Biology subjects

Laroche, F.

Publications and source records attributed to Laroche, F..

5 recordsLinked to original sources

bioRxiv2024

Large-scale informative priors to better predict the local occurrence rate of a rare tree-related microhabitat

Tree-related microhabitats (TreMs) are key features for forest biodi-versity, and knowing their accumulation rate is essential to design inte-grative management strategies. Many types of TreMs are associated to large old trees and show slow ontogenical processes. The rarity of such TreMs (particularly in intensively managed forests) hinder the estimation of their occurrence rate along tree growth. Here, we used a continental meta-analysis on TreMs occurrence rate along tree growth to build in-formative priors for a model of trunk-base rot-hole occurrence on oaks within the Gresigne forest, France -- a context where stand management and tree DBH were confounded. We explored whether the use of infor-mative priors could improve the identifiability, the precision of estimates and the predictive abilities of the model. Without prior information, the low variance of tree DBH within management modalities rendered the model poorly identifiable and prevented the detection of an effect of tree DBH per se across the range of explored tree DBH. By contrast, using informative priors contributed to improve the precision of estimates and lead to detecting a positive effect of tree DBH per se. Informative priors did not degrade the model fit and clearly improved predictive abilities on new stands. In particular, while the model without prior information did not predict the occurrence of trunk-base rot-holes significantly better than a purely random guess, the model with informative priors did. Ir-respective of the prior used, models suggested that the high recruitment of trunk-base rot-holes in Gresigne may be a temporary management ef-fect in stands undergoing conversion from coppice-with-standards to high forest through sprout thinning, which will lead to conservation issues for cavicolous saproxylic species when all conversions are complete. Because using informative priors was simple and beneficial in our study, it should be further explored in other local applied contexts to orientate forest man-agement.

ecology↗

bioRxiv2022

Efficient sampling designs to assess biodiversity spatial autocorrelation : should we go fractal?

Quantifying the autocorrelation range of species distribution in space is necessary for applied ecological questions, like implementing protected area networks or monitoring programs. However, the power of spatial sampling designs to estimate this range is negatively related with other objectives such as estimating environmental effects acting upon species distribution. Mixing random sampling points and systematic grid ( hy-brid designs) is a classic solution to make a trade-off. However, fractal designs (i.e. self-similar designs with well-identified scales) could make an even better compromise, because they cover a wide array of possible autocorrelation range values across scales. Using maximum likelihood estimation in an optimal design of experiments approach, we compared errors of hybrid and fractal designs when simultaneously estimating an effect acting upon a response variable and the residual autocorrelation range. We found that Pareto-optimal sampling strategies depended on the feasible grid mesh size (FGMS) over the study area, given the sampling budget. When the FMGS was shorter than expected autocorrelation range values, grid design was the best option on all criteria. When the FMGS was around or larger than expected autocorrelation range values, the choice of designs depended on the effect under study. Fractal designs outperformed hybrid designs when studying the effect of a monotonic environmental gradient across space, while grid design was more efficient for other types of question. Beyond the niche identified in our analysis, fractal designs may also appear interesting when studying response variables with more heterogeneous spatial structure across scales, and when considering more practical criteria of performance such as the distance needed to cover the design.

ecology↗

bioRxiv2022

The genetic architecture of local adaptation in a cline

Local adaptation is pervasive. It occurs whenever selection favors different phenotypes in different environments, provided that there is genetic variation for the corresponding traits and that the effect of selection is greater than the effect of drift and migration. In many cases, ecologically relevant traits are quantitative and controlled by many genes. It has been repeatedly proposed that the localization of these genes in the genome may not be random, but could be an evolved feature. In particular, the clustering of local adaptation genes may be theoretically expected and has been observed in several situations. Previous theory has focused on two-patch or continent-island models to investigate this phenomenon, reaching the conclusion that such clustering could evolve, but in relatively limited conditions. In particular, it required that migration rate was neither too low nor too large and that the full optimization of trait values could not be eventually achieved by a mutation at a single locus. Here, we investigate this question in a spatially-explicit model, considering two contiguous habitats with distinct trait optima on a circular stepping-stone. We find that clustering of local-adaptation genes is pervasive within clines during both the establishment phase of local adaptation and the subsequent "reconfiguration" phase where different genetic architectures compete with each other. We also show that changing the fitness function relating trait to fitness has a strong impact on the overall evolutionary dynamics and resulting architecture.

evolutionary biology↗

bioRxiv2019

Simulated neutral metacommunities support the habitat amount hypothesis

AO_SCPLOWBSTRACTC_SCPLOWThe Theory of Island Biogeography (TIB) promoted the idea that species richness within sites depends on site connectivity, i.e. its connection with surrounding potential sources of immigrants. TIB has been extended to a wide array of fragmented ecosystems, beyond archipelagoes, surfing on the analogy between habitat patches and islands and on the patch-matrix framework. However, patch connectivity often little contributes to explaining species richness in empirical studies. Before interpreting this trend as questioning the broad applicability of TIB principles, one first needs a clear identification of methods and contexts where strong effects of patch structural connectivity are likely to occur. Here, we use spatially explicit simulations of neutral metacommunities to show that patch connectivity effect on local species richness is maximized under a set of specific conditions: (i) patch delineation should be fine enough to ensure that no dispersal limitation occurs within patches, (ii) patch connectivity indices should be scaled according to target organisms dispersal distance and (iii) the habitat amount around sampled sites (within a distance adapted to organisms dispersal) should be highly variable. When those three criteria are met, the absence of an effect of connectivity on species richness should be interpreted as contradicting TIB hypotheses

ecology↗

bioRxiv2018

Assessing metacommunity processes through signatures in spatiotemporal turnover of community composition

Although metacommunity ecology has been a major field of research in the last decades, with both conceptual and empirical outputs, the analysis of the temporal dynamics of metacommunities has only emerged recently and consists mostly of repeated static analyses. Here, we propose a novel analytical framework to assess metacommunity processes using path analyses of spatial and temporal diversity turnovers. We detail the principles and practical aspects of this framework and apply it to simulated datasets to illustrate its ability to decipher the respective contributions of entangled drivers of metacommunity dynamics. We then apply it to four empirical datasets. Empirical results support the view that metacommunity dynamics may be generally shaped by multiple ecological processes acting in concert, with environmental filtering being variable across both space and time. These results reinforce our call to go beyond static analyses of metacommunities that are blind to the temporal part of environmental variability.

ecology↗