A5089560986- Genetic diversity and population structure
- Genetic Associations and Epidemiology
- Forensic and Genetic Research
- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Evolution and Genetic Dynamics
- Yersinia bacterium, plague, ectoparasites research
- Digestive system and related health
- Weed Control and Herbicide Applications
- melanin and skin pigmentation
- Race, Genetics, and Society
- RNA and protein synthesis mechanisms
- Legume Nitrogen Fixing Symbiosis
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Nutritional Studies and Diet
- Molecular Biology Techniques and Applications
- Brucella: diagnosis, epidemiology, treatment
- Animal Diversity and Health Studies
- Dyeing and Modifying Textile Fibers
- Pesticide and Herbicide Environmental Studies
- Nematode management and characterization studies
- Nutrition, Genetics, and Disease
- Fractal and DNA sequence analysis
- Plant Parasitism and Resistance
University of California, Berkeley
2018-2024
Berkeley College
2021
Acupuncture & Integrative Medicine College
2019
Northwestern University
2017
Abstract Western Eurasia witnessed several large-scale human migrations during the Holocene 1–5 . Here, to investigate cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from Mesolithic and Neolithic periods—from across northern western Eurasia. These were imputed alongside published data obtain diploid genotypes more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending Black Sea Baltic. hunter-gatherers highly...
Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that most prevalent in Northern Europe. Although it known inherited risk for MS located within or close proximity to immune-related genes, unknown when, where how this genetic originated
The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for dietary, physical and mental health present-day populations. Using a dataset more than 1,600 imputed ancient genomes
Abstract Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales 1–4 . However, insights into the population dynamics contact zones are hampered by a lack of ancient genomic data sampled high spatiotemporal resolution 5–7 Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years Mesolithic period, Neolithic period and Early Bronze Age Denmark integrated these with proxies for diet ( 13 C 15 N content),...
Most current methods for detecting natural selection from DNA sequence data are limited in that they either based on summary statistics or a composite likelihood, and as consequence, do not make full use of the information available data. We here present new importance sampling approach approximating likelihood function coefficient. Our method CLUES treats ancestral recombination graph (ARG) latent variable is integrated out using previously published Markov Chain Monte Carlo (MCMC) methods....
Summary Western Eurasia witnessed several large-scale human migrations during the Holocene 1–5 . To investigate cross-continental impacts we shotgun-sequenced 317 primarily Mesolithic and Neolithic genomes from across Northern Eurasia. These were imputed alongside published data to obtain diploid genotypes >1,600 ancient humans. Our analyses revealed a ‘Great Divide’ genomic boundary extending Black Sea Baltic. hunter-gatherers (HGs) highly genetically differentiated east west of this...
One of the most powerful and commonly used approaches for detecting local adaptation in genome is identification extreme allele frequency differences between populations. In this article, we present a new maximum likelihood method finding regions under positive selection. It based on Gaussian approximation to changes it incorporates admixture The can analyze multiple populations simultaneously retains power detect selection signatures specific ancestry components that are not representative...
Causal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack understanding of evolutionary history: the extent parallelism origins target-site resistance (TSR), how long these persist, quickly they spread, allelic interactions that mediate selective advantage. We addressed questions with genomic data from 19 populations common waterhemp (Amaranthus tuberculatus), which show to have undergone a massive expansion over past...
The Shine-Dalgarno (SD) sequence motif is frequently found upstream of protein coding genes and thought to be the dominant mechanism translation initiation used by bacteria. Experimental studies have shown that SD facilitates start codon recognition enhances directly interacting with highly conserved anti-SD on 30S ribosomal subunit. However, proportion SD-led within a genome varies across species factors governing this variation in mechanisms remain largely unknown. Here, we conduct...
Summary The Eurasian Holocene (beginning c. 12 thousand years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for dietary, physical and mental health present-day populations. Using an imputed dataset >1600 complete ancient genome sequences, new computational methods locating selection time space, we reconstructed landscape transition from hunting gathering, to farming pastoralism across West Eurasia. We identify major signals...
Inbred populations often suffer from increased mutational load and reduced fitness due to lower efficacy of purifying selection in groups with small effective population sizes. Genetic rescue (GR) is a conservation tool that studied deployed the aim increasing such inbred by assisted migration individuals closely related outbred populations. The success GR depends on several factors-such as their demographic history distribution dominance effects mutations-that may vary across While we...
Abstract We present a full-likelihood method to estimate and quantify polygenic adaptation from contemporary DNA sequence data. The combines population genetic data GWAS summary statistics up thousands of nucleotide sites in joint likelihood function the strength transient directional selection acting on trait. Through simulations trait architectures GWAS, we show that substantially improves power over current methods. examine robustness under uncorrected stratification, uncertainty...
SUMMARY Multiple sclerosis (MS) is a modern neuro-inflammatory and -degenerative disease, which most prevalent in Northern Europe. Whilst it known that inherited risk to MS located within or close proximity immune genes, unknown when, where how this genetic originated 1 . By using the largest ancient genome dataset from Stone Age 2 , along with new Medieval post-Medieval genomes, we show many of variants for rose higher frequency among pastoralists on Pontic Steppe, were brought into Europe...
Abstract Causal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack an understanding of evolutionary history: the extent parallelism origins target-site resistance (TSR), how long these persist, quickly they spread, allelic interactions that mediate selective advantage. We addressed questions with genomic data from 18 populations common waterhemp ( Amaranthus tuberculatus ), which show to have undergone a massive...
Abstract Inbred populations often suffer from heightened mutational load and decreased fitness due to lower efficiency of purifying selection at small effective population size. Genetic rescue (GR) is a tool that studied deployed with the aim increasing such inbred populations. The success GR known depend on certain factors may vary between different populations, as their demographic history distribution dominance effects mutations. While we understand these evolution overall ancestry in...
Abstract The Shine-Dalgarno (SD) sequence is often found upstream of protein coding genes across the bacterial kingdom, where it enhances start codon recognition via hybridization to anti-SD (aSD) on small ribosomal subunit. Despite widespread conservation aSD sequence, proportion SD-led within a genome varies widely species, and evolutionary pressures shaping this variation remain largely unknown. Here, we conduct phylogenetically-informed analysis show that species capable rapid growth...
Abstract Most current methods for detecting natural selection from DNA sequence data are limited in that they either based on summary statistics or a composite likelihood, and as consequence, do not make full use of the information available data. We here present new importance sampling approach approximating likelihood function coefficient. The method treats ancestral recombination graph (ARG) latent variable is integrated out using previously published Markov Chain Monte Carlo (MCMC)...