A5017497900- Genetic diversity and population structure
- Genetic and phenotypic traits in livestock
- Wildlife Ecology and Conservation
- Genomics and Phylogenetic Studies
- Amphibian and Reptile Biology
- Identification and Quantification in Food
- Genetic Mapping and Diversity in Plants and Animals
- Aquaculture disease management and microbiota
- Species Distribution and Climate Change
- Environmental DNA in Biodiversity Studies
- Aquaculture Nutrition and Growth
- Fish Ecology and Management Studies
- Fish Biology and Ecology Studies
- Primate Behavior and Ecology
- Semantic Web and Ontologies
- Animal Behavior and Reproduction
- Cancer-related molecular mechanisms research
- Parasite Biology and Host Interactions
- Biomedical Text Mining and Ontologies
- Avian ecology and behavior
- Natural Language Processing Techniques
- Animal Genetics and Reproduction
- Bat Biology and Ecology Studies
- Insect Utilization and Effects
- Microbial Community Ecology and Physiology
Cardiff University
2016-2025
International Union for Conservation of Nature (Bangladesh)
2025
Sabah Wildlife Department
2024
University of Wales
2022
United Nations Industrial Development Organization
2022
Millenium Nucleus for Planet Formation
2021
International Union for Conservation of Nature
2020
Durrell Wildlife Conservation Trust
2017
University of Veterinary Medicine Vienna
2009-2011
KeyGene (Netherlands)
2011
Recent statistical analyses suggest that sequencing of pooled samples provides a cost effective approach to determine genome-wide population genetic parameters. Here we introduce PoPoolation, toolbox specifically designed for the analysis sequence data from individuals. PoPoolation calculates estimates θ(Watterson), θ(π), and Tajima's D account bias introduced by pooling errors, as well divergence between species. Results can be graphically displayed in sliding window plot. is written Perl R...
Effective population size (Ne ) is a key genetic parameter that describes the amount of drift in population. Estimating Ne has been subject to much research over last 80 years. Methods estimate from linkage disequilibrium (LD) were developed ~40 years ago but depend on availability large amounts marker data only most recent advances DNA technology have made available. Here we introduce SNeP, multithreaded tool perform using LD standard PLINK input file format (.ped and.map files) or by...
The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as domestic species become genome-enabled. Before established worldwide, sheep goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence genomes Asiatic mouflon Bezoar ibex goat center compare with that domestics from local, traditional, improved breeds. Among genomic regions carrying...
Abstract The genomic basis of adaptation to novel environments is a fundamental problem in evolutionary biology that has gained additional importance the light recent global change discussion. Here, we combined laboratory natural selection (experimental evolution) Drosophila melanogaster with genome‐wide next generation sequencing DNA pools (Pool‐Seq) identify alleles are favourable environment and traced their trajectories during adaptive process. Already after 15 generations, identified...
Experimental evolution in combination with whole-genome sequencing (evolve and resequence [E&R]) is a promising approach to define the genotype–phenotype map understand adaptation evolving populations. Many previous studies have identified large number of putative selected sites (i.e., candidate loci), but it remains unclear what extent these loci are genuine targets selection or experimental noise. To address this question, we exposed same founder population two different regimes—a hot...
Cattle have been invaluable for the transition of human society from nomadic hunter-gatherers to sedentary farming communities throughout much Europe, Asia and Africa since earliest domestication cattle more than 10,000 years ago. Although current understanding relationships among ancestral populations remains limited, is thought occurred on two or three occasions, giving rise taurine (Bos taurus) indicine indicus) species that share aurochs primigenius) as common ancestor ~250,000 Indicine...
Since its introduction, landscape genomics has developed quickly with the increasing availability of both molecular and topo-climatic data. The current challenges field mainly involve processing large numbers models disentangling selection from demography. Several methods address latter, either by estimating a neutral model population structure or inferring simultaneously environmental demographic effects. Here we present Sam$\beta$ada, an integrated approach to study signatures local...
