Biology subjects

Joly, E.

Publications and source records attributed to Joly, E..

4 recordsLinked to original sources

bioRxiv2026

TMRCA is observable from the branch lengths of a coalescent

The height of ancestral trees, in other words the time to the most recent common ancestor in a genealogical tree, is an informative statistic in population genomics and used in contexts of genealogical dating, demographic history inference, and assessing signals of selection. Exploiting a general pathwise identity between the height of a tree and its branch lengths, we revisit Zeng et al.s mutation rate estimator to develop a model-free estimator for the product of the expected height of genealogical trees with the scaled mutation rate, both for single loci and genomic regions. This estimator is a linear function of the site frequency spectrum of a sample, i.e., of the distribution of allele counts at all segregating sites across the locus or genomic region and thus both observable and computationally cheap. We show that, under the infinite sites model of mutation, our estimator is unbiased and, for two genome-wide models of ancestries (sequential Markovian coalescents and common-pedigree ancestries), consistent. Furthermore, we show via simulation that our estimator performs smaller errors than averaging over reconstructed ancestral tree heights (extracted from reconstructed ancestral recombination graphs) when considering genome properties similar to human genomes across large genomic regions. We then revisit a publicly available genomic dataset of dogs and wolves and compare our method with extracting TMRCAs from ancestral recombination graph reconstructions.

genetics↗

bioRxiv2023

Estimating the Lambda measure in multiple-merger coalescents

Multiple-merger coalescents, also known as {Lambda}-coalescents, have been used to describe the genealogy of populations that have a skewed offspring distribution or that undergo strong selection. Inferring the characteristic measure {Lambda}, which describes the rates of the multiple-merger events, is key to understand these processes. So far, most inference methods only work for some particular families of {Lambda}-coalescents that are described by only one parameter, but not for more general models. This article is devoted to the construction of a non-parametric estimator of the density of {Lambda} that is based on the observation at a single time of the so-called Site Frequency Spectrum (SFS), which describes the allelic frequencies in a present population sample. First, we produce estimates of the multiple-merger rates by solving a linear system, whose coefficients are obtained by appropriately subsampling the SFS. Then, we use a technique that aggregates the information extracted from the previous step through a kernel type of re-construction to give a non-parametric estimation of the measure {Lambda}. We give a consistency result of this estimator under mild conditions on the behavior of {Lambda} around 0. We also show some numerical examples of how our method performs.

evolutionary biology↗

bioRxiv2021

Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae

The bitter taste, triggered via gustatory receptors, serves as an important natural defense against the ingestion of poisonous foods in animals, and the diversity of food diet is usually linked to an increase in the number of gustatory receptor genes. This has been especially observed in polyphagous insect species, such as noctuid species from the Spodoptera genus. However, the dynamic and physical mechanisms leading to these gene expansions and the evolutionary pressures behind them remain elusive. Among major drivers of genome dynamics are the transposable elements but, surprisingly, their potential role in insect gustatory receptors expansion has not been considered yet. In this work, we hypothesized that transposable elements and possibly positive selection would be involved in the active dynamic of gustatory receptor evolution in Spodoptera spp. We first sequenced de novo the full 465Mb genome of S. littoralis, and manually annotated all chemosensory genes, including a large repertoire of 373 gustatory receptor genes (including 19 pseudogenes). We also improved the completeness of S. frugiperda and S. litura gustatory receptor repertoires. Then, we annotated transposable elements and revealed that a particular category of class I retrotransposons, the SINE transposons, was significantly enriched in the vicinity of gustatory receptor gene clusters, suggesting a transposon-mediated mechanism for the formation of these clusters. Selection pressure analyses indicated that positive selection within the gustatory receptor gene family is cryptic, only 7 receptors being identified as positively selected. Altogether, our data provide a new good quality Spodoptera genome, pinpoint interesting gustatory receptor candidates for further functional studies and bring valuable genomic information on the mechanisms of gustatory receptor expansions in polyphagous insect species.

genomics↗

bioRxiv2021

SDR enzymes oxidize specific lipidic alkynylcarbinols into cytotoxic protein-reactive species

Hundreds of cytotoxic natural or synthetic lipidic compounds contain chiral alkynylcarbinol motifs, but the mechanism of action of those potential therapeutic agents remains unknown. Using a genetic screen in haploid human cells, we discovered that the enantiospecific cytotoxicity of numerous terminal alkynylcarbinols, including the highly cytotoxic dialkynylcarbinols, involves a bioactivation by HSD17B11, a short-chain dehydrogenase/reductase (SDR) known to oxidize the C-17 carbinol center of androstan-3-alpha,17-beta-diol to the corresponding ketone. A similar oxidation of dialkynylcarbinols generates dialkynylketones, that we characterize as highly protein-reactive electrophiles. We established that, once bioactivated in cells, the dialkynylcarbinols covalently modify several proteins involved in protein-quality control mechanisms, resulting in their lipoxidation on cysteines and lysines through Michael addition. For some proteins, this triggers their association to cellular membranes and results in endoplasmic reticulum stress, unfolded protein response activation, ubiquitin-proteasome system inhibition and cell death by apoptosis. Finally, as a proof-of-concept, we show that generic lipidic alkynylcarbinols can be devised to be bioactivated by other SDRs, including human RDH11 and HPGD/15-PGDH. Given that the SDR superfamily is one of the largest and most ubiquitous, this unique cytotoxic mechanism-of-action could be widely exploited to treat diseases, in particular cancer, through the design of tailored prodrugs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/460423v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@12daae1org.highwire.dtl.DTLVardef@12db406org.highwire.dtl.DTLVardef@1863517org.highwire.dtl.DTLVardef@7b548_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

biochemistry↗