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Section: Evolutionary Biology ; Topics: Ecology, Evolution, Population biology

Spatial autocorrelation and host anemone species drive variation in local components of fitness in a wild clownfish population

Marrot, Pascal; Fauvelot, Cécile; Berumen, Michael L; Srinivasan, Maya; Jones, Geoffrey P; Planes, Serge; Pujol, Benoit

10.24072/pcjournal.493 - Peer Community Journal, Volume 5 (2025), article no. e7.
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The susceptibility of species to habitat changes depends on which ecological drivers shape individual fitness components. To date, only a few studies have quantified fitness components such as the Lifetime Reproductive Success across multiple generations in wild marine species. Because of a long-term sampling effort, such information is available for the population of wild orange clownfish, Amphiprion percula, from Kimbe Island (Papua New Guinea). Previous work on the wild orange clownfish near Kimbe Island suggests that there is little adaptive potential and that variation in LRS is mainly driven by a breeder’s habitat. Whether the host anemone species, geographic location, density or depth contributed to LRS remains however unknown because they were combined into a unique variable. We tested whether it is the ecology or the spatial distribution of clownfish that shaped the individual variation of a local fitness component, which would affect the population self-recruitment process and ultimately the maintenance of this wild population. Our spatially explicit analysis disentangled the role of these factors. We found that the host anemone species had an impact on wild clownfish LRS independently from their spatial distribution. The spatial distribution nevertheless had an impact on its own, as reflected by the spatial autocorrelation of LRS. Depth and density of anemones did not show a significant impact. Our findings imply that this clownfish population is susceptible to modifications of the spatial distribution and local assembly of anemone species
Section: Evolutionary Biology ; Topics: Evolution, Physiology

Sex-biased gene expression across tissues reveals unexpected differentiation in the gills of the threespine stickleback

Sylvestre, Florent; Aubin-Horth, Nadia; Bernatchez, Louis

10.24072/pcjournal.507 - Peer Community Journal, Volume 5 (2025), article no. e6.
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Sexual dimorphism can evolve through sex-specific regulation of the same gene set. However, sex chromosomes can also facilitate this by directly linking gene expression to sex. Moreover, differences in gene content between heteromorphic sex chromosomes contribute to sexual dimorphism. Understanding patterns of sex-biased gene expression across organisms is important for gaining insight into the evolution of sexual dimorphism and sex chromosomes. Moreover, studying gene expression in species with recently established sex chromosomes can help understand the evolutionary dynamics of gene loss and dosage compensation. The three-spined stickleback is known for its strong sexual dimorphism, especially during the reproductive period. Sex is determined by a young XY sex chromosome pair with a non-recombining region divided into three strata, which have started to degenerate. Using the high multiplexing capability of 3′ QuantSeq to sequence the sex-biased transcriptome of the liver, gills, and brain, we provide the first characterization of sex-specific transcriptomes from ~80 sticklebacks (40 males and 40 females) collected from a natural population during the reproductive period. We find that the liver is extremely differentiated between sexes (36% of autosomal genes) and reflects ongoing reproduction, while the brain shows very low levels of differentiation (0.78%) with no functional enrichment. Finally, the gills exhibit high levels of differentiation (5%), suggesting that sex should be considered in physiological and ecotoxicological studies of gill responses in fishes. We also find that sex-biased gene expression in hemizygous genes is mainly driven by a lack of dosage compensation. However, sex-biased expression of genes that have conserved copies on both sex chromosomes is likely driven by the degeneration of Y allele expression and a down-regulation of male-beneficial mutations on the X chromosome.
Section: Microbiology ; Topics: Microbiology

Design of a new model yeast consortium for ecological studies of enological fermentation

Pourcelot, Eléonore; Vigna, Audrey; Marlin, Thérèse; Galeote, Virginie; Nidelet, Thibault