Species delimitation is one of the most contested areas in modern biology, with widespread disagreement about almost every aspect definition and implementation "species" label. While this debate intellectually stimulating, it also has real implications for conservation, where its impacts on taxonomic inflation or inertia can mean that specific populations receive adequate conservation measures are ignored. Recently, rise next generation sequencing phylogenomics revolutionised phylogenetic...
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step technology analytical approaches available to define, manage conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR terms technological continuity, capacity integrative methodologies needed fully exploit new, multidimensional data. final conference the ESF program aimed address...
Mouflon (Ovis aries musimon) became extinct from mainland Europe after the Neolithic, but remnant populations Mediterranean islands of Corsica and Sardinia have been used for reintroductions across since 19th-century. x sheep hybrids are larger-bodied than mouflon, potentially showing increased male reproductive success, little is known about genomic levels admixture, or adaptive significance introgression between resident mouflon local breeds. Here we analysed Ovine medium-density SNP array...
Stress experienced during early life may have lasting effects on the immune system, with impacts health and disease dependent nature duration of stressor. The epigenome is especially sensitive to environmental stimuli represents a potential mechanism through which stress cause long-lasting effects. However, extent responds differently chronic vs acute stressors unclear, for non-mammalian species. We examined (cold-shock embryogenesis) (absence tank enrichment larval-stage) global gene...
The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This suggested to be the consequence demographic bottleneck 10 000–12 000 years ago (ya) and also led assumption that only small differences exist between subspecies. However, analysing mitochondrial DNA microsatellites in samples from most historic range we found relatively deep phylogeographic breaks some investigated populations, methods assessed divergence time estimates predating...
Snub-nosed monkeys (genus Rhinopithecus) are a group of endangered colobines endemic to South Asia. Here, we re-sequenced the whole genomes 38 snub-nosed representing four species within this genus. By conducting population genomic analyses, observed similar load deleterious variation in living both smaller and larger populations found that diversity was lower than reported other primates. Reconstruction Rhinopithecus evolutionary history suggested episodes climatic over past 2 million...
The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca llama) archaeological sites based solely on morphological data challenging due to similarity with respect wild ancestors. Using genetic methods also presents challenges hybridization history species, which are thought have extensively hybridized following Spanish conquest America that resulted slaughtered en masse. In this study, we generated...
The effects of the direct interaction between hybridization and speciation-two major contrasting evolutionary processes--are poorly understood. We present here history Galápagos marine iguana (Amblyrhynchus cristatus) reveal a case incipient within--island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, land iguanas, around 4.5 million years ago (Ma), but divergence among extant...
The introduction of Iberian cattle in the Americas after Columbus' arrival imposed high selection pressures on a limited number animals over brief period time. Knowledge genomic regions selected during this process may help enhancing climatic resilience and sustainable animal production. We first determined taurine indicine contributions to structure modern Creole cattle. Second, we inferred their demographic history using approximate Bayesian computation (ABC), linkage disequilibrium (LD)...
Bitter taste perception is essential for species with selective food intake, enabling them to avoid unpalatable or toxic items. Previous studies noted a marked variation in the number of TAS2R genes among various vertebrate species, but underlying causes are not well understood. Laurasiatherian mammals have highly diversified dietary niche, showing repeated evolution specialized feeding preferences multiple lineages and offering unique chance investigate how niches associated copy bitter...
Captive animal populations, be it for food production or conservation programmes, are often maintained at densities far beyond those in natural environments, which can have profound effects on behaviour, immune and stress levels, ultimately welfare. How such alterations impact transcriptional responses to pathogen infection is a 'different kettle of fish' remains poorly understood. Here, we assessed survival gene expression profiles infected fish reared two different elucidate potential...
Abstract Background The rhesus macaque (RM, Macaca mulatta) is the most important nonhuman primate model in biomedical research. We present first genomic survey of wild RMs, sequencing 81 geo-referenced individuals five subspecies from 17 locations China, a large fraction species' natural distribution. Results Populations were structured into genetic lineages on mainland and Hainan Island, recapitulating current designations. These are estimated to have diverged 125.8 51.3 thousand years...