A5009787104- Genetic diversity and population structure
- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Animal Ecology and Behavior Studies
- Wildlife Ecology and Conservation
- Identification and Quantification in Food
- Mosquito-borne diseases and control
- melanin and skin pigmentation
- Species Distribution and Climate Change
- Evolution and Genetic Dynamics
- Plant and animal studies
- Insect symbiosis and bacterial influences
- Biochemical Analysis and Sensing Techniques
- Insect Resistance and Genetics
- Malaria Research and Control
- Circadian rhythm and melatonin
- Infectious Diseases and Mycology
- Genomic variations and chromosomal abnormalities
- Advanced Graph Neural Networks
- Viral Infections and Vectors
- T-cell and Retrovirus Studies
- Cancer-related molecular mechanisms research
- Actinomycetales infections and treatment
- Animal Genetics and Reproduction
University of Lausanne
2021-2025
SIB Swiss Institute of Bioinformatics
2024
Laboratoire d'Écologie Alpine
2017-2022
Université Savoie Mont Blanc
2018-2022
Université Grenoble Alpes
2018-2022
Centre National de la Recherche Scientifique
2018-2022
How humans got their goats Little is known regarding the location and mode of early domestication animals such as for husbandry. To investigate history goat, Daly et al. sequenced mitochondrial nuclear sequences from ancient specimens ranging hundreds to thousands years in age. Multiple wild populations contributed origin modern during Neolithic. Over time, one type spread became dominant worldwide. However, at whole-genome level, goat are a mix different sources provide evidence multilocus...
Multiple introductions are key features for the establishment and persistence of introduced species. However, little is known about contribution genetic admixture to invasive potential populations. To address this issue, we studied recent invasion Asian tiger mosquito (Aedes albopictus) in Europe. Combining genome-wide single nucleotide polymorphisms historical knowledge using an approximate Bayesian computation framework, reconstruct colonization routes establish demographic dynamics...
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 continuous their potentially oligo- or polygenic bases remains rare populations. We studied genetics continuously varying white-to-rufous plumage coloration European barn owl ( Tyto alba ) using a genome-wide association approach whole-genome data...
Regulation of melanin-based pigmentation is complex, involving multiple genes. Because different genes can contribute to the same phenotype, identified in model organisms may not necessarily apply wild species. In barn owl (Tyto alba), ventral plumage colour ranges from white rufous, with genetic variation melanocortin 1 receptor gene (MC1R) accounting for at least a third this variation. present study, we used transcriptomic data compare expression profiles growing feathers nestlings MC1R...
Motivation: Pangenome graphs integrate multiple assemblies to represent non-redundant genetic diversity. However, current evaluations of pangenome graph quality rely primarily on technical parameters (e.g., total length, number nodes/edges, growth curves), which fail assess how effectively the represents homologous stretches across integrated assemblies. Results: We introduce a novel method quantitatively well its Our quantifies many single-copy and universal k-mers (SCUnK) from source are...
By altering gene expression and creating paralogs, genomic amplifications represent a key component of short-term adaptive processes. In insects, the use insecticides can select causing an increased detoxification enzymes, supporting usefulness these DNA markers for monitoring dynamics resistance alleles in field. this context, present study aims to characterize amplification event associated with organophosphate mosquito
Abstract The climate fluctuations of the Quaternary shaped movement species in and out glacial refugia. In Europe, majority followed one described traditional postglacial recolonization routes from southern peninsulas towards north. Like most organisms, barn owls are assumed to have colonized British Isles by crossing over Doggerland, a land bridge that connected Britain northern Europe. However, while they dark rufous conspicuously white, contrast could suggest selective forces at play on...
Abstract By their paternal transmission, Y‐chromosomal haplotypes are sensitive markers of population history and male‐mediated introgression. Previous studies identified biallelic single‐nucleotide variants in the SRY , ZFY DDX3Y genes, which domestic goats four major haplotypes, Y1A, Y1B, Y2A Y2B, with a marked geographical partitioning. Here, we extracted goat from whole‐genome sequences 386 (75 breeds) seven wild species, were generated by VarGoats genome project. Phylogenetic analyses...
Abstract Homologous recombination is a meiotic process that generates diversity along the genome and interacts with all evolutionary forces. Despite its importance, studies of landscapes are lacking due to methodological limitations limited data. Frequently used approaches include linkage mapping based on familial data provides sex-specific broad-scale estimates realized inferences population LD reveal more fine scale resolution landscape, albeit dependent effective size selective forces...
Islands, and the particular organisms that populate them, have long fascinated biologists. Due to their isolation, islands offer unique opportunities study effect of neutral adaptive mechanisms in determining genomic phenotypical divergence. In Canary an archipelago rich endemics, barn owl (Tyto alba), present all islands, is thought diverged into a subspecies (T. a. gracilirostris) on eastern ones, Fuerteventura Lanzarote. Taking advantage 40 whole-genomes modern population genomics tools,...
