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Section: Ecology ; Topics: Ecology, Statistics

Using informative priors to account for identifiability issues in occupancy models with identification errors

Monchy, Célian; Etienne, Marie-Pierre; Gimenez, Olivier

10.24072/pcjournal.511 - Peer Community Journal, Volume 5 (2025), article no. e8.
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Non-invasive monitoring techniques like camera traps, autonomous recording units and environmental DNA are increasingly used to collect data for understanding species distribution. These methods have prompted the development of statistical models to suit specific sampling designs and get reliable ecological inferences. Site occupancy models estimate species occurrence patterns, accounting for the possibility that the target species may be present but unobserved. Here, two key processes are crucial: detection, when a species leaves signs of its presence, and identification where these signs are accurately recognized. While both processes are prone to error in general, wrong identifications are often considered as negligible with in situ observations. When applied to passive bio-monitoring data, characterized by datasets requiring automated processing, this second source of error can no longer be ignored as misclassifications at both steps can lead to significant biases in ecological estimates. Several model extensions have been proposed to address these potential errors. We propose an extended occupancy model that accounts for the identification process in addition to detection. Similar to other recent attempts to account for false positives, our model may suffer from identifiability issues, which usually require another source of data with perfect identification to resolve them. As an alternative when such data are unavailable, we propose leveraging existing knowledge of the identification process within a Bayesian framework by incorporating this knowledge through an informative prior. Through simulations, we compare different prior choices that encode varying levels of information, ranging from cases where no prior knowledge is available, to instances with accurate metrics on the performance of the identification, and scenarios based on generally accepted assumptions. We demonstrate that, compared to using a default prior, integrating information about the identification process as a prior reduces bias in parameter estimates. Overall, our approach mitigates identifiability issues, reduces estimation bias, and minimizes data requirements. In conclusion, we provide a statistical method applicable to various monitoring designs, such as camera trap, bioacoustics, or eDNA surveys, alongside non-invasive sampling technologies, to produce ecological outcomes that inform conservation decisions.
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.

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