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  • Mathematical & Computational Biology

    Population genetics: coalescence rate and demographic parameters inference

    10.24072/pcjournal.285 - Peer Community Journal, Volume 3 (2023), article no. e53.

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    Inferring the demographic history of species is a great challenge in population genetics. This history is classically represented as a history of size changes, ignoring population structure. We present here the work carried out over the last decade around the concept of IICR (Inverse Instantaneous Coalescence Rate), which makes it possible to link, on the one hand, the history of the true population size for a panmictic population, and the inferred size, sometimes called "effective size", when structure is taken into account. We show that population structure can lead to misinterpretations of some demographic history inference results, we propose a framework for inferring structure-specific demographic parameters (number and size of subpopulations, migration rates), and we analyze the link between IICR and some form of selection modeling on genetic sequences.

  • Many world fisheries display a declining mean trophic level of catches. This “fishing down the food web” is often attributed to reduced densities of high-trophic-level species. We show here that the fishing down pattern can actually emerge from the adaptive harvesting of two- and three-species food webs, where changes in fishing patterns are driven by the relative profitabilities of the harvested species. Shifting fishing patterns from a focus on higher trophic levels to a focus on lower trophic levels can yield abrupt changes in the system, strongly impacting species densities. In predator-prey systems, such regime shifts occur when the predator species is highly valuable relative to the prey, and when the top-down control on the prey is strong. Moreover, we find that when the two species are jointly harvested, high adaptation speeds can reduce the resilience of fisheries. Our results therefore suggest that flexibility in harvesting strategies will not necessarily benefit fisheries but may actually harm their sustainability.

  • The effective population size is an important concept in population genetics. It corresponds to a measure of the speed at which genetic drift affects a given population. Moreover, this is most of the time the only kind of population size that empirical population genetics can give access to. Dioecious populations are expected to display excesses of heterozygosity as compared to monoecious panmictic populations, as measured by Wright's FIS. It can be shown that these excesses are negatively correlated with the population size. This is why FIS can be used to estimate the eigenvalue effective population size of dioecious populations. In this paper, we propose a new approximation that provides a very accurate estimate of the eigenvalue effective population size of a dioecious population as a function of the real population size. We then explore the accuracy of different FIS-based methods using the leading eigenvalue of transition matrices or coalescence. It appears that the eigenvalue-based method provides more accurate results in very small populations, probably due to approximations made by the coalescence approach that are less valid in such situations. We also discuss the applicability of this method in the field.

  • 1. Trait-environment relationships have been described at the community level across tree species. However, whether interspecific trait-environment relationships are consistent at the intraspecific level is yet unknown. Moreover, we do not know how consistent is the response between organ vs. whole-tree level. 2. We examined phenotypic variability for 16 functional leaf (dimensions, nutrient, chlorophyll) and wood traits (density) across two soil types, Ferralitic Soil (FS) vs. White Sands (WS), on two sites for 70 adult trees of Cecropia obtusa Trécul (Urticaceae) in French Guiana. Cecropia is a widespread pioneer Neotropical genus that generally dominates early successional forest stages. To understand how soil types impact resource use through the processes of growth and branching, we examined the architectural development with a retrospective analysis of growth trajectories. We expect soil types to affect both, functional traits in relation to resource acquisition strategy as already described at the interspecific level, and growth strategies due to resource limitations with reduced growth on poor soils. 3. Functional traits were not involved in the soil response, as only two traits -leaf residual water content and K content-showed significant differences across soil types. Soil effects were stronger on growth trajectories, with WS trees having the slowest growth trajectories and less numerous branches across their lifespan. 4. The analysis of growth trajectories based on architectural analysis improved our ability to characterise the response of trees with soil types. The intraspecific variability is higher for growth trajectories than functional traits for  C. obtusa, revealing the complementarity of the architectural approach with the functional approach to gain insights on the way trees manage their resources over their lifetime. Soil-related responses of Cecropia functional traits are not the same as those at the interspecific level, suggesting that the effects of the acting ecological processes are different between the two levels. Apart from soil differences, much variation was found across sites, which calls for further investigation of the factors shaping growth trajectories in tropical forests.

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