed data from a variety of organisms, from domestic animals like cows and pigs, to model organisms, like Drosophila melanogaster. I learnt new methods and developed codes that others use and are publicly available. I am currently a postdoctoral researcher at CIBIO, where I disentangle the population genetics of Sus scrofa (wild boars and domestic pigs) and continue theoretical research and data analyses.

Review:  1

16 Nov 2022
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Divergence of olfactory receptors associated with the evolution of assortative mating and reproductive isolation in mice

Carole M. Smadja, Etienne Loire, Pierre Caminade, Dany Severac, Mathieu Gautier, Guila Ganem https://doi.org/10.1101/2022.07.21.500634

Tinder in mice: A match made with the sense of smell

Recommended by based on reviews by Angeles de Cara, Ludovic Claude Maisonneuve and 1 anonymous reviewer

Differentiation-based genome scans lie at the core of speciation and adaptation genomics research. Dating back to Lewontin & Krakauer (1973), they have become very popular with the advent of genomics to identify genome regions of enhanced differentiation relative to neutral expectations. These regions may represent genetic barriers between divergent lineages and are key for studying reproductive isolation. However, genome scan methods can generate a high rate of false positives, primarily if the neutral population structure is not accounted for (Bierne et al. 2013). Moreover, interpreting genome scans can be challenging in the context of secondary contacts between diverging lineages (Bierne et al. 2011), because the coupling between different components of reproductive isolation (local adaptation, intrinsic incompatibilities, mating preferences, etc.) can occur readily, thus preventing the causes of differentiation from being determined.

Smadja and collaborators (2022) applied a sophisticated genome scan for trait association (BAYPASS, Gautier 2015) to underlie the genetic basis of a polygenetic behaviour: assortative mating in hybridizing mice. My interest in this neat study mainly relies on two reasons. First, the authors used an ingenious geographical setting (replicate pairs of “Choosy” versus “Non-Choosy” populations) with multi-way comparisons to narrow down the list of candidate regions resulting from BAYPASS. The latter corrects for population structure, handles cost-effective pool-seq data and allows for gene-based analyses that aggregate SNP signals within a gene. These features reinforce the set of outlier genes detected; however, not all are expected to be associated with mating preference. 

The second reason why this study is valuable to me is that Smadja et al. (2022) complemented the population genomic approach with functional predictions to validate the genetic signal. In line with previous behavioural and chemical assays on the proximal mechanisms of mating preferences, they identified multiple olfactory and vomeronasal receptor genes as highly significant candidates. Therefore, combining genomic signals with functional analyses is a clever way to provide insights into the causes of reproductive isolation, especially when multiple barriers are involved. This is typically true for reinforcement (Butlin & Smadja 2018), suspected to occur in these mice because, in that case, assortative mating (a prezygotic barrier) evolves in response to the cost of hybridization (for example, due to hybrid inviability). 

As advocated by the authors, their study paves the way for future work addressing the genetic basis of reinforcement, a trait of major evolutionary importance for which we lack empirical data. They also make a compelling case using complementary approaches that olfactory and vomeronasal receptors have a central role in mammal speciation.


References:

Bierne N, Welch J, Loire E, Bonhomme F, David P (2011) The coupling hypothesis: why genome scans may fail to map local adaptation genes. Mol Ecol 20: 2044–2072. https://doi.org/10.1111/j.1365-294X.2011.05080.x

Bierne N, Roze D, Welch JJ (2013) Pervasive selection or is it…? why are FST outliers sometimes so frequent? Mol Ecol 22: 2061–2064. https://doi.org/10.1111/mec.12241 

Butlin RK, Smadja CM (2018) Coupling, Reinforcement, and Speciation. Am Nat 191:155–172. https://doi.org/10.1086/695136 

Gautier M (2015) Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates. Genetics 201:1555–1579. https://doi.org/10.1534/genetics.115.181453 

Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of the theory of selective neutrality of polymorphisms. Genetics 74: 175–195. https://doi.org/10.1093/genetics/74.1.175 

Smadja CM, Loire E, Caminade P, Severac D, Gautier M, Ganem G (2022) Divergence of olfactory receptors associated with the evolution of assortative mating and reproductive isolation in mice. bioRxiv, 2022.07.21.500634, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.07.21.500634
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DE CARA Angeles

  • Agrigenomics, Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Universidade de Porto, Vairão, Portugal
  • Adaptation, Evolutionary Applications, Evolutionary Theory, Population Genetics / Genomics, Quantitative Genetics, Speciation

Recommendations:  0

Review:  1

Areas of expertise
I am a population geneticist with a focus on evolutionary and conservation biology. I apply computational and analytical methods to make hypothesis which I test in silico and with data from a wide range of organisms. I obtained my PhD in Physics analysing the Minority Game, where individuals have strategies to take decisions. I applied this framework to understand the dynamics of colonial breeding, collaborating with behavioural ecologists who worked with raptors. I first learnt population genetics during a stay abroad in my PhD and decided to move into that field, where I could apply my quantitative knowledge into biological questions with identifiable units. I thus obtained a position at the University of Edinburgh, where I worked on a debated topic, whether speciation can occur with of gene flow. I tackled that problem using a mathematical formalism which gave me deep insight into fundamental population and quantitative genetics. This led to two major contributions on the role of how small associations (linkage disequilibria) can slowly build up in the genome, leading to barriers to introgression between emerging species. After a break to look after my children, I obtained a postdoctoral position at the department of animal breeding at INIA (Spain), where I evaluated if marker arrays were better to maintain diversity in conservation programmes. There my programming skills and evolutionary knowledge were crucial and resulted in several key studies. Firstly, I established that using high density markers maintained most diversity compared with using genealogies. The precise density was established in a later study. Secondly, I studied how by maintaining the most diversity, deleterious variants could increase in frequency in the population, with negative long-term effects on their viability. Lastly, by using regions of the genome instead of single markers, I established how to reach a compromise between maintaining diversity and viability. I then moved to France, where I combined simulations and mathematical approximations with whole-genome data analyses. I analysed which method is best to understand adaptation at the genomic level, while I also studied demography and selection in Heliconius numata. During that period, I hosted three researchers and collaborated with people from previous departments and elsewhere. I analysed data from a variety of organisms, from domestic animals like cows and pigs, to model organisms, like Drosophila melanogaster. I learnt new methods and developed codes that others use and are publicly available. I am currently a postdoctoral researcher at CIBIO, where I disentangle the population genetics of Sus scrofa (wild boars and domestic pigs) and continue theoretical research and data analyses.