Nicolas Lartillot

Nicolas Lartillot
French National Centre for Scientific Research | CNRS · Laboratoire de Biométrie et Biologie Évolutive (LBBE)

About

138
Publications
14,362
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10,902
Citations
Citations since 2016
56 Research Items
5731 Citations
20162017201820192020202120220200400600800
20162017201820192020202120220200400600800
20162017201820192020202120220200400600800
20162017201820192020202120220200400600800

Publications

Publications (138)
Preprint
Full-text available
Adaptation in protein-coding sequences can be detected from multiple sequence alignments across species, or alternatively by leveraging polymorphism data inside a population. Across species, quantification of the adaptive rate relies on phylogenetic codon models, classically formulated in terms of the ratio of non-synonymous over synonymous substit...
Article
Reconstructing ancestral characters on a phylogeny is an arduous task because the observed states at the tips of the tree correspond to a single realization of the underlying evolutionary process. Recently, it was proposed that ancestral traits can be indirectly estimated with the help of molecular data, based on the fact that life history traits i...
Article
Full-text available
Molecular sequences are shaped by selection, where the strength of selection relative to drift is determined by effective population size (Ne). Populations with high Ne are expected to undergo stronger purifying selection, and consequently to show a lower substitution rate for selected mutations relative to the substitution rate for neutral mutatio...
Article
Full-text available
Mutation-selection phylogenetic codon models are grounded on population genetics first principles and represent a principled approach for investigating the intricate interplay between mutation, selection and drift. In their current form, mutation-selection codon models are entirely characterized by the collection of site-specific amino-acid fitness...
Article
Full-text available
The nearly-neutral theory predicts specific relations between effective population size (Ne ) and patterns of divergence and polymorphism, which depend on the shape of the distribution of fitness effects (DFE) of new mutations. However, testing these relations is not straightforward, owing to the difficulty in estimating Ne. Here, we introduce an i...
Article
We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. I...
Article
Full-text available
A Correction to this paper has been published: https://doi.org/10.1038/s42003-021-01922-8
Article
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Bivalves represent valuable taxonomic group for aging studies given their wide variation in longevity (from 1–2 to >500 years). It is well known that aging is associated to the maintenance of Reactive Oxygen Species homeostasis and that mitochondria phenotype and genotype dysfunctions accumulation is a hallmark of these processes. Previous studies...
Article
Full-text available
Statistical phylogenetic analysis currently relies on complex, dedicated software packages, making it difficult for evolutionary biologists to explore new models and inference strategies. Recent years have seen more generic solutions based on probabilistic graphical models, but this formalism can only partly express phylogenetic problems. Here, we...
Preprint
Full-text available
Molecular sequences are shaped by selection, where the strength of selection relative to drift is determined by effective population size ( N e ). Populations with high N e are expected to undergo stronger purifying selection, and consequently to show a lower substitution rate for selected mutations relative to the substitution rate for neutral mut...
Preprint
Full-text available
Mutation-selection phylogenetic codon models are grounded on population genetics first principles and represent a principled approach for investigating the intricate interplay between mutation, selection and drift. In their current form, mutation-selection codon models are entirely characterized by the collection of site-specific amino-acid fitness...
Article
Full-text available
In recent years, codon substitution models based on the mutation-selection principle have been extended for the purpose of detecting signatures of adaptive evolution in protein-coding genes. However, the approaches used to date have either focused on detecting global signals of adaptive regimes—across the entire gene—or on contexts where experiment...
Article
Full-text available
Gall wasps (Hymenoptera: Cynipidae) induce complex galls on oaks, roses and other plants, but the mechanism of gall induction is still unknown. Here we take a comparative genomic approach to revealing the genetic basis of gall induction. We focus on Synergus itoensis, a species that induces galls inside oak acorns. Previous studies suggested that t...
Article
Full-text available
Biochemical demands constrain the range of amino acids acceptable at specific sites resulting in across-site compositional heterogeneity of the amino acid replacement process. Phylogenetic models that disregard this heterogeneity are prone to systematic errors, which can lead to severe long branch attraction artifacts. State-of-the-art models accou...
Preprint
Full-text available
