Biology subjects

Achaz, G.

Publications and source records attributed to Achaz, G..

At least 19 recordsLinked to original sources

bioRxiv2026

Three phylogenetic metrics are compatible with natural evolution of the earliest SARS-CoV-2 sequence

Comparative analyses of coronavirus sequences can unravel important aspects of their complex evolution. Here we develop a method to infer past recombination breakpoints based on minimizing homoplasies count. We test it on three outbreak viruses (SARS-CoV-1, MERS-CoV, and SARS-CoV-2) and various chimeric coronaviruses as positive controls. We identify genomic regions evolving under distinct selective pressures. We also trace possible signs of human-made manipulations using metrics such as synonymous and non-synonymous mutation rates, codon usage and insertion patterns. Our pipeline appears to efficiently detect synthetic sequence optimization or genome re-encoding, but does not identify chimeras of natural viruses. Unlike in positive controls, with our method no signal of human-made manipulation is detected in SARS-CoV-1, MERS-CoV, nor SARS-CoV-2.

evolutionary biology↗

bioRxiv2026

Blockbuster meets the theoretical limit of genome-wide SFS-based inference of recent demography

1The molecular diversity of a sample of DNA sequences from the same species is traditionally summarized by the so-called Site Frequency Spectrum (SFS). Past variations in population size leave a trace in the shape of this histogram that several popular programs leverage to infer demography. The ability of inference methods using genome-wide SFS to document recent demography for conservation purposes needs to be evaluated both theoretically and practically. Assuming population size is piecewise constant, we predict analytically that the date of the most recent demographic change that leaves a statistically detectable trace in the SFS is on the order of [Formula] generations, where n is the sample size and N is the effective population size before the change. We further show that robust parameter estimation is achieved at N3/4/n generations for both the date and intensity of the most recent change. We release Blockbuster, a deterministic program that reliably infers a demographic scenario with piecewise-constant population size through time from a genome-wide SFS. Blockbuster consistently outperforms recent similar programs in accuracy, robustness, and computational time. More importantly, it reaches the theoretical limit on the most recent demographic changes. Finally, we propose a simple yet efficient method to circumvent the presence of population structure, a well-known and pervasive complication that prevents reliable inference of demographic history.

genetics↗

bioRxiv2025

Repeated losses of self-fertility shaped heterozygosity and polyploidy in yeast evolution

Evolutionary transitions in mating strategy have profound consequences for genetic variation and adaptation. In Saccharomyces cerevisiae, mating-type switching is a central feature of the life cycle that enables homothallism, i.e., mating between mitotic descendants of the same haploid cell. Yet heterothallic isolates that have lost this ability are found across diverse niches, indicating that this trait is polymorphic. Here we experimentally characterized loss of mating-type switching in a representative panel of strains. Analysis of 117 telomere- to-telomere genome assemblies revealed multiple independent loss-of-function mutations in the Ho endonuclease gene and structural variants in the silent HML and HMR cassettes, the three loci essential for switching. We estimated that at least 13 independent transitions from homothallism to heterothallism have occurred in the species history. Analysis of the HO genotype of 2,915 strains show that at least 27% are heterothallic. We found that heterothallism is strongly associated with polyploidy and elevated genome-wide heterozygosity, although the strength of these associations varies between populations. Heterothallic isolates are most prevalent in domesticated and clinical clades, consistent with an origin linked to human-associated environments. However, they are also found, though less frequently, in natural niches. Signatures of recombination in HO sequences suggest that outcrossing contributed to the ecological and geographical distribution of the trait. Our findings reveal that mating-type switching has undergone repeated losses in S. cerevisiae evolution, with major consequences for genome architecture and ecological diversification. Significance StatementMating-type switching evolved multiple times in yeasts, enabling haploid selfing, which became a key feature of their life cycles. We show that this trait has been lost repeatedly in the history of Saccharomyces cerevisiae, producing heterothallic isolates that cannot switch mating type. Analysis of thousands of genomes reveals that these losses involve multiple mutations in the Ho endonuclease and structural changes in the silent mating-type cassettes. Heterothallism is associated with polyploidy and increased genome-wide heterozygosity. It is more frequent in domesticated and clinical lineages, but also occurs in natural ecological niches. Our findings illustrate how repeated changes in a single life-history trait can reshape genome architecture and highlight the dynamic interplay between genetics, environment, and evolution in a model eukaryote.

evolutionary biology↗

bioRxiv2025

Combining population genomics with ancient DNA to understand island colonization history of the Madagascar turtle dove

