Jerome Goudet

University of Lausanne | UNIL · Department of Ecology and Evolution

Homologous recombination is a meiotic process that generates diversity along the genome and interacts with all evolutionary forces. Despite its importance, studies of recombination landscapes are lacking due to methodological limitations and limited data. Frequently used approaches include linkage mapping based on familial data that provides sex-sp...

The Jacquard genetic identity coefficients are of fundamental importance in relatedness research. We address the estimation of these coefficients as well as other relationship parameters that derive from them such as kinship and inbreeding coefficients using a concise matrix framework. Estimation of the Jacquard coefficients via likelihood methods...

A key aspect of assessing the risk of extinction/extirpation for a particular wild species or population is the status of inbreeding, but the origin of inbreeding and the current mutational load are also two crucial factors to consider when determining survival probability of a population. In this study, we used samples from 502 barn owls from cont...

Measuring inbreeding and its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the best method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. We simulated traits based on si...

An important aspect of assessing endangered levels and managing conservation is the study of inbreeding status, identifying its origin as well as assessing the mutation load in wild populations. In this study, we used 502 barn owls from continental and island populations across Europe. In addition to comparing inbreeding status, we determined wheth...

Homologous recombination is a meiotic process that generates diversity along the genome and interacts with all evolutionary forces. Despite its importance, studies of recombination landscapes are lacking due to methodological limitations and a dearth of appropriate data. Linkage mapping based on familial data gives unbiased sex-specific broad-scale...

The Jacquard genetic identity coefficients are of fundamental importance in relatedness research. We address the estimation of these coefficients as well as other relatedness parameters that derive from them such as kinship and inbreeding coefficients using a concise matrix framework. Estimation of the Jacquard coefficients via likelihood methods a...

[This corrects the article DOI: 10.1371/journal.pgen.1010871.].

Mitochondria are known to play an essential role in the cell. These organelles contain their own DNA, which is divided in a coding and non-coding region (NCR). While much of the NCR’s function is unknown, tandem repeats have been observed in several vertebrates, with extreme intra-individual, intraspecific and interspecific variation. Taking advant...

The maintenance of colour variation in wild populations has long fascinated evolutionary biologists, although most studies have focused on discrete traits exhibiting rather simple inheritance patterns and genetic architectures. However, the study of continuous colour traits and their potentially oligo- or polygenic genetic bases remains rare in wil...

Being able to properly quantify genetic differentiation is key to understanding the evolutionary potential of a species. One central parameter in this context is FST, the mean coancestry within populations relative to the mean coancestry between populations. Researchers have been estimating FST globally or between pairs of populations for a long ti...

Background After its nearly eradication in the 1940’s, the bed bug (Cimex lectularius) experienced a global resurgence with some populations displaying insecticide resistance. Two distinct lineages of bed bugs have been identified, one of which is associated with humans and the other with bats. Given that bat roosts can be shared within human shelt...

Measuring inbreeding as well as its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the most appropriate method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. In this proj...

Being able to properly quantify genetic differentiation is key to understanding the evolutionary potential of a species. One central parameter in this context is F ST , the mean coancestry within populations relative to the mean coancestry between populations. Researchers have been estimating F ST globally or between pairs of populations for a long...

The maintenance of color polymorphism in populations has fascinated evolutionary biologists for decades. Studies of color variation in wild populations often focus on discrete color traits exhibiting simple inheritance patterns, while studies on continuously varying traits remain rare. Here, we studied the continuous white to rufous color polymorph...

Climatic variations subject living species to evolutionary stresses and shape their distributions. Since the Last Glacial Maximum (LGM) and the subsequent temperature rise, species (re-) colonised higher latitudes. Among the evolutionary mechanisms involved during this process, local adaptation is thought to be one of the keystones of species persi...

Despite their paramount importance in molecular ecology and conservation, genetic diversity and structure remain challenging to quantify with traditional genotyping methods. Next-generation sequencing holds great promises, but this has not been properly tested in highly mobile species. In this article, we compared microsatellite and RAD-sequencing...

Genomic measures of inbreeding based on Identical-by-Descent (IBD) segments are increasingly used to measure inbreeding and mostly estimated on SNP arrays and whole-genome-sequencing (WGS) data. However, some softwares recurrently used for their estimation assume that genomic positions which have not been genotyped are non-variant. This might be tr...

