A5018346231- Genetic diversity and population structure
- Genetic and phenotypic traits in livestock
- Genomics and Phylogenetic Studies
- Animal Behavior and Reproduction
- Genetic Mapping and Diversity in Plants and Animals
- Turtle Biology and Conservation
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Animal Disease Management and Epidemiology
- Evolution and Genetic Dynamics
- Cancer-related molecular mechanisms research
- Wildlife Ecology and Conservation
- Amphibian and Reptile Biology
- Microbial infections and disease research
- T-cell and B-cell Immunology
- Identification and Quantification in Food
- Molecular Biology Techniques and Applications
- Species Distribution and Climate Change
- Yersinia bacterium, plague, ectoparasites research
- Forensic and Genetic Research
- CRISPR and Genetic Engineering
- interferon and immune responses
- Fish Ecology and Management Studies
- Ubiquitin and proteasome pathways
- Spider Taxonomy and Behavior Studies
- Genomics and Rare Diseases
Swiss Federal Institute for Forest, Snow and Landscape Research
2023-2024
University of Zurich
2013-2024
Institut de Biologia Evolutiva
2014-2023
University of British Columbia
2016-2018
University of Lausanne
2010-2018
Kunming Institute of Zoology
2014
State Key Laboratory of Genetic Resources and Evolution
2014
Human activity has caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of species with unknown consequences for health. A key factor survival is evolution deleterious mutation load, but how bottleneck strength and load interact lacks empirical evidence. We analyze 60 complete genomes six ibex domestic goat. show that historic rather than current conservation status predict levels genome-wide variation. By analyzing...
Non-recombining sex chromosomes are expected to undergo evolutionary decay, ending up genetically degenerated, as has happened in birds and mammals. Why then so often homomorphic cold-blooded vertebrates? One possible explanation is a high rate of turnover events, replacing master sex-determining genes by new ones on other chromosomes. An alternative that X-Y similarity maintained occasional recombination occurring sex-reversed XY females. Based mitochondrial nuclear gene sequences, we...
Abstract Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions high relative differentiation (i.e., “islands differentiation” in F ST ), but there is much debate regarding the causes this pattern. We briefly review prominent models islands and compare patterns three closely related pairs New World warblers with goal evaluating support for four models. Each pair (MacGillivray's/mourning warblers; Townsend's/black‐throated green...
In sharp contrast with mammals and birds, many cold-blooded vertebrates present homomorphic sex chromosomes. Empirical evidence supports a role for frequent turnovers, which replace nonrecombining chromosomes before they have time to decay. Three main mechanisms been proposed such relying either on neutral processes, sex-ratio selection, or intrinsic benefits of the new sex-determining genes (due, e.g., linkage sexually antagonistic mutations). Here, we suggest an additional mechanism,...
The major histocompatibility complex (MHC) is a crucial component of the vertebrate immune system and shows extremely high levels genetic polymorphism. extraordinary variation thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for at MHC in Alpine ibex (Capra ibex). At usually very polymorphic exon involved pathogen recognition (DRB 2), carried only two...
Sex determination is often seen as a dichotomous process: individual sex assumed to be determined either by genetic (genotypic determination, GSD) or environmental factors (environmental ESD), most temperature (temperature TSD). We endorse an alternative view, which sees GSD and TSD the ends of continuum. Both effects interact priori, because can affect gene expression at any step along sex‐determination cascade. propose define systems population‐ (rather than individual) level, via...
Abstract Restoration of lost species ranges to their native distribution is key for the survival endangered species. However, reintroductions often fail and long‐term genetic consequences are poorly understood. Alpine ibex ( Capra ) wild goats that recovered from <100 individuals ~50,000 within a century by population reintroductions. We analyzed genomic reintroduction strategy. genotyped 101,822 genomewide single nucleotide polymorphism loci in 173 ibex, closely related Iberian pyrenaica...
Crucial for the long-term survival of wild populations is their ability to fight diseases. Disease outbreaks can lead severe population size reductions, which makes endangered and reintroduced species especially vulnerable. In vertebrates, major histocompatibility complex (MHC) plays an important role in determining immune response. Species that went through bottlenecks often show very low levels genetic diversity at MHC. Due known link between MHC response, such are expected be particular...
Abstract Mating with attractive or dominant males is often predicted to offer indirect genetic benefits females, but it still largely unclear how important such non‐random mating can be regard embryo viability. We sampled a natural population of adult migratory brown trout ( Salmo trutta ), bred them in vitro half‐sib breeding design separate from maternal environmental effects, raised 2098 embryos singly until hatching, and exposed experimentally different levels pathogen stress at late...
Recombination arrest between X and Y chromosomes, driven by sexually antagonistic genes, is expected to induce their progressive differentiation. However, in contrast birds mammals (which display the predicted pattern), most cold-blooded vertebrates have homomorphic sex chromosomes. Two main hypotheses been proposed account for this, namely high turnover rates of sex-determining systems occasional XY recombination. Using individual-based simulations, we formalize evolution recombination...
