A5060910782- Genetic diversity and population structure
- SARS-CoV-2 and COVID-19 Research
- Mycobacterium research and diagnosis
- Tuberculosis Research and Epidemiology
- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- Yersinia bacterium, plague, ectoparasites research
- Forensic and Genetic Research
- Zoonotic diseases and public health
- Antibiotic Resistance in Bacteria
- Genetic and phenotypic traits in livestock
- Bat Biology and Ecology Studies
- Plant and animal studies
- Gut microbiota and health
- COVID-19 Clinical Research Studies
- Bacterial Identification and Susceptibility Testing
- Race, Genetics, and Society
- Wildlife Ecology and Conservation
- Amphibian and Reptile Biology
- Genetic Mapping and Diversity in Plants and Animals
- COVID-19 epidemiological studies
- Animal Virus Infections Studies
- Bacterial Infections and Vaccines
- Plant Virus Research Studies
- Reproductive tract infections research
University College London
2016-2025
ORCID
2021-2022
University College Lahore
2022
Great Ormond Street Hospital for Children NHS Foundation Trust
2018
Institute of Genetics
2017
Medical Research Council
2010-2014
Imperial College London
2008-2013
Faculty of 1000 (United Kingdom)
2010
Laboratoire de Biométrie et Biologie Evolutive
2010
Université Claude Bernard Lyon 1
2010
The dramatic progress in sequencing technologies offers unprecedented prospects for deciphering the organization of natural populations space and time. However, size datasets generated also poses some daunting challenges. In particular, Bayesian clustering algorithms based on pre-defined population genetics models such as STRUCTURE or BAPS software may not be able to cope with this amount data. Thus, there is a need less computer-intensive approaches. Multivariate analyses seem particularly...
A novel influenza (H1N1) virus has spread rapidly across the globe. Judging its pandemic potential is difficult with limited data, but nevertheless essential to inform appropriate health responses. By analyzing outbreak in Mexico, early data on international spread, and viral genetic diversity, we make an assessment of transmissibility severity. Our estimates suggest that 23,000 (range 6000 32,000) individuals had been infected Mexico by late April, giving estimated case fatality ratio (CFR)...
Whole-genome data indicate that early modern humans expanded into Australia 62,000 to 75,000 years ago.
Abstract Large structural variations (SVs) within genomes are more challenging to identify than smaller genetic variants but may substantially contribute phenotypic diversity and evolution. We analyse the effects of SVs on gene expression, quantitative traits intrinsic reproductive isolation in yeast Schizosaccharomyces pombe . establish a high-quality curated catalogue worldwide library S. strains, including duplications, deletions, inversions translocations. show that copy number (CNVs)...
The consequences of variable rates clonal reproduction on the population genetics neutral markers are explored in diploid organisms within a subdivided (island model). We use both analytical and stochastic simulation approaches. High will positively affect heterozygosity. As consequence, nearly twice as many alleles per locus can be maintained differentiation estimated F(ST) value is strongly decreased purely populations compared to sexual ones. With increasing reproduction, effective size...
Abstract Colistin represents one of the few available drugs for treating infections caused by carbapenem-resistant Enterobacteriaceae . As such, recent plasmid-mediated spread colistin resistance gene mcr-1 poses a significant public health threat, requiring global monitoring and surveillance. Here, we characterize distribution using data set 457 mcr-1- positive sequenced isolates. We find in various plasmid types but identify an immediate background common to all sequences. Our analyses...
How and when the Americas were populated remains contentious. Using ancient modern genome-wide data, we found that ancestors of all present-day Native Americans, including Athabascans Amerindians, entered as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) after more an 8000-year isolation period in Beringia. After their arrival to Americas, ancestral Americans diversified into two basal genetic branches around 13 ka, one is now dispersed across North South...
Panzootic chytrid fungus out of Asia Species in the fungal genus Batrachochytrium are responsible for severe declines populations amphibians globally. The sources these pathogens have been uncertain. O'Hanlon et al. used genomics on a panel more than 200 isolates to trace source frog pathogen B. dendrobatidis hyperdiverse hotspot Korean peninsula (see Perspective by Lips). Over past century, trade amphibian species has accelerated, and now all lineages occur traded amphibians; become...
Abstract Many recent studies report that individual heterozygosity at a handful of apparently neutral microsatellite markers is correlated with key components fitness, most invoking inbreeding depression as the likely underlying mechanism. The implicit assumption an individual's coefficient can be estimated reliably using only 10 or so markers, but validity this unclear. Consequently, we have used individual‐based simulations to examine conditions under which and are correlated. Our results...
Batrachochytrium dendrobatidis ( Bd ) is a globally ubiquitous fungal infection that has emerged to become primary driver of amphibian biodiversity loss. Despite widespread effort understand the emergence this panzootic, origins infection, its patterns global spread, and principle mode evolution remain largely unknown. Using comparative population genomics, we discovered three deeply diverged lineages associated with amphibians. Two these were found in multiple continents are known...
The widespread use of antibiotics in association with high-density clinical care has driven the emergence drug-resistant bacteria that are adapted to thrive hospitalized patients. Of particular concern globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clones cause outbreaks and epidemics associated health care. most rapidly spreading tenacious health-care-associated clone Europe currently is EMRSA-15, which was first detected UK early 1990s subsequently spread...
Abstract Summary: adephylo is a package for the R software dedicated to analysis of comparative evolutionary data. Phylogenetic methods initially aimed at accounting or removing effects phylogenetic signal in biological traits. However, recent approaches have shown that considerable information can be gathered from study signal. In particular, close examination structures unveil interesting patterns. For this purpose, we developed provides tools quantifying and describing implements tests...