The combined actions of climatic variations and landscape barriers shape the history natural populations. When organisms follow their shifting niches, obstacles in can lead to splitting populations, on which evolution will then act independently. two such populations are reunited, secondary contact occurs a broad range admixture patterns, from narrow hybrid zones complete dissolution lineages. A previous study suggested that barn owls colonized Western Palearctic after last glaciation...
During domestication processes, changes in selective pressures induce multiple phenotypical, physiological, and behavioral target species. The rise of next-generation sequencing has provided a chance to study the genetics bases these changes, most time based on single nucleotide polymorphisms (SNPs). However, several studies have highlighted impact structural variations (SVs) individual fitness, particularly domestic We aimed at unraveling role SVs during later improvement small ruminants by...
The study of insular populations was key in the development evolutionary theory. successful colonisation an island depends on geographic context, and specific characteristics organism island, but also stochastic processes. As a result, apparently identical islands may harbour with contrasting histories. Here, we use whole genome sequences 65 barn owls to investigate patterns inbreeding genetic diversity eastern Mediterranean Sea. We focus Crete Cyprus, similar size, climate distance...
Abstract Homologous recombination is a meiotic process that generates diversity along the genome and interacts with all evolutionary forces. Despite its importance, studies of landscapes are lacking due to methodological limitations dearth appropriate data. Linkage mapping based on familial data gives unbiased sex-specific broad-scale estimates while linkage disequilibrium (LD) inference population provides finer resolution albeit depending effective size acting selective In this study, we...
ABSTRACT Next-generation sequencing technologies have opened a new era of research in genomics. Among these, restriction enzyme-based techniques such as restriction-site associated DNA (RADseq) or double-digest RAD-sequencing (ddRADseq) are now widely used many population genomics fields. From sampling to SNP calling, both wet and dry protocols been discussed the literature identify key parameters for an optimal loci reconstruction. The impact these on downstream analyses biological results...
Abstract The maintenance of color polymorphism in populations has fascinated evolutionary biologists for decades. Studies variation wild often focus on discrete traits exhibiting simple inheritance patterns, while studies continuously varying remain rare. Here, we studied the continuous white to rufous European barn owl ( Tyto alba ). Using a Genome Wide Association approach whole-genome data 75 owls sampled across Europe, identified, addition previously known MC1R mutation, two regions...
Abstract The male-specific part of the Y-chromosome is in mammalian and many other species longest haplotype that inherited without recombination. By its paternal transmission it has a small effective population size with dominant males. In several species, Y-chromosomal haplotypes are sensitive markers history introgression. Previous studies have identified domestic goats four major Y1A, Y1B, Y2A Y2B marked geographic differentiation regional variants. this study we used published...
Abstract The combined actions of climatic variations and landscape barriers shape the history natural populations. When organisms follow their shifting niches, obstacles in can lead to splitting populations, on which evolution will then act independently. two such populations are reunited, secondary contact occurs a broad range admixture patterns, from narrow hybrid zones complete dissolution lineages. A previous study suggested that barn owls colonized Western Palearctic after last...
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which domestic goats four major Y1A, Y1B, Y2A Y2B with a marked geographic partitioning. Here, we analyze whole-genome sequences 386 from 75 modern breeds 7 wild goat species that were generated by VarGoats genome project. Phylogenetic analyses indicated haplogroups...
Abstract Climatic variations subject living species to evolutionary stresses and shape their distributions. Since the Last Glacial Maximum (LGM) subsequent temperature rise, (re-) colonised higher latitudes. Among mechanisms involved during this process, local adaptation is thought be one of keystones persistence. However, its relative role location in space remain elusive. The Western Palearctic barn owl ( Tyto alba ) recolonised Europe after LGM (from Italian Iberic peninsulas) offers an...
Mitochondria are known to play an essential role in the cell. These organelles contain their own DNA, which is divided a coding and non-coding region (NCR). While much of NCR’s function unknown, tandem repeats have been observed several vertebrates, with extreme intra-individual, intraspecific interspecific variation. Taking advantage new complete reference for mitochondrial genome Afro-European Barn Owl ( Tyto alba ), as well 172 whole genome-resequencing; we (i) describe special focus on...
<title>Abstract</title> An important aspect of assessing endangered levels and managing conservation is the study inbreeding status, identifying its origin as well mutation load in wild populations. In this study, we used 502 barn owls from continental island populations across Europe. addition to comparing determined whether due non-random mating or high co-ancestry within population. We show that islands have higher than populations, mainly small effective population sizes rather recent...
A key aspect of assessing the risk extinction/extirpation for a particular wild species or population is status inbreeding, but origin inbreeding and current mutational load are also two crucial factors to consider when determining survival probability population. In this study, we used samples from 502 barn owls continental island populations across Europe, with aim quantifying comparing level between differing demographic histories. addition status, determined whether due non-random mating...