publications

2022

1. The Impact of Genetic Surfing on Neutral Genomic Diversity

   Flávia Schlichta, Stephan Peischl, and Laurent Excoffier

   Molecular Biology and Evolution, Nov 2022

   1 citations (Crossref) [2023-03-10]

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   Range expansions have been common in the history of most species. Serial founder effects and subsequent population growth at expansion fronts typically lead to a loss of genomic diversity along the expansion axis. A frequent consequence is the phenomenon of “gene surfing,” where variants located near the expanding front can reach high frequencies or even fix in newly colonized territories. Although gene surfing events have been characterized thoroughly for a specific locus, their effects on linked genomic regions and the overall patterns of genomic diversity have been little investigated. In this study, we simulated the evolution of whole genomes during several types of 1D and 2D range expansions differing by the extent of migration, founder events, and recombination rates. We focused on the characterization of local dips of diversity, or “troughs,” taken as a proxy for surfing events. We find that, for a given recombination rate, once we consider the amount of diversity lost since the beginning of the expansion, it is possible to predict the initial evolution of trough density and their average width irrespective of the expansion condition. Furthermore, when recombination rates vary across the genome, we find that troughs are over-represented in regions of low recombination. Therefore, range expansions can leave local and global genomic signatures often interpreted as evidence of past selective events. Given the generality of our results, they could be used as a null model for species having gone through recent expansions, and thus be helpful to correctly interpret many evolutionary biology studies.

2. Strong neutral sweeps occurring during a population contraction

   Antoine Moinet, Flávia Schlichta, Stephan Peischl, and Laurent Excoffier

   Genetics, Feb 2022

   https://web.archive.org/web/20220311001657/https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyac021/6529544?redirectedFrom=fulltext

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   A strong reduction in diversity around a specific locus is often interpreted as a recent rapid fixation of a positively selected allele, a phenomenon called a selective sweep. Rapid fixation of neutral variants can however lead to a similar reduction in local diversity, especially when the population experiences changes in population size, e.g. bottlenecks or range expansions. The fact that demographic processes can lead to signals of nucleotide diversity very similar to signals of selective sweeps is at the core of an ongoing discussion about the roles of demography and natural selection in shaping patterns of neutral variation. Here, we quantitatively investigate the shape of such neutral valleys of diversity under a simple model of a single population size change, and we compare it to signals of a selective sweep. We analytically describe the expected shape of such “neutral sweeps” and show that selective sweep valleys of diversity are, for the same fixation time, wider than neutral valleys. On the other hand, it is always possible to parametrize our model to find a neutral valley that has the same width as a given selected valley. Our findings provide further insight into how simple demographic models can create valleys of genetic diversity similar to those attributed to positive selection.

2021

1. Demographic inference

   Nina Marchi, Flávia Schlichta, and Laurent Excoffier

   Current Biology, Mar 2021

   5 citations (Crossref) [2022-02-16]
2. Aggression towards neonates and possible infanticide in the boto, or Amazon river dolphin (Inia geoffrensis)

   V.M.F. Silva, P.M. Silva, F. Schlichta, N.A.S. Carmo, G.L. Olson, and 3 more authors

   Behaviour, Jul 2021

   0 citations (Crossref) [2022-02-16]

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   Recent observed attacks by male Amazon river dolphins on conspecific calves, together with postmortem examinations, indicate that infanticide occurs in this species but that not all attacked calves are killed. If mortality occurs, it might therefore be an inadvertent consequence of the behaviour rather than the motive for it. Our observations suggest that males who commit infanticide are unlikely to gain direct fitness benefits. Evidence does not fit the sexual selection hypothesis. Aggression towards calves usually ‘drew a crowd’ and may represent socio-sexual display or simply be a form of social pathology, as found in other infanticidal mammals.

2019

1. Are all patterns created equal? Cooperation is more likely in spatially simple habitats

   Camilla Bertolini, Kasper Hlebowicz, Flavia Schlichta, Jacob J. Capelle, Johan Koppel, and 1 more author

   Marine Ecology, Jul 2019

   _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/maec.12572

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   Cooperative behaviours, such as aggregation with neighbouring conspecifics, can enhance resilience in habitats where risks (i.e. predation, physical disturbances) are high, exerting positive feedback loops to maintain a healthy population. At the same time, cooperation behaviours can involve some extra energy expenditures and increasing resource competition. For sessile reefs, like mussels, simulation models predict increased cooperation under increasing levels of environmental stress. Predation risk is viewed as a behaviour-modifying stressor, but its role on cooperation mechanisms, such as likelihood of reciprocity, has not yet been empirically tested. This study harnesses this framework to understand how cooperation changes under different perceived levels of predation risk, using mussel beds as model of a complex “self-organised” system. Hence, we assessed the context dependency of cooperation response in different “landscapes of fear,” created by changes in predator cues, substratum availability and body size. Our experiments demonstrated that i) cooperation in a mussel bed system increases when predator cues are present, but that this relationship was found to be both, ii) strongly context-dependent, particularly upon substratum availability and iii) size-dependent. That is, while cooperation is in general greater for larger individuals, the response to risk results in greater cooperation when alternative attachment substratum is absent, meaning that simpler landscapes may be perceived as riskier. The context dependency of structural complexity is also an essential finding to consider in a changing world where habitats are losing complexity and cooperative strategies should be maximised.