The Mascarene archipelago (Mauritius, Reunion and Rodrigues), characterized by first human arrival being recent, offers a unique setting to study species colonization. Here we use a combination of modern and ancient DNA data as a case study to investigate the recent colonization history of a species of concern in relation to conservation programs - the Madagascar turtle dove (Nesoenas picturata) on Mauritius and Reunion. We generated a reference genome and re-sequenced genomes from contemporary N. picturata populations, as well as genome-wide data from relevant subfossils. A combination of model-free inferences, site frequency spectrum (SFS) based demographic modelling, and analyses of population structure including that of subfossils indicate that N. picturata colonized both islands independently and naturally from Madagascar, long before human arrival. Summary statistics and SFS-based modeling reveal large effective population sizes (Ne) and high genetic diversity in island populations, conflicting with historical accounts of human-induced demographic collapse. Based on goodness-of-fit, genetic structure and diversity indices do not discriminate between two solutions, one of which posits large recent Ne and negligible translocation rates, while the other supports recent severe bottlenecks followed by high post-human translocation from Madagascar. Nonetheless, linkage disequilibrium provides stronger evidence for the latter scenario, which may also explain high genetic diversity. Both modern and ancient DNA data sources independently support the classification of N. picturata as native to both islands. Our findings highlight the importance of validating demographic models with multiple summary statistics, and potential of using a combination of different data sources to resolve colonization history in recent time.

evolutionary biology↗

bioRxiv2025

The Baldwin effect reloaded: Intermediate levels of phenotypic plasticity favor evolutionary rescue

Since the late 1890s and until today, how phenotypic plasticity interacts with genetic adaptation is a debated issue. Proponents of a positive causal role of phenotypic plasticity -James M. Bald-win in the first place- supported the view that, in altered environmental conditions, phenotypic plasticity is a key factor allowing a population to avoid extinction and then genetic evolution to catch up ("Original Baldwin Effect", thereafter OBE). Opponents, like for instance Ernst Mayr, regularly pointed out that phenotypic plasticity, by masking genetic variation, slows gene-level evolution ("Mayr Effect", thereafter ME). For decades this opposition remained only verbal and qualitative. To resolve it, we propose here a stochastic model that, following Baldwins intuitive take, combines the minimal number of ingredients to account for extinction, selection, mutation and plasticity. We study evolutionary rescue of the population (arrival and invasion of an adaptive genetic mutant) in the altered environment for different values of phenotypic plasticity, here quantified as the probability p that the maladapted genotype develops into the adapted phenotype. Our claim is that OBE can be a genuine evolutionary mechanism, depending on the level of phenotypic plasticity with respect to a threshold value p[*]: when p < p[*], increasing p promotes evolutionary rescue by delaying extinction ("Strong" OBE); when p > p[*], plasticity sustains population survival and increasing p has two antagonistic effects: to accelerate adaptation by increasing the supply of adaptive mutants ("Weak" OBE, intermediate values of p), and to slow down adaptation by decreasing their fitness advantage (ME, high values of p).

evolutionary biology↗

bioRxiv2023

Chromosome-level genome assembly of the European Green woodpecker Picus viridis

The European Green Woodpecker, Picus viridis, is a widely distributed species found in the Western Palearctic region. Here we assembled a highly contiguous genome assembly for this species using a combination of short and long reads sequencing and scaffolded with chromatin conformation capture (Hi-C). The final genome assembly was 1.28 Gb and features a scaffold N50 of 37Mb and a scaffold L50 of 39.165 Mb. The assembly incorporates 89.4% of the genes identified in birds in OrthoDB. Gene and repetitive content annotation on the assembly detected 15,805 genes and a [~]30.1% occurrence of repetitive elements, respectively. Analysis of synteny demonstrates the fragmented nature of the Picus viridis genome when compared to the chicken (Gallus gallus). The assembly and annotations produced in this study will certainly help for further research into the genomics of P. viridis and the comparative evolution of woodpeckers.

genomics↗

bioRxiv2023

How demography shapes linkage disequilibrium with or without recombination

Linkage Disequilibrium (LD) is a measure of the statistical association, within a population, between alleles present at different loci. Here, we produce detailed characterizations of LD statistics in different demographic scenarios, with simulations and with analytic results, focusing on several widely used measures of LD (D, |D'|, and r2), and introducing a fourth class of statistics: 2-site configuration probabilities, which correspond to the frequencies of different allelic association patterns. By studying these measures under no recombination, a single recombination event, and between fully independent loci, we are able to gain new insights to how these measures vary across recombination scales. We also classify recombination events into four types and rank them according to their respective frequencies and effects on LD measures. Using previously published human data, we show how tree-sequence information can be used to partition the genome and to analyze LD in relation to theoretical expectations. Finally, we provide recommendations for the use of the different statistics and suggest applications of LD measures in the absence of recombination.

