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Section: Genomics ; Topics: Evolution, Genetics/genomics

Factors influencing the accuracy and precision in dating single gene trees

Louvel, Guillaume; Roest Crollius, Hugues

10.24072/pcjournal.556 - Peer Community Journal, Volume 5 (2025), article no. e51.
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Molecular dating is the inference of divergence time from genetic sequences. Knowing the time of appearance of a taxon sets the evolutionary context by connecting it with past ecosystems and species. Knowing the divergence times of gene lineages would provide a context to understand adaptation at the genomic level. However, molecular clock inference faces uncertainty due to the variability of the rate of substitution between species, between genes, and between sites within genes. When dating speciations, per-lineage rate variability can be informed by fossil calibrations, and gene-specific rates can be either averaged out or modeled by concatenating multiple genes. By contrast, when dating gene-specific events, fossil calibrations only inform about speciation nodes, and concatenation does not apply to divergences other than speciations. This study aims to benchmark the accuracy of molecular dating applied to single gene trees and identify how it is affected by gene tree characteristics. We analyze 5205 alignments of genes from 21 Primates in which no duplication or loss is observed. We also simulated alignments based on characteristics from Primates under a relaxed clock model to analyze the dating accuracy. Divergence times were estimated with the Bayesian program Beast2. From the empirical dataset, we find that the date estimates deviate more from the median age with shorter alignments, high rate heterogeneity between branches, and low average rate, features that underlie the amount of dating information in alignments, hence, statistical power. The smallest deviation is associated with core biological functions such as ATP binding and cellular organization, categories that are expected to be under strong negative selection. We then investigated the accuracy of dating with simulated alignments, by controlling the three above parameters separately. It confirmed the factors of precision, but also revealed biases when branch rates are highly heterogeneous. This suggests that in the case of the relaxed uncorrelated molecular clock, biases arise from the tree prior when calibrations are lacking and rate heterogeneity is high. Our study finally reports the scale of the gene tree features that influence the dating consistency with median ages, so that comparisons can be made with other genes and taxa. To tackle the molecular dating of events only observed in single gene trees, like deep coalescence, horizontal gene transfers, and gene duplications, future models should overcome the lack of power due to limited information from single genes.
Section: Genomics ; Topics: Genetics/genomics, Plant biology

Natural variation in chalcone isomerase defines a major locus controlling radial stem growth variation among Populus nigra populations

Duruflé, Harold; Déjardin, Annabelle; Jorge, Véronique; Pégard, Marie; Pilate, Gilles; Rogier, Odile; Sanchez, Leopoldo; Segura, Vincent

10.24072/pcjournal.559 - Peer Community Journal, Volume 5 (2025), article no. e50.
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Poplar is a promising resource for wood production and the development of lignocellulosic biomass, but currently available varieties have not been optimized for these purposes. Therefore, it is critical to investigate the genetic variability and mechanisms underlying traits that affect biomass yield. Previous studies have shown that target traits in different poplar species are complex, with a small number of genetic factors having relatively low effects compared to medium to high heritability. In this study, a systems biology approach was implemented, combining genomic, transcriptomic, and phenotypic information from a large collection of individuals from natural populations of black poplar from Western Europe. Such an approach identified a QTL and a gene, coding for chalcone isomerase (CHI), as a candidate for controlling radial growth. Additionally, analysis of the structure and diversity of traits as well as CHI gene expression revealed a high allelic fixation index, linked to the geographical origin of the natural populations under study. These findings provide insights into how adaptive traits arise, are selected, and maintained in the populations. Overall, this study contributes to enhancing the use of poplar as a valuable resource for sustainable biomass production.
Section: Microbiology ; Topics: Microbiology

The cutting type of vegetables influences the spontaneous fermentation rate

Valence, Florence; Junker, Romane; Baty, Céline; Rué, Olivier; Mariadassou, Mahendra; Madec, Marie Noëlle; Maillard, Marie-Bernadette; Bage, Anne-Sophie; Chuat, Victoria; Marché, Laurent; Thierry, Anne

