A5051535161- Genetic Mapping and Diversity in Plants and Animals
- Genetic diversity and population structure
- Genetic Associations and Epidemiology
- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- Forensic and Genetic Research
- Genetic and phenotypic traits in livestock
- Pleistocene-Era Hominins and Archaeology
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Forensic Anthropology and Bioarchaeology Studies
- Plant and animal studies
- Colorectal Cancer Screening and Detection
- BRCA gene mutations in cancer
- Rice Cultivation and Yield Improvement
- Epigenetics and DNA Methylation
- Wildlife Ecology and Conservation
- Evolution and Paleontology Studies
- Genomics and Rare Diseases
- Race, Genetics, and Society
- Single-cell and spatial transcriptomics
- Crop Yield and Soil Fertility
- Human-Animal Interaction Studies
- Archaeology and ancient environmental studies
Harvard University
2022-2025
University of Southern California
2023-2025
Broad Institute
2023-2025
University of California, Los Angeles
2017-2022
Max Planck Institute for Plant Breeding Research
2017
University of Vienna
2017
Vienna Biocenter
2017
University of California, Davis
2015-2016
Selection, recombination, and hybrid evolution Hybridization is an important force in evolution. The effects of hybridization across the whole genome are not understood. Using a fine-scale genetic map, Schumer et al. examined local ancestry replicate natural populations swordtail fish. Each parental species contributes different proportions material to genomes their descendants. Genes from “minor” (less well-represented) parent occur regions that subject higher recombination rates where...
Over the past 20 y, many studies have examined history of plant ecological and molecular model, Arabidopsis thaliana, in Europe North America. Although these informed us about recent species, early has remained elusive. In a large-scale genomic analysis African A. we sequenced genomes 78 modern herbarium samples from Africa analyzed together with over 1,000 previously Eurasian samples. striking contrast to expectations, find that all individuals sampled are native this continent, including...
The explosion in population genomic data demands ever more complex modes of analysis, and increasingly, these analyses depend on sophisticated simulations. Recent advances genetic simulation have made it possible to simulate large models, but specifying such models for a particular engine remains difficult error-prone task. Computational genetics researchers currently re-implement independently, leading inconsistency duplication effort. This situation presents major barrier empirical seeking...
Multiple West African populations inherited genes from a population that diverged before modern humans and Neanderthals split.
Dominance is a fundamental concept in molecular genetics and has implications for understanding patterns of genetic variation, evolution, complex traits. However, despite its importance, the degree dominance natural populations poorly quantified. Here, we leverage multiple mating systems Arabidopsis to co-estimate distribution fitness effects coefficients new amino acid changing mutations. We find that more deleterious mutations are likely be recessive than less Further, this pattern holds...
The genetic variants introduced into the ancestors of modern humans from interbreeding with Neanderthals have been suggested to contribute an unexpected extent complex human traits. However, testing this hypothesis has challenging due idiosyncratic population properties introgressed variants. We developed rigorous methods assess contribution Neanderthal heritable trait variation and applied these analyze 235,592 96 distinct phenotypes measured in about 300,000 unrelated white British...
All published methods for learning about demographic history make the simplifying assumption that genome evolves neutrally, and do not seek to account effects of natural selection on patterns variation. This is a major concern, as ample work has demonstrated pervasive in particular background (BGS) genetic variation diverse species. Simulations theoretical have shown infer changes effective population size over time (
Abstract A recently proposed model suggests a severe bottleneck in the panmictic ancestral population of modern humans during Early to Middle Pleistocene transition. Here, we show this provides worse fit data than without bottleneck.
Phenotype prediction is a key goal for medical genetics. Unfortunately, most genome-wide association studies are done in European populations, which reduces the accuracy of predictions via polygenic scores non-European populations. Here, we use population genetic models to show that human demographic history and negative selection on complex traits can result population-specific architectures. For where alleles with largest effect trait under strongest selection, approximately half...
Metabolic pathways differ across species but are expected to be similar within a species. We discovered two functional, incompatible versions of the galactose pathway in
Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection introgressed genomic regions. Although widely used, intersecting are vulnerable to high false-negative rate as the power different varies, especially complex events. Moreover, population genetic processes unrelated AI, such background heterosis, may create similar...