Abstract Introgression can be an important evolutionary force but it also lead to species extinction and as such is a crucial issue for conservation. However, introgression difficult detect, morphologically well genetically. Hybridization with domestic cats ( F elis silvestris catus ) major concern the conservation of European wildcats s. ). The available morphologic genetic markers two Felis subspecies are not sufficient reliably detect hybrids beyond first generation. Here we present...
Populations that have experienced long periods of geographic isolation will diverge over time. The application high-throughput sequencing technologies to study the genomes related taxa now allows us quantify, at a fine scale, consequences this divergence across genome. Throughout number studies, notable pattern has emerged. In many cases, estimates differentiation genome are strongly heterogeneous; however, evolutionary processes driving striking still unclear. Here we quantified genomic...
High-throughput sequencing is a powerful tool, but suffers biases and errors that must be accounted for to prevent false biological conclusions. Such include batch effects; technical only present in subsets of data due procedural changes within study. If overlooked multiple batches are combined, spurious signals can arise, particularly if correlated with variables. Batch effects minimized through randomization sample groups across batches. However, long-term or multiyear studies where added...
Abstract Human activity caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of species with unknown consequences for health. A key factor survival is evolution deleterious mutation load, but how bottleneck strength and load interact lacks empirical evidence. Here, we take advantage exceptionally well-characterized once nearly extinct Alpine ibex. survived one most known successfully restored We analyze 60 complete...
Abstract Hybridization can result in the transfer of adaptive genetic material from one species to another, known as introgression. Bottlenecked (and hence genetically depleted) are expected be particularly receptive introgression, since introgression introduce new or previously lost variation. The Alpine ibex ( Capra ), which recently recovered near extinction, is hybridize with domestic goat aegagrus hircus and signals found at major histocompatibility complex were suggested potentially...
Despite increasing appreciation of the "speciation continuum", delimiting and describing new species is a major yet necessary challenge modern phylogeography to help optimize conservation efforts. In amphibians, lack phenotypic differences between closely-related taxa, their complex, sometimes unresolved phylogenetic relationships, potential hybridize all act blur taxonomic boundaries. Here we implement multi-disciplinary approach evaluate nature two deeply-diverged mitochondrial lineages...
Abstract Population bottlenecks can have dramatic consequences for the health and long‐term survival of a species. Understanding historic population size standing genetic variation prior to contraction allows estimating impact bottleneck on species' diversity. Although sizes be modelled based extant genomics, uncertainty is high last 10–20 millenia. Hence, integrating ancient genomes provides powerful complement retrace evolution diversity through fluctuations. Here, we recover 15...
Hybrid zones allow the measurement of gene flow across genome, producing insight into genomic architecture speciation. Such analysis is particularly powerful when applied to multiple pairs hybridizing species, as patterns differentiation can then be related age providing a view build-up over time. We examined 33 809 single nucleotide polymorphisms (SNPs) in three woodpecker species: Red-breasted, Red-naped and Yellow-bellied sapsuckers (Sphyrapicus ruber, Sphyrapicus nuchalis varius), two...
In the last decades, several endangered breeds of livestock species have been re-established effectively. However, successful revival Dutch and Danish Landrace goats involved crossing with exotic ancestry current populations is therefore not clear. We generated genotypes for 27 FAO-recommended microsatellites these landraces three phenotypically similar Nordic-type compared central European, Mediterranean south-west Asian goats. found decreasing levels genetic diversity increasing distance...
Identifying local adaptation in bottlenecked species is essential for conservation management. Selection detection methods have an important role management plans, assessments of adaptive capacity, and looking responses to climate change. Yet, the allele frequency changes exploited selection are similar those caused by strong neutral genetic drift expected during a bottleneck. Consequently, it often unclear what accuracy across populations. In this study, simulations were used explore if...
Balanced lethal systems are more than biological curiosities: as theory predicts, they should quickly be eliminated through the joint forces of recombination and selection. That such might become fixed in natural populations poses a challenge to evolutionary theory. Here we address case balanced system crested newts related species, which makes 50% offspring die early development. All adults heteromorphic for chromosome pair 1. The two homologues (1A 1B) have different recessive deleterious...
The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two species left in the world. endemic to Atoll Seychelles and listed as Vulnerable on International Union for Conservation Nature Red List (v2.3) due its limited distribution threats posed by climate change. Genomic resources A. gigantea are lacking, hampering conservation efforts both wild ex situpopulations. A high-quality genome would also open avenues investigate genetic basis species' exceptionally long life span. We...
Polymorphism for immune functions can explain significant variation in health and reproductive success within species. Drastic loss genetic diversity at such loci constitutes an extinction risk should be monitored species of conservation concern. However, effective implementations genome-wide polymorphism sets into high-throughput genotyping assays are scarce. Here, we report the design validation a microfluidics-based amplicon sequencing assay to comprehensively capture Alpine ibex (Capra...