Islands, and the particular organisms that populate them, have long fascinated biologists. Due to their isolation, islands offer unique opportunities to study the effect of neutral and adaptive mechanisms in determining genomic and phenotypical divergence. In the Canary Islands, an archipelago rich in endemics, the barn owl (Tyto alba), present in...

Runs of homozygosity (ROHs) are proxy for genomic Identical-by-Descent segments and are increasingly used to measure individual inbreeding. ROHs analyses are mostly carried out on SNPs-arrays and whole-genome-sequencing data. Softwares recurrently used for their detection usually assume that genomic positions which have not been genotyped are non-v...

In his 1972 paper ‘The apportionment of human diversity’, Lewontin showed that, when averaged over loci, genetic diversity is predominantly attributable to differences among individuals within populations. However, selection can alter the apportionment of diversity of specific genes or genomic regions. We examine genetic diversity at the human leuc...

Islands, and the particular organisms that populate them, have long fascinated biologists. Due to their isolation, islands offer unique opportunities to study the effect of neutral and adaptive mechanisms in determining genomic and phenotypical divergence. In the Canary Islands, an archipelago rich in endemics, the barn owl (Tyto alba) is thought t...

The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad ran...

The study of insular populations was key in the development of evolutionary theory. The successful colonisation of an island depends on the geographic context, and specific characteristics of the organism and the island, but also on stochastic processes. As a result, apparently identical islands may harbour populations with contrasting histories. H...

The two alleles an individual carries at a locus are identical by descent (ibd) if they have descended from a single ancestral allele in a reference population, and the probability of such identity is the inbreeding coefficient of the individual. Inbreeding coefficients can be predicted from pedigrees with founders constituting the reference popula...

In his 1972 "The apportionment of human diversity", Richard Lewontin showed that, when averaged over loci, genetic diversity is predominantly attributable to differences among individuals within populations. However, selection on specific genes and genomic regions can alter the apportionment of diversity. We examine genetic diversity at the HLA loc...

The climate fluctuations of the Quaternary shaped the movement of species in and out of glacial refugia. In Europe, the majority of species followed one of the described traditional postglacial recolonization routes from the southern peninsulas towards the north. Like most organisms, barn owls are assumed to have colonized the British Isles by cros...

The study of insular populations was key in the development of evolutionary theory. The successful colonisation of an island depends on the geographic context, and specific characteristics of the organism and the island, but also on stochastic processes. As a result, apparently identical islands may harbour populations with contrasting histories. H...

The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad ran...

The climate fluctuations of the Quaternary shaped the movement of species in and out of glacial refugia. In Europe, the majority of species followed one of the described traditional postglacial recolonization routes from the southern peninsulas towards the north. Like most organisms, barn owls are assumed to have colonized the British Isles by cros...

Common garden experiments are precious to study adaptive phenomenon and adaptive potential, in that they allow to study local adaptation without the confounding effect of phenotypic plasticity. The QST − FST comparison framework, comparing genetic differentiation at the phenotypic and molecular level, is the usual way to test and measure whether lo...

Assessing the degree to which climate explains the spatial distributions of different taxonomic and functional groups is essential for anticipating the effects of climate change on ecosystems. Most effort so far has focused on aboveground organisms, which offer only a partial view on the response of biodiversity to environmental gradients. Here, in...

New genomic tools open doors to study ecology, evolution, and population genomics of wild animals. For the Barn owl species complex, a cosmopolitan nocturnal raptor, a very fragmented draft genome was assembled for the American species (Tyto furcata pratincola) (Jarvis et al. 2014). To improve the genome, we assembled de novo Illumina and Pacific B...

For at least 40 years now, evolutionary biologists have discussed the relative roles of natural selection and genetic drift in shaping the genetic composition of populations. Range expansions are of particular interest in this discussion: They normally occur over environmental gradients allowing local adaptation to take place, but the demographic p...

The concept of kinship permeates many domains of fundamental and applied biology ranging from social evolution to conservation science to quantitative and human genetics. Until recently, pedigrees were the gold standard to infer kinship, but the advent of next generation sequencing and the availability of dense genetic markers in many species make...

Non-random gene flow is a widely neglected force in evolution and ecology. This genotype-dependent dispersal is difficult to assess, yet can impact the genetic variation of natural populations and their fitness. In this work, we demonstrate a high immigration rate of barn owls (Tyto alba) inside a Swiss population surveyed during 15 years. Using te...