10.24072/pcjournal.553 - Peer Community Journal, Volume 5 (2025), article no. e49.
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Fermented vegetables are mainly produced by the spontaneous fermentation of raw vegetables that are roughly or thinly cut, salted and incubated in an oxygen-free environment. Despite the variety of cutting types and their potential role in the rate of solute diffusion from vegetable tissue, and hence the fermentation rate, the effect of this factor has been little studied. Our aim was to investigate how cutting and small variations in salt concentrations impact the microbial and biochemical changes that occur during the spontaneous fermentation of vegetables. A 2 × 3 experimental design was set up with vegetable type (carrot/cabbage), cutting type (thin/rough), and salt concentration (0.8%/1%) as the different factors. The vegetables were pressed down in 500 mL-jars and then filled with brine, and two independent jars used at four stages to characterise microbial dynamics and biochemical changes by combining culturomics, 16S rRNA V5-V7 and gyrB metataxonomics, and targeted metabolomics. Culturomic and metataxonomic results revealed similar successions of the main bacterial groups in both vegetables, with Enterobacteriaceae (8 vs 7 log colony-forming units(CFU)/g) quickly replacing the initial microbiota, further replaced within a few days by lactic acid bacteria (9 vs 8 logCFU/g), mainly represented by Leuconostoc sp. The pH fell to 3.8 within 40 h in carrot and about two weeks in cabbage. Mannitol, lactic acid and acetic acid were the main metabolites produced in both vegetables. Viable Enterobacteriaceae were no longer detected after two weeks of fermentation, except in some roughly-cut cabbage samples. No pathogenic bacteria were found. Taxonomic profiles varied depending on the marker used, e.g. Leuconostoc was only detected with gyrB and vice-versa for Clostridium. The gyrB marker enabled markedly better resolution at the species level (for 97% of ASV vs only 20% for the 16S marker). Significant effects of the cutting type, and, to a limited extent, of the NaCl concentration, were observed. Thinly-cut vegetables generally displayed more rapid fermentation compared to roughly-cut vegetables, together with higher titratable acidity, e.g. 0.8% vs 0.3%, respectively, in grated and sliced carrot after 64 h incubation. In line with this, acids were produced more rapidly and levels of viable enterobacteria fell more quickly in thinly-cut vegetables, and particularly cabbage, where the surface area generated by cutting was ~20-fold greater in shredded cabbage than in leaf cabbage. Some leaf cabbage samples displayed atypical fermentations, with particular taxa and atypical metabolite profiles producing high levels of ethanol. These general trends were modulated by quantitative and qualitative differences between replicate jars. This study therefore confirms the highly diverse microbiota of spontaneously fermented vegetables and the tight competition between Enterobacteriaceae and lactic acid bacteria regarding their colonisation. For the first time it documents the effects of cutting type on the fermentation rate.
Section: Ecology ; Topics: Ecology

A framework to quantify the vulnerability of insular biota to global changes

Bellard, Céline; Marino, Clara; Butt, Nathalie; Fernández-Palacios, José María; Rigal, François; Robuchon, Marine; Lenoir, Jonathan; Irl, Severin; Benítez-López, Ana; Capdevila, Pol; Zhu, G.; Caetano, Gabriel; Denelle, Pierre; Philippe-Lesaffre, Martin; Schipper, Aafke M; Foden, Wendy; Kissling, W. Daniel; Leclerc, Camille

10.24072/pcjournal.557 - Peer Community Journal, Volume 5 (2025), article no. e48.
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The majority of vulnerability assessments of biodiversity to global changes have so far been applied to, and designed for, mainland systems, overlooking islands. However, islands harbour unique biodiversity and are epicentres of ongoing extinctions. We thus introduce a specific framework for quantifying the vulnerability of terrestrial insular biota to multiple threats. This framework uses markers of exposure, sensitivity, and adaptive capacity to account for the unique characteristics of island biodiversity. Our assessment framework involves five steps: (1) defining the scope of the vulnerability assessment, (2) selecting the most appropriate markers, (3) computing the vulnerability metric, (4) evaluating uncertainties, and (5) providing recommendations for conservation. The development of this vulnerability framework tailored for island systems is part of a larger initiative to meet international policy targets that better integrate biodiversity threats and dimensions. We thus discuss the need and urgency for applying this framework to guide evidence-based decisions for the conservation of insular biodiversity, and for increased attention to insular biota at the science-policy interface.

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