Pigmentation is often used to understand how natural selection affects genetic variation in wild populations since it can have a simple basis, and affect variety of fitness-related traits (e.g., camouflage, thermoregulation, sexual display). In gray wolves, the K locus, β-defensin gene, causes black coat color via dominantly inherited KB allele. The allele derived from dog-wolf hybridization at high frequency North American wolf populations. We designed DNA capture array probe geographic...
Statistical analyses of genomic data from diverse human populations have demonstrated that archaic hominins, such as Neanderthals and Denisovans, interbred or admixed with the ancestors present-day humans. Central to these are methods for inferring ancestry along genomes individuals (archaic local ancestry). Methods inference rely on availability reference ancestral accurate inference. However, several instances admixture lack genomes, making it difficult characterize events. We present a...
Admixture, the interbreeding between previously distinct populations, is a pervasive force in evolution. The evolutionary history of populations presence admixture can be modeled by augmenting phylogenetic trees with additional nodes that represent events. While enabling more faithful representation history, graphs present formidable inferential challenges, and there an increasing need for methods are accurate, fully automated computationally efficient. One key challenge arises from size...
Abstract The role of gene-environment (GxE) interaction in disease and complex trait architectures is widely hypothesized, but currently unknown. Here, we apply three statistical approaches to quantify distinguish different types GxE for a given E variable. First, detect locus-specific by testing genetic correlation ( r g ) < 1 across bins. Second, genome-wide effects the variable on variance leveraging polygenic risk scores (PRS) test significant PRSxE regression phenotypes PRS, E,...
Abstract The analysis of longitudinal data from electronic health records (EHRs) has the potential to improve clinical diagnoses and enable personalized medicine, motivating efforts identify disease subtypes patient comorbidity information. Here we introduce an age-dependent topic modeling (ATM) method that provides a low-rank representation hundreds distinct diseases in large EHR datasets. We applied ATM 282,957 UK Biobank samples, identifying 52 with heterogeneous profiles; analyses...
High-throughput sequencing has changed many aspects of population genetics, molecular ecology and related fields, affecting both experimental design data analysis. The software package angsd allows users to perform a number genetic analyses on high-throughput data. uses probabilistic approaches which can directly make use genotype likelihoods; thus, SNP calling is not required for comparative analyses. This takes advantage all the produces more accurate results samples with low depth. Here,...
Abstract While introgression from Neanderthals and Denisovans has been well-documented in modern humans outside Africa, the contribution of archaic hominins to genetic variation present-day Africans remains poorly understood. Using 405 whole-genome sequences four sub-Saharan African populations, we provide complementary lines evidence for into these populations. Our analyses site frequency spectra indicate that populations derive 2-19% their ancestry an population diverged prior split...
Abstract While hybridization between species is increasingly appreciated to be a common occurrence, little known about the forces that govern subsequent evolution of hybrid genomes. We considered this question in three independent, naturally-occurring populations formed swordtail fish Xiphophorus birchmanni and X. malinche. To end, we built fine-scale genetic map inferred patterns local ancestry along genomes 690 individuals sampled from populations. In all cases, found more regions high...
Abstract Dominance is a fundamental concept in molecular genetics and has implications for understanding patterns of genetic variation, evolution, complex traits. However, despite its importance, the degree dominance yet to be quantified natural populations. Here, we leverage multiple mating systems populations Arabidopsis co-estimate distribution fitness effects coefficients new amino acid changing mutations. We find that more deleterious mutations are likely recessive than less Further,...
Accurate genetic risk prediction is a key goal for medical genetics and great progress has been made toward identifying individuals with extreme across several traits diseases (Collins Varmus, 2015). However, many of these studies are done in predominantly European populations (Bustamante et al., 2011; Popejoy Fullerton, 2016). Although GWAS effect sizes correlate ancestries (Wojcik 2019), scores show substantial reductions accuracy when applied to non-European (Kim 2018; Martin 2019;...
Abstract The explosion in population genomic data demands ever more complex modes of analysis, and increasingly these analyses depend on sophisticated simulations. Recent advances genetic simulation have made it possible to simulate large models, but specifying such models for a particular engine remains difficult error-prone task. Computational genetics researchers currently re-implement independently, leading inconsistency duplication effort. This situation presents major barrier empirical...