10.24072/pcjournal.500 - Peer Community Journal, Volume 5 (2025), article no. e5.
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Wine fermentation involves complex microbial communities of non-Saccharomyces yeast species besides the well-known Saccharomyces cerevisiae. While extensive research has enhanced our understanding of S. cerevisiae, the development of multi-species fermentation starters has led to increased interest in yeast interactions and the role of microbial diversity in winemaking. Consequently, molecular methods have emerged to identify the different species at different stages of the winemaking process. Model microbial communities or consortia, which provide simplified systems resembling natural microbial diversity, offer opportunities to investigate population dynamics and understand the role of community diversity in ecosystem performance. Here, this work aims to design a yeast consortium reflecting the diversity of wine yeasts and to develop a method for accurately tracking their population dynamics during fermentation. We developed and characterized a six-species consortium, with S. cerevisiae, Hanseniaspora uvarum, Starmerella bacillaris, Metschnikowia pulcherrima, Lachancea thermotolerans and Torulaspora delbrueckii. By tagging each yeast species with distinct fluorescent markers, the study enables real-time monitoring of individual species within the consortium using flow cytometry. We have carried out a complete analysis of this consortium, studying the evolution of populations over time and examining factors such as metabolite production and fermentation kinetics. In addition, the yeast consortium was used to test the diversity-function relationship as a proof of concept. We sought to determine the impact of the initial evenness on communities’ performances subjected to osmotic stress. To this end, ten randomly designed consortia with varying initial species proportions were followed in enological fermentation with 200 and 280 g/L of initial sugars. The initial proportion of certain species affected the population dynamics and metabolite production however no demonstrable effect of the initial evenness on the response to osmotic stress was shown. These results demonstrated the usefulness of the presented consortium, which is now available to the scientific community and can contribute to future work trying to decipher multispecies dynamics and the role of yeast diversity in wine fermentation.
Section: Mathematical & Computational Biology ; Topics: Agricultural sciences, Statistics

Bayesian joint-regression analysis of unbalanced series of on-farm trials

Turbet Delof, Michel; Rivière, Pierre; Dawson, Julie C; Gauffreteau, Arnaud; Goldringer, Isabelle; van Frank, Gaëlle; David, Olivier

10.24072/pcjournal.495 - Peer Community Journal, Volume 5 (2025), article no. e4.
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Participatory plant breeding (PPB) is aimed at developing varieties adapted to agroecologically-based systems. In PPB, selection is decentralized in the target environments, and relies on collaboration between farmers, farmers' organisations and researchers. By doing so, evaluation of new genotypes takes genotype x environment (GxE) interactions into account to select for specific adaptation. In many cases, there is little overlap among genotypes assessed from farm to farm because the farmers participating in a PPB project choose which ones to assess on their farm. In addition, on-farm trials can often generate more extreme observations than trials carried out on research stations. These features make the estimation of genotype, environment and interaction effects more difficult. This challenge is not unique to PPB, as many breeding programs use sparse testing or incomplete block designs to evaluate more genotypes, however in PPB genotypes are not always assigned randomly to environments. To explore methods of overcoming these challenges, this article tests various data analysis scenarios using a Bayesian approach with different models and a real wheat PPB dataset over 11 years. Four morpho-agronomic traits were studied, representing over 1000 GxE combinations from 189 on-farm trials. This dataset was severely unbalanced with more than 90% of GxE combinations missing. We compared various Bayesian Finlay-Wilkinson models and found that placing hierarchical distributions on model parameters and modelling residuals using a Student's t distribution jointly improved the estimates of main effects and interactions. Environment effects were the most important and explained more than 50% of the variance of observations. This statistical framework allowed us to estimate two indicators of genotype stability (one static and one dynamic) despite the high disequilibrium of the data. We found differences in mean and stability between genotype categories, with registred varieties consistently shorter (-30 cm) and containing less protein (-0.3%) than other types of varieties. The methods developed could be used for evaluation and/or selection within networks of various stakeholders such as farmers, gardeners, plant breeders or managers of genetic resource centres.

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The network image was drawn by Martin Grandjean: A force-based network visualization CC BY-SA