Statistical phylogenetic analysis currently relies on complex, dedicated software packages, making it difficult for evolutionary biologists to explore new models and inference strategies. Recent years have seen more generic solutions based on probabilistic graphical models, but this formalism can only partly express phylogenetic problems. Here we s...
Preprint
Full-text available
We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. I...
Preprint
Full-text available
A bstract The nearly-neutral theory predicts specific relations between effective population size ( N e ), and patterns of divergence and polymorphism, which depend on the shape of the distribution of fitness effects (DFE) of new mutations. However, testing these relations is not straightforward since N e is difficult to estimate in practice. For t...
Preprint
Full-text available
Biochemical demands constrain the range of amino acids acceptable at specific sites resulting in across-site composition heterogeneity of the amino acid replacement process. Phylogenetic models that disregard this heterogeneity are prone to systematic errors, which can lead to severe long branch attraction artifacts. State-of-the-art models account...
Article
Full-text available
In evolutionary genomics, researchers have taken an interest in identifying substitutions that subtend convergent phenotypic adaptations. This is a difficult question that requires distinguishing foreground convergent substitutions that are involved in the convergent phenotype from background convergent substitutions. Those may be linked to other a...
Article
The rate of molecular evolution varies widely among species. Life history traits have been proposed as a major driver of these variations. However, the relative contribution of each trait is poorly understood. Here, we test the influence of metabolic rate, longevity and generation time on the nuclear and mitochondrial synonymous substitution rates...
Preprint
Full-text available
In evolutionary genomics, researchers have taken an interest in identifying in the genomes substitutions that subtend convergent phenotypic adaptations. This is a difficult question to address, because genomes contain billions of sites, many of which have substituted in the lineages where the adaptations took place, and yet are not linked to them....
Article
The rate of molecular evolution varies widely among species. Life history traits have been proposed as a major driver of these variations. However, the relative contribution of each trait is poorly understood. Here, we test the influence of metabolic rate, longevity and generation time on the nuclear and mitochondrial synonymous substitution rates...
Article
Full-text available
A key question in molecular evolutionary biology concerns the relative roles of mutation and selection in shaping genomic data. Moreover, features of mutation and selection are heterogeneous along the genome and over time. Mechanistic codon substitution models based on the mutation-selection framework are promising approaches to separating these ef...
Article
Full-text available
Rubisco (Ribulose-1, 5-biphosphate carboxylase/oxygenase) is the most important enzyme on earth, catalyzing the first step of photosynthetic CO2 fixation. So, without it, there would be no storing of the sun’s energy in plants. Molecular adaptation of Rubisco to C4 photosynthetic pathway has attracted a lot of attention. C4 plants, which comprise l...
Data
C4 differential sequence logo for rbcL sequence in Amaranthaceae family. (DOCX)
Data
Estimates of posterior mean differential selection effects across all amino acids and all sites for two independent chains, for C3 plants (a) and C4 plants (b). (DOCX)
Data
List of 179 species from Amaranthaceae family. (DOCX)
Data
Alignment of 179 sequences. (TXT)
Article
Full-text available
In humans and many other species, recombination events cluster in narrow and short-lived hot spots distributed across the genome, whose location is determined by the Zn-finger protein PRDM9. To explain these fast evolutionary dynamics, an intra-genomic Red Queen model has been proposed, based on the interplay between two antagonistic forces: biased...
Preprint
Full-text available
This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology ( http://dx.doi.org/10.24072/pci.evolbiol.100042 ). Reconstructing ancestral characters on a phylogeny is an arduous task because the observed states at the tips of the tree correspond to a single realization of the underlying evolutionary process. Recently, i...
Article
Full-text available
The relationships at the root of the animal tree have proven difficult to resolve, with the current debate focusing on whether sponges (phylum Porifera) or comb jellies (phylum Ctenophora) are the sister group of all other animals [1–5]. The choice of evolu- tionary models seems to be at the core of the prob- lem because Porifera tends to emerge as...
Article
Full-text available
Background Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these...
Article
Full-text available
Codon substitution models have traditionally attempted to uncover signatures of adaptation within protein-coding genes by contrasting the rates of synonymous and nonsynonymous substitutions. Another modeling approach, known as the mutation-selection framework, attempts to explicitly account for selective patterns at the amino acid level, with some...