evolutionary biology↗

bioRxiv2023

Weak genetic draft and the Lewotin's paradox

Recurrent selective sweeps reduce diversity at linked neutral loci, a regime known as genetic draft. Most theoretical work has focused on the tight draft regime, where the selected and neutral loci are closely linked, leading to Multiple Merger Coalescents and a diversity largely insensitive to population size. Here, we investigate the neglected regime of loose genetic draft, where sweeps at a distant linked locus have individually negligible effects but collectively drive diversity. To explore this regime systematically, we make extensive use of the RIF model (Random Initial and Final conditions), a semi-deterministic approximation of selective sweeps that is 103 times faster than standard Wright-Fisher simulations and equally accurate. Using this framework, we derive novel analytical approximations for the coalescence probability under a single sweep, valid for a wide range of recombination-to-selection ratios A = c/s, and show that they outperform several previous approximations from the literature, which are only accurate for small A. Under recurrent loose draft (0.1 < A < 0.5), the effective population size scales as a power law of census size, Ne {propto} N 2A, which could contribute to the observed non-linear dependence of diversity on population size. Crucially, despite this strong reduction in diversity, the genealogy converges to a Kingman coalescent, making loose draft patterns indistinguishable from neutrality by standard tests.

evolutionary biology↗

bioRxiv2023

Chance favors the prepared genomes: horizontal transfer shapes the emergence of antibiotic resistance mutations in core genes.

Bacterial lineages vary in the frequency with which they acquire novel traits, like antibiotic resistance or virulence. While previous studies have highlighted the impact of the genetic background on the successful acquisition of novel traits through horizontal gene transfer, the impact of the latter on the subsequent evolution of bacterial genomes by point mutations remains poorly understood. Here, we studied the evolution of resistance to quinolones in thousands of Escherichia coli genomes. Resistance-conferring point mutations in the core genes are frequent and accumulate very quickly. We searched for gene gains and losses significantly associated with the subsequent acquisition of these resistance mutations. This revealed 60 groups of genes in genetic linkage whose gain or loss induced a change in the probability of subsequently becoming resistant to quinolones by point mutations in gyrA and parC. Although some of these chronologies may reflect epidemiological trends, most of these groups encoded functions that were previously associated with antibiotic resistance, tolerance, or persistence, often specifically under quinolone treatment. A lot of the largest groups were found in prophages or plasmids, and they usually increased the likelihood of subsequent resistance mutations. Conversely groups of lost genes were typically small and chromosomal. Quinolone resistance was among the first resistances acquired in the extant lineages of E. coli and its acquisition was associated with an increased likelihood of acquiring other types of resistances, including to aminoglycosides and beta-lactams. Our findings suggest that gene flow shapes the subsequent fixation rate of adaptive mutations in core genes. Given the substantial gene flow within bacterial genomes, interactions between horizontal transfer and point mutations in core genes may be key to the success of adaptation processes.

evolutionary biology↗

bioRxiv2023

The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Contiguous assemblies are fundamental to decipher the exact composition of extant genomes. In molluscs, this task is considerably challenging owing to their large size, heterozygosity, and widespread content of repetitive content. Consequently, the usage of long-read sequencing technologies is fundamental to achieve high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, has been produced recently. However, the current genome is highly fragmented since the assembly relied solely on short-read approaches. To overcome this caveat, here, a new improved reference genome assembly is produced using a combination of PacBio CLR long reads and Illumina paired-end short reads. This novel genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4Mbp. The ab initio gene prediction resulted in a total of 48,314 protein-coding genes. This new assembly represents a substantial improvement and is an essential resource for studying this species unique biological and evolutionary features that ultimately will help to promote its conservation.

genomics↗

bioRxiv2022

Evo-Scope: Fully automated assessment of correlated evolution on phylogenetic trees

