Latest Articles

Section: Ecology ; Topics: Ecology, Evolution

Disentangling urbanisation, climate effects and their interaction on ornamental colourations

Sandmeyer, Lisa; López-Idiáquez, David; Fargevieille, Amélie; Giovannini, Pablo; Perret, Samuel; Del Rey, Maria; Charmantier, Anne; Doutrelant, Claire; Grégoire, Arnaud

10.24072/pcjournal.664 - Peer Community Journal, Volume 5 (2025), article no. e137
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Urbanisation and climate change can both affect phenotype expression across taxa. Most evidence collected so far has focused on exploring these two phenomena on isolation. Currently, the combined effects of climate change and urbanisation remain underexplored, despite being among the greatest challenges faced by biodiversity. Here, we use a decade-long, individual-based study of urban and forest great tits (Parus major) to analyse urbanisation, climate and their interactive effects on yellow breast colouration, a carotenoid-based trait. We find that urban birds exhibit duller colourations than forest counterparts, being 10-20% less chromatic, with first-year birds and males being more negatively impacted by cities. Additionally, birds in the city are more sexually dichromatic than in the forest. Over the decade, colouration differences between habitats remain stable, following a similar quadratic temporal pattern. Finally, while climate has a weak effect on colouration, urban birds appear more sensitive to its influence than forest birds. Our results indicate urbanisation has a stronger impact than last decade climatic variation on great tit colouration, though both factors may interact. The heightened sensitivity of first-year birds and increased sexual dichromatism in cities may alter the strength of natural and sexual selection on this trait in urban environments.
Section: Genomics ; Topics: Genetics/genomics

Bulk-based hypothesis weighing increases power in single-cell differential expression analysis

Germain, Pierre-Luc; Wang, Jiayi; Robinson, Mark D.

10.24072/pcjournal.663 - Peer Community Journal, Volume 5 (2025), article no. e136
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Due to the costs of single-cell sequencing, sample sizes are often relatively limited, sometimes leading to poorly reproducible results. In many contexts, however, larger bulk RNAseq data is available for the same conditions or experimental paradigm, which can be used as additional evidence of a generalizable differential expression pattern. Here, we show how such data can be used, via bulk-based hypothesis weighing (bbhw), to increase the power and robustness of single-cell differential state analysis. We find that all methods improve performance, with the best results obtained by applying a grouped Benjamini-Hochberg procedure on bins based on proportion-adjusted significance (PAS). These methods are implemented in the muscat package, and should be applicable to a broader range of scenarios.
Section: Archaeology ; Topics: Archaeology, Anthropology

Isobiography of the first farmers: effects of age-estimating referential and statistical models on reconstructing infant life from dentinal isotopic sequences

Bédécarrats, Samuel; Le Roy, Mélie; Sayle, Kerry L.; Blaizot, Frédérique; Couvrat, Maëlle; Gleize, Yves; Leduc, Guillaume; Rottier, Stéphane; Goude, Gwenaëlle

10.24072/pcjournal.657 - Peer Community Journal, Volume 5 (2025), article no. e135
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The use of isotopic sequence allowing a longitudinal life tracking of an individual (isobiography), by taking a series of isotope measurements on dentine sections and estimating the age of the individual at their formation, provides a means of tracing dietary and environmental variations during childhood. This approach is based on the use of standards for estimating the age at which teeth are formed. By using a dual mathematical model, linear and a generalised additive model, and by testing two standards commonly used in biological anthropology to estimate dental age, we have characterised the isobiography of 4 Neolithic individuals from France. Our study shows the importance of the choice of mathematical model and standard in age estimates. Depending on the choices made, there can be gaps of several years between the estimates, underscoring the difficulty and precautions that need to be taken when making inferences on social ages. The statistical processing protocol developed can be re-used or adapted for new studies.
Section: Evolutionary Biology ; Topics: Ecology, Environmental sciences, Evolution

Increased clonality and genetic differentiation across the Arctic Ocean in tetraploid sea anemone Aulactinia stella

Bocharova, Ekaterina; Volkov, Aleksandr; Stoeckel, Solenn

10.24072/pcjournal.656 - Peer Community Journal, Volume 5 (2025), article no. e134
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Reproductive mode is a key factor shaping genetic diversity, evolutionary potential, and the processes of dispersal and colonization. Clonality is particularly common in harsh environments and at the margins of species ranges, where it supports persistence, enables rapid growth, and promotes the maintenance of locally adapted genotypes. In the rapidly changing Arctic, increasing ecological connectivity is eroding historical barriers for sessile species. Evaluating genetic diversity in this context, before global change further alters Arctic ocean, is essential for understanding evolutionary dynamics during range expansion and for informing conservation strategies. Aulactinia stella is a circumpolar sea anemone with physiological characteristics in laboratory conditions suggesting a potential for clonal reproduction. In this study, we investigated its reproductive modes in natural populations across the Arctic ocean, from the northern Pacific to the Atlantic, and examined how genetic diversity is structured between adults and juveniles at five sampled sites. Across all study sites, we observed only females or individuals lacking gonads, with the exception of Kamchatka, where males were also present. Genetic indices and changes in genotype frequencies between adults and juveniles confirmed that this species reproduces partially by parthenogenesis. Populations on the Atlantic side were highly clonal with clonal rates (c) estimated at 80-99%, whereas populations on the Pacific side reproduced more sexually (c around 50%). Allelic diversity was twice as high in Kamchatka and Kuril populations, suggesting North Pacific coasts being the main last glacial refugia of A. stella. We found a stepping-stone pattern of genetic structure from Kamchatka to Atlantic populations, consistent with contemporary ocean currents and melted summer sea ice. Only a subset of the juvenile genetic diversity, mostly of local origin, was found in the established adults, while juveniles exhibited lower levels of genetic differentiation across the Arctic Ocean. Our findings underscore the need for further ecological and behavioral investigations to elucidate the mechanisms allowing the current possibilities of dispersal of this species across the Arctic Ocean.

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