A5056381387- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
- Genetic and phenotypic traits in livestock
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Forensic and Genetic Research
- Cancer Genomics and Diagnostics
- Microbial Metabolic Engineering and Bioproduction
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Evolutionary Game Theory and Cooperation
- Genomics and Rare Diseases
- Archaeology and ancient environmental studies
- Receptor Mechanisms and Signaling
- Protein Structure and Dynamics
- Vascular Malformations and Hemangiomas
- Bayesian Methods and Mixture Models
- Coral and Marine Ecosystems Studies
- RNA Research and Splicing
- Animal Diversity and Health Studies
- Mathematical and Theoretical Epidemiology and Ecology Models
University of Arizona
2016-2025
Environmental Education Exchange
2022
University of Arizona Cancer Center
2022
Prostate Cancer Research
2016
Institut de Biologie Moléculaire et Cellulaire
2011
Los Alamos National Laboratory
2009-2010
Cornell University
2005-2009
California Institute of Technology
2003
Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null genome scans for selection. We introduce an inference method based on the joint frequency spectrum of variants within between populations. For candidate we numerically compute expected using a diffusion approximation to one-locus two-allele Wright-Fisher process, involving up three simultaneous Our approach is composite likelihood scheme, since linkage neutral loci alters...
Quantitative computational models play an increasingly important role in modern biology. Such typically involve many free parameters, and assigning their values is often a substantial obstacle to model development. Directly measuring vivo biochemical parameters difficult, collectively fitting them other experimental data yields large parameter uncertainties. Nevertheless, earlier work we showed growth-factor-signaling that collective could yield well-constrained predictions, even when it...
High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental populations and present an approach for combining complementary aspects whole-genome, low-coverage data targeted high-coverage data. We apply this to generated by pilot phase Thousand Genomes Project, including whole-genome 2–4× coverage 179 samples from HapMap European, Asian, African panels as well target exons 800...
The genome of the Southeast Asian great ape or orang-utan has been sequenced — specifically a draft assembly Sumatran female individual and short-read sequence data from five further Bornean orang-utan, Pongo abelii pygmaeus, respectively. Orang-utan species appear to have split around 400,000 years ago, more recent than most previous estimates suggested, resulting in an average Bornean–Sumatran nucleotide identity 99.68%. Structural evolution seems proceeded much slowly that other apes,...
Balancing selection is potentially an important biological force for maintaining advantageous genetic diversity in populations, including variation that responsible long-term adaptation to the environment. By serving as a means maintain variation, it may be particularly relevant phenotypic natural populations. Nevertheless, its prevalence and specific targets human genome remain largely unknown. We have analyzed patterns of divergence 13,400 genes two populations using unbiased...
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...
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well processes timing their differentiation, remain largely unknown. Demogenomic modeling high-quality ancient genomes reveals that early farmers Anatolia emerged from a multiphase mixing Asian population with strongly bottlenecked western hunter-gatherer after last glacial maximum. Moreover, ancestors went through period extreme drift during westward range expansion, contributing highly...
Secondary bacterial infections are a leading cause of illness and death during epidemic pandemic influenza. Experimental studies suggest lethal synergism between influenza certain bacteria, particularly Streptococcus pneumoniae, but the precise processes involved unclear. To address mechanisms determine influences pathogen dose strain on disease, we infected groups mice with either H1N1 subtype A virus A/Puerto Rico/8/34 (PR8) or version expressing 1918 PB1-F2 protein (PR8-PB1-F2(1918)),...
Characterizing patterns of genetic variation within and among human populations is important for understanding evolutionary history careful design medical studies. Here, we analyze across 443,434 single nucleotide polymorphisms (SNPs) genotyped in 3845 individuals from four continental regions. This unique resource allows us to illuminate diversity previously under-studied at the genome-wide scale including Latin America, South Asia, Southern Europe. Key insights afforded by our analysis...
Past demographic changes can produce distortions in patterns of genetic variation that mimic the appearance natural selection unless effects are explicitly removed. Here we fit a detailed model human demography incorporates divergence, migration, admixture, and population size to directly sequenced data from 13,400 protein coding genes 20 European-American 19 African-American individuals. Based on this model, use several new established statistical methods for identifying with extreme...
