Biology subjects

Tricou, T.

Publications and source records attributed to Tricou, T..

9 recordsLinked to original sources

bioRxiv2024

Gene flow can reveal ghost lineages

Ghost species, encompassing extinct, unknown, and unsampled taxa, vastly outnumber those typically included in phylogenetic analyses. This hidden diversity has been shown to influence the study of horizontal gene flow (e.g., introgression and horizontal gene transfer) by complicating the phylogenetic signals commonly used for their detection. In this work, we explore the potential of horizontal gene transfer (HGT) detection methods based on phylogenies (i.e., reconciliation methods) to detect and quantify ghost diversity . We briefly outline the theoretical framework underpinning our approach. Then, using simple simulations and empirical data from Cyanobacteria, we show that HGT signals, as interpreted by reconciliation methods, can reveal the presence and phylogenetic position of ghost clades, despite the absence of genomic data for these taxa. We anticipate possible limitations and difficulties in using HGT detection to explore ghost diversity and suggest promising approaches to address or circumvent them. Altogether, this proof of concept opens new lines of research for the future: a scarce fossil record and a large proportion of unknown lineages, especially in Archaea and Bacteria, does not equate to an absence of information for evolutionary studies.

evolutionary biology↗

bioRxiv2024

HGTs are not SPRs: In the presence of ghost lineages, series of Horizontal Gene Transfers do not result in series of Subtree Pruning and Regrafting

When a gene is horizontally transferred (HGT), under the "replacement" model where the transferred gene replaces its homolog in the recipient genome, the corresponding gene phylogeny departs from the species phylogeny by a Subtree Prune and Regraft (SPR) operation: the "recipient branch" is moved from its initial position to attach to the "donor branch". Based on this observation, various methods have used SPRs to infer HGTs. We examine this apparent equivalence in the light of ghost lineages, i.e. related species absent from the phylogeny because they are extinct, unknown or have not been sampled. In this case an SPR is not directly interpretable by an HGT from the donor branch, because HGTs can have ghost lineages as donors. A possible and frequent interpretation - that we call "induced HGT" - is that the transferred gene leaves the sampled phylogeny for a ghost lineage at the donor branch, and is transferred back from a ghost lineage at the recipient branch. We show by simulations that this interpretation is misleading in a significant number of cases. For instance if the studied phylogeny represents 1% of all the species susceptible to exchange genetic material with the 100 sampled species, and 11 transfers occurred, then SPRs do not correspond to induced HGTs in around 50% of the cases. This leaves the question of a coherent interpretation of SPR in the presence of ghosts open, and applies to a certain extent to other phylogenetic simulation or inference methods of HGT, like reconciliation, or phylogenetic networks.

bioinformatics↗

bioRxiv2024

Relaxed purifying selection is associated with an accumulation of transposable elements in flies

Although the mechanisms driving the evolution of genome size are not yet fully understood, one potentially important factor is the dynamics of the accumulation of mobile selfish genetic elements called transposable elements (TEs). Since most of these sequences are neutral or slightly deleterious, a negative correlation between genome size and selection efficacy is expected. However, previous studies based on empirical data from closely related species with contrasting life history traits (thought to result in contrasting levels of selection efficacy) have yielded inconsistent results, leaving this issue controversial. In this study, we perform the first large-scale analysis of the effect of drift on genome size evolution, without any prior assumption about the amount of drift in each sampled species. We reconstructed a phylogeny based on whole-genome data (2,242 genes) for 77 Drosophilid species to examine correlations between genome size, TE content, and measures of selection efficacy (especially using dN/dS ratios of non-synonymous to synonymous divergence). We highlight a strong phylogenetic inertia in genome size and confirm that TEs are the major components of genome size. Using an integrative approach that controls for shared history, we find that genome-wide dN/dS are strongly positively correlated with genome size and TE content, particularly in GC-poor genes. This study highlights the critical importance of controlling for heterogeneity in base composition when testing the controversial correlation between evolutionary rates and genome size. Furthermore, our review of previous studies reveals that the absence of evidence for TE accumulation in association with increased genetic drift may be attributed to a secondary effect of changes in life history traits on TE dynamics. In conclusion, this work provides evidence for TE proliferation in fly genomes when purifying selection is reduced and genetic drift increases, shedding new light on the role of transposable elements and genetic drift in the evolution of genome architecture.

evolutionary biology↗

bioRxiv2023

High prevalence of Prdm9-independentrecombination hotspots in placental mammals

In many mammals, recombination events are concentrated into hotspots directed by a sequence specific DNA-binding protein named Prdm9. This protein facilitates chromosome pairing and its inactivation has been shown to induce fertility losses in mice and rats. Intriguingly, Prdm9 has been lost several times in vertebrates, and notably among mammals, it has been pseudogenized in the ancestor of canids (dogs, wolves foxes). When this gene is inactive, either naturally in dogs, or through knock-out experiments in mice, recombination hotspots still exist, but they tend to occur in promoter-like features such as CpG islands. It has thus been proposed that one role of Prdm9 could be to direct recombination away from those Prdm9-independent hotspots. However, the ability of Prdm9 to direct recombination hotspots has been assessed only in a handful of species, and a clear picture of how much recombination occurs outside of Prdm9-directed hotspots in mammals is still lacking. In this study, we derived an estimator of past recombination activity based on signatures of GC-biased gene conversion in substitution patterns. We applied it to quantify recombination activity in Prdm9-independent hotspots in 52 species of boreoeutherian mammals. We observed a wide range of recombination rate at these loci: several species (such as mice, humans, some felids or cetaceans) show a deficit of recombination, while a majority of mammals display a clear peak of recombination. Our results demonstrate that Prdm9-directed and Prdm9-independent hotspots can co-exist in mammals, and that their co-existence seem to be the rule rather than an exception.