O_LICorrelated evolution describes how multiple biological traits evolve together. Recently developed methods provide increasingly detailed results of correlated evolution, sometimes at elevated computational costs. C_LIO_LIHere, we present evo-scope, a fast and fully-automated pipeline with minimal input requirements to compute correlation between discrete traits evolving on a phylogenetic tree. Notably, we improve two of our previously developed tools that efficiently compute statistics of correlated evolution to characterize the nature, such as synergy or antagonism, and the strength of the interdependence between the traits. C_LIO_LIFurthermore, we improved the running time and implemented several additional features, such as genetic mapping, Bayesian Markov Chain Monte Carlo estimation, consideration of missing data and phylogenetic uncertainty. C_LIO_LIAs an application, we scan a published penicillin resistance data set of Streptococcus pneumoniae and characterize genetic mutations that correlate with antibiotic resistance. The pipeline is accessible both as a self-contained github repository (https://github.com/Maxime5G/EvoScope) and through a graphical galaxy interface (https://galaxy.pasteur.fr/u/maximeg/w/evoscope). C_LI

evolutionary biology↗

bioRxiv2022

Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences

Cultural Transmission of Reproductive Success (CTRS) has been observed in many human populations as well as other animals. It consists in a positive correlation of non-genetic origin between the progeny size of parents and children. This correlation can result from various factors, such as the social influence of parents on their children, the increase of childrens survival through allocare from uncle and aunts, or the transmission of resources. Here, we study the evolution of genomic diversity through time under CTRS. We show that CTRS has a double impact on population genetics: (1) effective population size decreases when CTRS starts, mimicking a population contraction, and increases back to its original value when CTRS stops; (2) coalescent trees topologies are distorted under CTRS, with higher imbalance and higher number of polytomies. Under long-lasting CTRS, effective population size stabilises but the distortion of tree topology remains, which yields U-shaped Site Frequency Spectra (SFS) under constant population size. We show that this CTRS impact yields a bias in SFS-based demographic inference. Considering that CTRS was detected in numerous human and animal populations worldwide, one should be cautious that inferring population past histories from genomic data can be biased by this cultural process.

genetics↗

bioRxiv2022

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

The standard neutral model of molecular evolution has traditionally been used as the null model for population genomics. We gathered a collection of 45 genome-wide site frequency spectra from a diverse set of species, most of which display an excess of low and high frequency variants compared to the expectation of the standard neutral model, resulting in U-shaped spectra. We show that multiple merger coalescent models often provide a better fit to these observations than the standard Kingman coalescent. Hence, in many circumstances these under-utilized models may serve as the more appropriate reference for genomic analyses. We further discuss the underlying evolutionary processes that may result in the widespread U-shape of frequency spectra.

evolutionary biology↗

bioRxiv2020

Simulation of bacterial populations with SLiM

Simulation of genomic data is a key tool in population genetics, yet, to date, there is no forward-in-time simulator of bacterial populations that is both computationally efficient and adaptable to a wide range of scenarios. Here we demonstrate how to simulate bacterial populations with SLiM, a forward-in-time simulator built for eukaryotes. SLiM has gained many users in recent years, due to its speed and power, and has extensive documentation showcasing various scenarios that it can simulate. This paper focuses on a simple demographic scenario, to explore unique aspects of modeling bacteria in SLiMs scripting language. In addition, we illustrate the flexibility of SLiM by simulating the growth of bacteria on a Petri dish with antibiotic. To foster the development of bacterial simulations based upon this recipe, we explain the inner workings of its code. We also validate the simulator, by extensively testing the results of simulations against existing simulators, and against theoretical expectations for some summary statistics. This protocol, with the flexibility and power of SLiM, will enable the community to simulate bacterial populations efficiently under a wide range of evolutionary scenarios.

evolutionary biology↗

bioRxiv2020

A minimal yet flexible likelihood framework to assess correlated evolution

An evolutionary process is reflected in the sequence of changes of any trait (e.g. morphological, molecular) through time. Yet, a better understanding of evolution would be procured by characterizing correlated evolution, or when two or more evolutionary processes interact. Many previously developed parametric methods often require significant computing time as they rely on the estimation of many parameters. Here we propose a minimal likelihood framework modelling the joint evolution of two traits on a known phylogenetic tree. The type and strength of correlated evolution is characterized by few parameters tuning mutation rates of each trait and interdependencies between these rates. The framework can be applied to study any discrete trait or character ranging from nucleotide substitution to gain or loss of a biological function. More specifically, it can be used to 1) test for independence between two evolutionary processes, 2) identify the type of interaction between them and 3) estimate parameter values of the most likely model of interaction. In its current implementation, the method takes as input a phylogenetic tree together with mapped discrete evolutionary events on it and then maximizes the likelihood for one or several chosen scenarios. The strengths and limits of the method, as well as its relative power when compared to a few other methods, are assessed using both simulations and data from 16S rRNA sequences in a sample of 54 {gamma}-enterobacteria. We show that even with datasets of fewer than 100 species, the method performs well in parameter estimation and in the selection of evolutionary scenario.