Preprint
Full-text available
Rubisco (Ribulose-1, 5-biphosphate carboxylase/oxygenase) is the most important enzyme on earth, catalyzing the first step of CO2 fixation in photosynthesis. Its molecular adaptation to C4 photosynthetic pathway has attracted a lot of attention. C4 plants, which comprise less than 5% of land plants, have evolved more efficient photosynthesis compar...
Preprint
Full-text available
Background Phylogenetic codon models are often used to characterize the selective regimes acting on protein coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by explicitly modelling the amino acid fitness landscape along the sequence. However, thus far, mo...
Article
Full-text available
Over recent years, several alternative relaxed clock models have been proposed in the context of Bayesian dating. These models fall in two distinct categories: uncorrelated and autocorrelated across branches. The choice between these two classes of relaxed clocks is still an open question. More fundamentally, the true process of rate variation may...
Article
Full-text available
Total-evidence dating (TED) allows evolutionary biologists to incorporate a wide range of dating information into a unified statistical analysis. One might expect this to improve the agreement between rocks and clocks but this is not necessarily the case. We explore the reasons for such discordance using a mammalian dataset with rich molecular, mor...
Article
Full-text available
Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed...
Article
Full-text available
Significance Clarifying the phylogeny of animals is fundamental to understanding their evolution. Traditionally, sponges have been considered the sister group of all other extant animals, but recent genomic studies have suggested comb jellies occupy that position instead. Here, we analyzed the current genomic evidence from comb jellies and found no...
Article
Full-text available
In spite of substantial work and recent progress, a global and fully resolved picture of the macroevolutionary history of eukaryotes is still under construction. This concerns not only the phylogenetic relations among major groups, but also the general characteristics of the underlying macroevolutionary processes, including the patterns of gene fam...
Article
Full-text available
Recombination is an essential process in eukaryotes, which increases diversity by disrupting genetic linkage between loci and ensures the proper segregation of chromosomes during meiosis. In the human genome, recombination events are clustered in hotspots, whose location is determined by the PRDM9 protein. There is evidence that the location of hot...
Article
Full-text available
Motivation: Brownian models have been introduced in phylogenetics for describing variation in substitution rates through time, with applications to molecular dating or to the comparative analysis of variation in substitution patterns among lineages. Thus far, however, the Monte Carlo implementations of these models have relied on crude approximati...
Article
Full-text available
In recent years, there has been an increasing interest in the potential of codon substitution models for a variety of applications. However, the computational demands of these models have sometimes lead to the adoption of over-simplified assumptions, questionable statistical methods, or a limited focus on small data sets. Here, we offer a scalable,...
Article
Full-text available
Correlation between life-history or ecological traits and genomic features such as nucleotide or amino-acid composition can be used for reconstructing the evolutionary history of the traits of interest along phylogenies. Thus far, however, such ancestral reconstructions have been done using simple linear regression approaches that do not account fo...
Article
Full-text available
The nearly-neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of non-synonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino-acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous...
Article
Full-text available
The exact evolutionary origin of the zinc finger (ZF) domain is unknown, as it is still not clear from which organisms it was first derived. However, the unique features of the ZF domains have made it very easy for evolution to tinker with them in a number of different manners, including their combination, variation of their number by unequal cross...
Article
Full-text available
Modeling across site variation of the substitution process is increasingly recognized as important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models have been proposed, and have been shown to significantly improve on classical single-matrix models. Compared to their finite counterparts, infinite mixtu...
Article
Full-text available
In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. B...
Article
Full-text available
GC Biased gene conversion (gBGC) is a major evolutionary force shaping genomic nucleotide landscapes, distorting the estimation of the strength of selection, and having potentially deleterious effects on genome-wide fitness. Yet, a global quantitative picture, at large evolutionary scale, of the relative strength of gBGC compared to selection and r...