genetics↗

bioRxiv2023

PhylteR: efficient identification of outlier sequences in phylogenomic datasets

In phylogenomics, incongruences between gene trees, resulting from both artifactual and biological reasons, can decrease the signal-to-noise ratio and complicate species tree inference. The amount of data handled today in classical phylogenomic analyses precludes manual error detection and removal. However, a simple and efficient way to automate the identification of outliers from a collection of gene trees is still missing. Here, we present PhylteR, a method that allows a rapid and accurate detection of outlier sequences in phylogenomic datasets, i.e. species from individual gene trees that do not follow the general trend. PhylteR relies on DISTATIS, an extension of multidimensional scaling to 3 dimensions to compare multiple distance matrices at once. In PhylteR, these distance matrices extracted from individual gene phylogenies represent evolutionary distances between species according to each gene. On simulated datasets, we show that PhylteR identifies outliers with more sensitivity and precision than a comparable existing method. We also show that PhylteR is not sensitive to ILS-induced incongruences, which is a desirable feature. On a biological dataset of 14,463 genes for 53 species previously assembled for Carnivora phylogenomics, we show (i) that PhylteR identifies as outliers sequences that can be considered as such by other means, and (ii) that the removal of these sequences improves the concordance between the gene trees and the species tree. Thanks to the generation of numerous graphical outputs, PhylteR also allows for the rapid and easy visual characterisation of the dataset at hand, thus aiding in the precise identification of errors. PhylteR is distributed as an R package on CRAN and as containerized versions (docker and singularity).

evolutionary biology↗

bioRxiv2022

Ghost lineages invalidate or reverse several results on gene flow

Introgression, endosymbiosis and gene transfer, i.e. Horizontal Gene Flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection, and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data re-analysis, that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies.

evolutionary biology↗

bioRxiv2021

Ghost lineages deceive introgression tests and call for a new null hypothesis

Most species are extinct; those that are not are often unknown. Sequenced and sampled species are often a minority of known ones. Past evolutionary events involving horizontal gene flow, such as horizontal gene transfer, hybridization, introgression and admixture, are therefore likely to involve "ghosts", i.e. extinct, unknown or unsampled lineages. The existence of these ghost lineages is widely acknowledged, but their possible impact on the detection of gene flow and on the identification of the species involved is largely overlooked. It is generally considered as a possible source of error that, with reasonable approximation, can be ignored. We explore the possible influence of absent species on an evolutionary study by quantifying the effect of ghost lineages on introgression as detected by the popular D-statistic method. We show from simulated data that under certain frequently encountered conditions, the donors and recipients of horizontal gene flow can be wrongly identified if ghost lineages are not taken into account. In particular, having a distant outgroup, which is usually recommended, leads to an increase in the error probability and to false interpretations in most cases. We conclude that introgression from ghost lineages should be systematically considered as an alternative possible, even probable, scenario.

evolutionary biology↗

bioRxiv2021

Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes.

O_LIWe recently described, in Cannabis sativa, the oldest sex chromosome system documented so far in plants. Based on our estimate of its age, we predicted that it should be shared by its sister genus Humulus, which is known to also possess XY sex chromosomes. C_LIO_LIHere, we used transcriptome sequencing of a F1 family of Humulus lupulus to identify and study the sex chromosomes in this species using the probabilistic method SEX-DETector. C_LIO_LIWe identified 265 sex-linked genes in H. lupulus, located on the chromosome that is also the C. sativa sex chromosome pair. Using phylogenies of sex-linked genes, we show that a region of these chromosomes had already stopped recombining in the common ancestor of the two species. Furthermore, as in C. sativa, Y gene expression was reduced in correlation to the position on the X chromosome, and strongly Y degenerated genes showed dosage compensation. C_LIO_LIHere we report, for the first time in the Angiosperms, a sex chromosome system that is shared by two different genera. Recombination suppression started at least 21-25 My ago, and then (either gradually or step-wise) spread to a large part of the sex chromosomes, leading to a strongly degenerated Y. C_LI

evolutionary biology↗

bioRxiv2018

Zombi: A simulator of species, genes and genomes that accounts for extinct lineages.

SummaryHere we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have not to date been combined in a single simulator, such as the possibility of generating species trees with a pre-defined variation of speciation and extinction rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree - species tree reconciliations.\n\nAvailability and implementationSource code and manual are freely available in https://github.com/AADavin/ZOMBI/\n\nContactaaredav@gmail.com

bioinformatics↗