Many population genetics tools employ composite likelihoods, because fully modeling genomic linkage is challenging. But traditional approaches to estimating parameter uncertainties and performing model selection require full so these have relied on computationally expensive maximum-likelihood estimation (MLE) bootstrapped data. Here, we demonstrate that statistical theory can be applied adjust likelihoods perform robust efficient inference in two demographic tools: ∂a∂i TRACTS. On both...
Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances archaic admixture through interbreeding between the ancestors modern non-Africans now extinct hominids such as Neanderthals Denisovans. One implication these findings is that some adaptive features in humans may entered population via gene flow with forms Eurasia. Within Africa, fossil evidence suggests anatomically (AMH) various coexisted for much last 200,000 yr; however, absence...
The allele frequency spectrum (AFS) consists of counts the number single nucleotide polymorphism (SNP) loci with derived variants present at each given in a sample. Multiple approaches have recently been developed for parameter estimation and calculation model likelihoods based on joint AFS from two or more populations. We conducted simulation study one these approaches, implemented Python module δaδi, to compare selection accuracy different sample sizes under one- two-population models. Our...
As both natural selection and population history can affect genome-wide patterns of variation, disentangling the contributions each has remained as a major challenge in genetics. We here discuss historical recent progress towards this goal-highlighting theoretical computational challenges that remain to be addressed, well inherent difficulties dealing with model complexity violations-and offer thoughts on potentially fruitful next steps.
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains major obstacle. Today, more realistic are possible thanks to large increases quantity quality available genetic data, sophistication inference simulation software. However, implementing these still requires substantial time specialized knowledge. These challenges especially pronounced simulating genomes...
In a variety of contexts, physicists study complex, nonlinear models with many unknown or tunable parameters to explain experimental data. We why such systems so often are sloppy: the system behavior depends only on few "stiff" combinations and is unchanged as other "sloppy" parameter vary by orders magnitude. observe that eigenvalue spectra for sensitivity sloppy have striking, characteristic form density logarithms eigenvalues which roughly constant over large range. suggest common...
Partially recessive variants under positive selection are expected to go fixation more quickly on the X chromosome as a result of hemizygosity, an effect known faster-X.Conversely, purifying is reduce substitution rates effectively chromosome.Previous work in humans contrasted divergence autosomes and chromosome, with results tending support faster-X effect.However, no study has yet incorporated both polymorphism quantify effects selection, which opposing forces respect divergence.In this...
Abstract Demographic modelling is often used with population genomic data to infer the relationships and ages among populations. However, relatively few analyses are able validate these inferences independent data. Here, we leverage written records that describe distinct Brassica rapa crops corroborate demographic models of domestication. renowned for their outstanding morphological diversity, but order domestication remain unclear. We generated genomewide SNP s from 126 accessions collected...
Using data from 83 isolates a single population, the population genomics of microcrustacean Daphnia pulex are described and compared to current knowledge for only other well-studied invertebrate, Drosophila melanogaster These two species quite similar with respect effective sizes mutation rates, although some features recombination appear be different, linkage disequilibrium being elevated at short ([Formula: see text] bp) distances in D. long The study adheres closely expectations under...
African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, they likely experienced strong selective pressures due to their unique in the Central rainforest. To identify genomic targets of adaptation, we sequenced genomes four Biaka Republic jointly analyzed these data with genome sequences three Baka Cameroon nine Yoruba famers. account for complex demographic history populations that includes both...
Abstract Understanding the demographic history of populations is a key goal in population genetics, and with improving methods data, ever more complex models are being proposed tested. Demographic current interest typically consist set discrete populations, their sizes growth rates, continuous pulse migrations between those over number epochs, which can require dozens parameters to fully describe. There currently no standard format define such models, significantly hampering progress field....
Polyploidy is an important generator of evolutionary novelty across diverse groups in the Tree Life, including many crops. However, impact whole-genome duplication depends on mode formation: doubling within a single lineage (autopolyploidy) versus after hybridization between two different lineages (allopolyploidy). Researchers have historically treated these scenarios as completely separate cases based patterns chromosome pairing, but represent ideals continuum chromosomal interactions among...