Balancing selection is defined as a class of selective regimes that maintain polymorphism above what is expected under neutrality. Theory predicts that balancing selection reduces population differentiation, as measured by FST. However, balancing selection regimes in which different sets of alleles are maintained in different populations could incr...

The rate of aquatic invasions by planktonic organisms has increased considerably in recent decades. In order to effectively direct funding and resources to control the spread of such invasions, a methodological framework for identifying high-risk transport vectors, as well as ruling out vectors of lesser concern will be necessary. A number of estua...

Although it is generally accepted that geography is a major factor shaping human genetic differentiation, it is still disputed how much of this differentiation is a result of a simple process of isolation-by-distance, and if there are factors generating distinct clusters of genetic similarity. We address this question using a geographically explici...

Distribution of the populations used in this study (red crosses). The origin of the expansion of humans in East Africa is marked as the green dot. Map following Fuller’s Dymaxion projection, the same applied to the maps used in the simulations. The modeled map contained 20,384 square demes (5,094 on land), each with an approximate area of 160 x 160...

ABC-GLM estimation of the model parameters. Gray lines represent the prior distributions; black lines, the posteriors; the gray dashed vertical lines, the modes for the posteriors (point estimates). The estimations were carried out on 5,000 out of ~1 million simulations which were the closest to the observations in six pattern statistics (see mater...

Estimates of the most likely number of groups within the worldwide sample of populations. The figure contains the results obtained both for observations (Observed) and simulations (Simulated). L(K) is the direct assessment of likelihood for each number of groups. Delta-K is the estimate based on Evanno et al.’s 2005 approach. (TIF)

Population samples as they were analyzed in this study. Populations marked with “a” were merged together due to their geographical proximity (less than 160km apart) and were considered to inhabit the same deme in the simulations and also in the analyses applied to the read dataset. Populations marked with “b” were removed from the pattern statistic...

Prior distributions and values of the parameters explored in the ABC analysis. (PDF)

Schematic representation of the pipeline used in the study. ABC framework shows the basic structure of an ABC analysis focused in parameter estimation. Full-dataset simulations represents the following step in which simulations were run based on the estimations above and for which complete allele frequency data was retained. In Pattern comparison,...

Comparison between the STRUCTURE results obtained for observed (OBS) and simulated (SIM) data. Vertical bars represent the 70 populations as used in the simulations and the colors code for the proportion of each inferred ancestry group (K = 5, 6 and 7). One can observe that particular populations become highlighted in the observations (Suruí with K...

ABC-GLM estimation of the model parameters using five PLS components calculated from the whole set of statistics retaining 1000 simulations. Gray lines represent the realized priors; blue dashed lines represent the distribution of the parameter values in the retained simulations; red lines represent the posterior distributions. The PLS calculation...

Comparison of patterns generated with gene diversity (heterozygosity, hs). A, comparison of the patterns generated for the cline in heterozigosity between observation and a simulation based on the point estimates. B, convergence of different pattern statistics related to the heterozigosity cline across different samplings from prior or posterior. (...

The canonical model of sex-chromosome evolution predicts that sex-antagonistic (SA) genes play an instrumental role in the arrest of XY recombination and ensuing Y-chromosome degeneration. Although this model might account for the highly differentiated sex chromosomes of birds and mammals, it does not fit the situation of many lineages of fish, amp...

Balancing selection is defined as a class of selective regimes that maintain polymorphism above what is expected under neutrality. Theory predicts that balancing selection reduces population differentiation, as measured by F ST . However, balancing selection regimes in which different sets of alleles are maintained in different populations could in...

Although it is generally accepted that geography is a major factor shaping human genetic differentiation, it is still disputed how much of this differentiation is a result of a simple process of isolation-by-distance, and if there are factors generating distinct clusters of genetic similarity. We address this question using a geographically explici...

Many population genetic activities, ranging from evolutionary studies to association mapping to forensic identification, rely on appropriate estimates of population structure or relatedness. All applications require recognition that quantities with an underlying meaning of allelic dependence are not defined in an absolute sense, but instead are mad...

Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties base...

List and details on the Cannabis accessions. (XLSX)

List and details on the STRs markers. (XLSX)

List and details on test samples. (XLSX)

Tree of genetic distances (pairwise Fst) between Cannabis accessions. Monoecious hemp are highlighted in grey. (TIF)

Genetic structure among marijuana samples. (TIF)

Plant interactions with arbuscular mycorrhizal fungi have long attracted interest for their potential to promote more efficient use of mineral resources in agriculture. Their use, however, remains limited by a lack of understanding of the processes that determine the outcome of the symbiosis. In this study, the impact of host genotype on growth res...