evolutionary biology↗

bioRxiv2019

Revisiting use of DNA characters in taxonomy with MolD - a tree independent algorithm to retrieve diagnostic nucleotide characters from monolocus datasets

AO_SCPLOWBSTRACTC_SCPLOWWhile DNA characters are increasingly used for phylogenetic inference, taxa delimitation and identification, their use for formal description of taxa (i.e. providing either a formal description or a diagnosis) remains scarce and inconsistent. The impediments are neither nomenclatural, nor conceptual, but rather methodological issues: lack of agreement of what DNA character should be provided, and lack of a suitable operational algorithm to identify such characters. Furthermore, the reluctance of using DNA data in taxonomy may also be due to the concerns of insufficient reliability of DNA characters as robustness of the DNA based diagnoses has never been thoroughly assessed. Removing these impediments will enhance integrity of systematics, and will enable efficient treatment of traditionally problematic cases, such as for example, cryptic species. We have developed a novel versatile and scalable algorithm MolD to recover diagnostic combinations of nucleotides (DNCs) for pre-defined groups of DNA sequences, corresponding to taxa. We applied MolD to four published monolocus datasets to examine 1) which type of DNA characters compilation allows for more robust diagnosis, and 2) how the robustness of DNA based diagnosis changes depending on the sampled fraction of taxons diversity. We demonstrate that the redundant DNCs, termed herein sDNCs, allow for higher robustness. Furthermore, we show that a reliable DNA-based diagnosis may be obtained when a rather small fraction of the entire data set is available. Based on our results we propose improvements to the existing practices of handling DNA data in taxonomic descriptions, and discuss a workflow of contemporary systematic study, where the integrative taxonomy part precedes the proposition of a DNA based diagnosis and the diagnosis itself can be efficiently used as a DNA barcode. Our analysis fills existing methodological gaps, thus setting stage for a wider use of the DNA data in taxa description.

bioinformatics↗

bioRxiv2019

Testing for population decline using maximal linkage disequilibrium blocks

Only 6% of known species have a conservation status. Methods that assess conservation statuses are often based on individual counts and are thus too laborious to be generalized to all species. Population genomics methods that infer past variations in population size are easy to use but limited to the relatively distant past. Here we propose a population genomics approach that tests for recent population decline and may be used to assess species conservation statuses. More specifically, we study Maximal Recombination Free (MRF) blocks, that are segments of a sequence alignment inherited from a common ancestor without recombination. MRF blocks are relatively longer in small than in large populations. We use the distribution of MRF block lengths rescaled by their mean to test for recent population decline. However, because MRF blocks are difficult to detect, we also consider Maximal Linkage Disequilibrium (MLD) blocks, which are runs of single nucleotide polymorphisms compatible with a single tree. We develop a new method capable of inferring a very recent decline (e.g. with a detection power of 50% for populations which size was halved to N, 0.05 xN generations ago) from rescaled MLD block lengths. Our framework could serve as a basis for quantitative tools to assess conservation status in a wide range of species.

evolutionary biology↗

bioRxiv2019

The rapid divergence of the Antarctic crinoid species Promachocrinus kerguelensis

Climatic oscillations in Antarctica caused a succession of expansion and reduction of the ice sheets covering the continental shelf of the Southern Ocean. For marine invertebrates, these successions are suspected to have driven allopatric speciation, endemism and the prevalence of cryptic species, leading to the so-called Antarctic biodiversity pump hypothesis. Here we took advantage of the recent sampling effort influenced by the International Polar Year (2007-8) to test for the validity of this hypothesis for 1,797 samples of two recognized crinoid species: Promachocrinus kerguelensis and Florometra mawsoni. Species delimitation analysis identified seven phylogroups. As previously suggested, Promachocrinus kerguelensis forms a complex of six cryptic species. Conversely, despite the morphological differences, our results show that Florometra mawsoni is a lineage nested within Promachocrinus kerguelensis. It suggests that Florometra mawsoni and Promachocrinus kerguelensis belong to the same complex of species. Furthermore, this study indicates that over time and space the different sectors of the Southern Ocean show a remarkable rapid turn-over in term of phylogroups composition and also of genetic variants within phylogroups. We argue that strong \"apparent\" genetic drift causes this rapid genetic turn-over. Finally, we dated the last common ancestor of all phylogroups at less than 1,000 years, raising doubts on the relevance of the Antarctic \"biodiversity pump\" for this complex of species. This work is a first step towards a better understanding of how life is diversifying in the Southern Ocean.

evolutionary biology↗