Latest Articles
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Section: Evolutionary Biology ; Topics: Evolution, Genetics/genomics, Population biology
Detection of domestication signals through the analysis of the full distribution of fitness effects
10.24072/pcjournal.540 - Peer Community Journal, Volume 5 (2025), article no. e35.
Get full text PDFDomestication is a process marked by complex interactions between demographic changes and selective pressures, which together shape genetic diversity. While the phenotypic outcomes of domestication are well documented, its genetic basis—particularly the dynamics of selection—remain less well understood. To investigate these dynamics, we performed simulations designed to approximate the demographic history of large domestic mammals. These simulations used selection coefficients as a modeling tool to represent changes in selection pressures, recognizing that such coefficients are abstractions rather than direct representations of biological reality. Specifically, we analyzed site frequency spectra (SFS) under varying distributions of fitness effects (DFE) and proportions of mutations with divergent selective pressures. Our results show that the discretized deleterious DFE can be reliably inferred from the SFS of a single population, but reconstructing the beneficial DFE and demographic history remains challenging, even when using the joint SFS of both populations. We further developed a novel joint DFE inference model to estimate the proportion of mutations with divergent selection coefficients (pc), although we found that signals of classic hard sweeps can mimic increases in pc, complicating interpretation. These findings underscore both the utility and limitations of DFE inference and highlight the need for caution when interpreting demographic histories in domesticated populations based on such modeling assumptions.
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Section: Ecology ; Topics: Ecology, Population biology ; Conference: Euring 2023
The importance of sampling design for unbiased estimation of survival using joint live-recapture and live resight models
10.24072/pcjournal.533 - Peer Community Journal, Volume 5 (2025), article no. e34.
Get full text PDFSurvival is a key life history parameter that can inform management decisions and basic life history research. Because true survival is often confounded with emigration from the study area, many studies are forced to estimate apparent survival (i.e., probability of surviving and remaining inside the study area), which can be much lower than true survival for highly mobile species. One method for estimating true survival is the Barker joint live-recapture/live-resight (JLRLR) model, which combines capture data from a study area (hereafter the ‘capture site’) with resighting data from a broader geographic area. This model assumes that live resights occur throughout the entire area where animals can disperse to and this assumption is often not met in practice. Here we use simulation to evaluate survival bias from a JLRLR model under study design scenarios that differ in the site selection for resights: global, random, fixed including the capture site, and fixed excluding the capture site. Simulation results indicate that fixed designs that included the capture site showed negative survival bias, whereas fixed designs that excluded the capture site exhibited positive survival bias. The magnitude of the bias was dependent on movement and survival, where scenarios with high survival and frequent movement had minimal bias. In an effort to help minimize bias, we developed a multistate version of the JLRLR and demonstrated reductions in survival bias compared to the single-state version for most designs. Our results suggest minimizing bias can be accomplished by: 1) using a random resight design when feasible if global sampling is not possible, 2) using the multistate JLRLR model when appropriate, 3) including the capture site in the resight sampling frame when possible, and 4) reporting survival as apparent survival if fixed sites are used for resight with the single state JLRLR model.
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Section: Ecotoxicology & Environmental Chemistry ; Topics: Agricultural sciences, Environmental sciences, Microbiology
Evaluating the effects of environmental disturbances and pesticide mixtures on N-cycle related soil microbial endpoints
10.24072/pcjournal.537 - Peer Community Journal, Volume 5 (2025), article no. e33.
Get full text PDFPesticides are widely used in conventional agriculture, either applied separately or incombination during the culture cycle. Due to their occurrence and persistence in soils, pesticideresidues may have an impact on soil microbial communities and on supported ecosystemservices. In this regard, the EFSA (European Food Safety Authority) recently published ascientific opinion inciting to change pesticide risk assessment to better protect soil microbe-mediated processes. Climate change is another major concern for all living organisms includingsoil microbial community stability. Extreme climatic events, such as heat waves or heavyrainfalls, are becoming more and more frequent and their impact on soil microbial diversity andfunctions have already been demonstrated.The objectives of this study were to evaluate the effects of temperature and humiditydisturbances and pesticide active ingredients exposure on soil microbial community structureand functions. To this end, 250 soil microcosms were exposed to either a heat disturbance, ahigh humidity to mimic heavy rain, or no environmental disturbance. After three days ofrecovery, soil microcosms were treated with different active ingredients: clopyralid (herbicide),cypermethrin (insecticide) and pyraclostrobin (fungicide). The treatments were applied aloneor in combination at 1x or 10x of the agronomical dose. We then evaluated the effects of thedisturbances and the active ingredients on various microbial endpoints related to the diversityand the structure of soil microbial communities, and with a specific focus on microbial guildsinvolved in nitrification.Overall, we demonstrated that the impact of environmental disturbances applied to soilmicrocosms, especially heat, on microbial endpoints was stronger than that of the activeingredients applied alone or in combinations. Compounded effects of environmentaldisturbances and active ingredients were detected, but sparsely and were of small scale for thechosen pesticides and applied doses.
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Section: Ecology ; Topics: Ecology, Population biology
Delayed dichromatism in waterfowl as a convenient tool for assessing vital rates
Tableau, Adrien;
Henderson, Iain;
Reeber, Sébastien;
Guillemain, Matthieu;
Maillard, Jean-François;
Caizergues, Alain
10.24072/pcjournal.531 - Peer Community Journal, Volume 5 (2025), article no. e32.
Get full text PDFMonitoring the number of individuals is by far the most popular strategy for studying the environmental factors that determine population dynamics and for measuring the effectiveness of management actions aimed at population recovery, control or eradication. Unfortunately, population size monitoring is inefficient in identifying the mechanisms underlying demographic processes and, in particular, in assessing the extent to which population growth rate is influenced by changes in adult survival rather than variations in reproductive parameters. In many waterfowl species, sexual dichromatism is observed in adults, while immatures of both sexes display a plumage pattern similar to that of adult females. In these species, the apparent proportion of males increases as the female-like immature males gradually take on the plumage of adult males. The difference between the apparent sex ratio before and after the young reach sexual maturity then provides information about the age ratio of a population. Using winter counts that distinguished between female-like and male-like individuals of two non-native populations of Ruddy duck Oxyura jamaicensis, a species that exhibits such a plumage pattern, we present a non-invasive method based on the apparent sex ratio to split population growth rate into adult survival and recruitment rates (the latter also referred to as productivity). This method can correctly detect annual changes in vital rates, supporting the assumption that counts conducted in an appropriate time window reflect the age structure of a population. We exemplify how the respective contributions of survival and productivity to the population growth rate are essential for understanding the processes behind demographic dynamics. Finally, we point out some best practices to correctly apply the ``apparent sex ratio'' method described here.
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