Many population genetic activities, ranging from evolutionary studies to association mapping to forensic identification, rely on appropriate estimates of population structure or relatedness. All applications require recognition that quantities with an underlying meaning of allelic identity by descent are not defined in an absolute sense, but instea...

Many population genetic activities, ranging from evolutionary studies to association mapping to forensic identification, rely on appropriate estimates of population structure or relatedness. All applications require recognition that quantities with an underlying meaning of allelic identity by descent are not defined in an absolute sense, but instea...

Plant interactions with arbuscular mycorrhizal fungi have long attracted interest for their potential to promote more efficient use of mineral resources in agriculture. Their widespread use, however, remains limited by understanding of the processes that determine the outcome of the symbiosis. In this study, variation in growth response to mycorrhi...

Sexual conflict arises when selection in one sex causes the displacement of the other sex from its phenotypic optimum, leading to an inevitable tension within the genome – called intralocus sexual conflict. Although the autosomal melanocortin-1-receptor gene (MC1R) can generate colour variation in sexually dichromatic species, most previous studies...

Population genetics and genomics have developed and been treated as independent fields of study despite having common roots. The continuous progress of sequencing technologies is contributing to (re-)connect these two disciplines. We review the challenges faced by data analysts and software developers when handling very big genetic data sets collec...

Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria, and Eucaryotes. While such data may sometimes be treated as a single locus, in practice a number of biological and statistical phenomena can lead to phylogenetic incongruence. In such cases different loci should, at least...

Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey ( Lampetra fluviatilis ) and brook lamprey (L. planeri) show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and...

Raw data used in the manuscript

Supplementary material

Script to reproduce the major analysis step

Uncovering the genetic basis of phenotypic variation and the population history under which it established is key to understand the trajectories along which local adaptation evolves. Here, we investigated the genetic basis and evolutionary history of a clinal plumage color polymorphism in European barn owls (Tyto alba). Our results suggest that bar...

Clines in chromosomal inversion polymorphisms - presumably driven by climatic gradients - are common but there is surprisingly little evidence for selection acting on them. Here we address this long-standing issue in Drosophila melanogaster by using diagnostic SNP markers to estimate inversion frequencies from 28 whole-genome Pool-seq samples colle...

Uncovering the genetic basis of phenotypic variation and the population history under which it established is key to understand the trajectories along which local adaptation evolves. Here, we investigated the genetic basis and evolutionary history of a clinal plumage color polymorphism in European barn owls (Tyto alba). Our results suggest that bar...

Next Generation Sequencing (NGS) technologies have become the standard for data generation in studies of population genomics, as the 1000 Genomes Project (1000G). However, these techniques are known to be problematic when applied to highly polymorphic genomic regions, such as the Human Leukocyte Antigen (HLA) genes. Because accurate genotype calls...

Parasite population structure is often thought to be largely shaped by that of its host. In the case of a parasite with a complex life cycle, two host species, each with their own patterns of demography and migration, spread the parasite. However, the population structure of the parasite is predicted to resemble only that of the most vagile host sp...

Next Generation Sequencing (NGS) technologies have become the standard for data generation in studies of population genomics, as the 1000 Genomes Project (1000G). However, these techniques are known to be problematic when applied to highly polymorphic genomic regions, such as the Human Leukocyte Antigen ( HLA ) genes. Because accurate genotype call...

Gradients of variation – or clines – have always intrigued biologists. Classically, they have been interpreted as the outcomes of antagonistic interactions between selection and gene flow. Alternatively, clines may also establish neutrally with isolation-by-distance or secondary contact between previously isolated populations. The relative importan...

Extensive gene flow between wheat (Triticum sp.) and several wild relatives of the genus Aegilops has recently been detected despite notoriously high levels of selfing in these species. Here, we assess and model the spread of wheat alleles into natural populations of the barbed goatgrass (Aegilops triuncialis), a wild wheat relative prevailing in t...

Studying patterns of species distributions along elevation gradients is frequently used to identify the primary factors that determine the distribution, diversity and assembly of species. However, despite their crucial role in ecosystem functioning, our understanding of the distribution of below-ground fungi is still limited, calling for more compr...