A5005571919- Genetic diversity and population structure
- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Cephalopods and Marine Biology
- Insect Resistance and Genetics
- Genetic Associations and Epidemiology
- Genomics and Chromatin Dynamics
- Mosquito-borne diseases and control
- Chemical synthesis and alkaloids
- Malaria Research and Control
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Wildlife Ecology and Conservation
- Species Distribution and Climate Change
- Insect and Arachnid Ecology and Behavior
- Neurobiology and Insect Physiology Research
- Animal Behavior and Reproduction
- RNA Research and Splicing
- Gene expression and cancer classification
- RNA modifications and cancer
- Genomics and Rare Diseases
- Genetics, Aging, and Longevity in Model Organisms
University of Oregon
2019-2025
University of British Columbia
2023
The University of Melbourne
2023
Knoxville College
2023
University of Tennessee at Knoxville
2023
Rutgers, The State University of New Jersey
2012-2018
Rutgers Sexual and Reproductive Health and Rights
2013-2018
University of North Carolina at Chapel Hill
2017
Pediatrics and Genetics
2016
Rütgers (Germany)
2014
The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within between closely related species. Here we present a analysis Drosophila simulans based on whole-genome shotgun sequencing multiple inbred lines comparison resulting data to genome assemblies species, D. melanogaster yakuba. We discovered previously unknown, large-scale fluctuations along chromosome arms,...
Comparative genomics allow us to search the human genome for segments that were extensively changed in last approximately 5 million years since divergence from our common ancestor with chimpanzee, but are highly conserved other species and thus likely be functional. We found 202 genomic elements vertebrates show evidence of significantly accelerated substitution rates human. These mostly non-coding DNA, often near genes associated transcription DNA binding. Resequencing confirmed five most...
This report of independent genome sequences two natural populations Drosophila melanogaster (37 from North America and 6 Africa) provides unique insight into forces shaping genomic polymorphism divergence. Evidence interactions between selection genetic linkage is abundant not only in centromere- telomere-proximal regions, but also throughout the euchromatic arms. Linkage disequilibrium, which decays within 1 kbp, exhibits a strong bias toward coupling more frequent alleles high-resolution...
Descriptions of recently evolved genes suggest several mechanisms origin including exon shuffling, gene fission/fusion, retrotransposition, duplication-divergence, and lateral transfer, all which involve recruitment preexisting or genetic elements into new function. The importance noncoding DNA in the novel remains an open question. We used well annotated genome model system Drosophila melanogaster sequences related species to carry out a whole-genome search for D. that are derived from DNA....
Abstract Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and usually only way of obtaining ground-truth data to evaluate inferences. Because this, large number specialized programs have been developed, each filling particular niche, but with largely overlapping functionality substantial duplication effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry mutation simulations based on...
In this perspective, we evaluate the explanatory power of neutral theory molecular evolution, 50 years after its introduction by Kimura. We argue that was supported unreliable theoretical and empirical evidence from beginning, in light modern, genome-scale data, can firmly reject universality. The ubiquity adaptive variation both within between species means a more comprehensive evolution must be sought.
Detecting the targets of adaptive natural selection from whole genome sequencing data is a central problem for population genetics. However, to date most methods have shown sub-optimal performance under realistic demographic scenarios. Moreover, over past decade there has been renewed interest in determining importance standing variation adaptation populations, yet very few inferring this model at scale introduced. Here we introduce new method, S/HIC, which uses supervised machine learning...
The degree to which adaptation in recent human evolution shapes genetic variation remains controversial. This is part due the limited evidence humans for classic "hard selective sweeps", wherein a novel beneficial mutation rapidly sweeps through population fixation. However, positive selection may often proceed via "soft sweeps" acting on mutations already present within population. Here, we examine across six populations using powerful machine learning approach that sensitive both hard and...
Abstract The availability of large-scale population genomic sequence data has resulted in an explosion efforts to infer the demographic histories natural populations across a broad range organisms. As events alter coalescent genealogies, they leave detectable signatures patterns genetic variation within and between populations. Accordingly, variety approaches have been designed leverage uncover footprints change genome. vast majority these methods make simplifying assumption that measures...
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...
Ultraconserved elements in the human genome are defined as stretches of at least 200 base pairs DNA that match identically with corresponding regions mouse and rat genomes. Most ultraconserved noncoding have been evolutionarily conserved since mammal bird ancestors diverged over 300 million years ago. The reason for this extreme conservation remains a mystery. It has speculated they mutational cold spots or where every site is under weak but still detectable negative selection. However,...
Determining the genetic basis of environmental adaptation is a central problem evolutionary biology. This issue has been fruitfully addressed by examining differentiation between populations that are recently separated and/or experience high rates gene flow. A good example this approach decades-long investigation selection acting along latitudinal clines in Drosophila melanogaster. Here we use next-generation genome sequencing to reexamine well-studied Australian D. melanogaster cline. We...
The mutational origin and subsequent evolution of de novo genes, which are hypothesized to be genes recent that not obviously related ancestral coding sequence, poorly understood. However, accumulating evidence suggests such may often function in male reproduction. Here we use testis-derived expressed sequence tags (ESTs) from Drosophila yakuba identify have likely arisen either D. or the yakuba/D. erecta ancestor. We found several show testis-biased expression X-linked. Comparative data...
Identifying selective sweeps in populations that have complex demographic histories remains a difficult problem population genetics. We previously introduced supervised machine learning approach, S/HIC, for finding both hard and soft genomes on the basis of patterns genetic variation surrounding window genome. While S/HIC was shown to be powerful precise, utility limited by use phased genomic data as input. In this report we describe deep variant our method, diploS/HIC, uses unphased...
Abstract Accurately inferring the genome-wide landscape of recombination rates in natural populations is a central aim genomics, as patterns linkage influence everything from genetic mapping to understanding evolutionary history. Here, we describe estimation using recurrent neural networks (ReLERNN), deep learning method for estimating map that accurate even with small numbers pooled or individually sequenced genomes. Rather than use summaries disequilibrium its input, ReLERNN takes columns...
Abstract Drosophila melanogaster, an ancestrally African species, has recently spread throughout the world, associated with human activity. The species served as focus of many studies investigating local adaptation relating to latitudinal variation in non-African populations, especially those from United States and Australia. These have documented existence shared, genetically determined phenotypic clines for several life history morphological traits. However, there are no designed formally...
Mosquito control remains a central pillar of efforts to reduce malaria burden in sub-Saharan Africa. However, insecticide resistance is entrenched vector populations, and countries with high face daunting challenge sustain limited set surveillance intervention tools. Here we report on the second phase project build an open resource high-quality data genome variation among natural populations major African species Anopheles gambiae coluzzii . We analyzed whole genomes 1142 individual...
Hybridization and gene flow between species appears to be common. Even though it is clear that hybridization widespread across all surveyed taxonomic groups, the magnitude consequences of introgression are still largely unknown. Thus crucial develop statistical machinery required uncover which genomic regions have recently acquired haplotypes via from a sister population. We developed novel machine learning framework, called FILET (Finding Introgressed Loci Extra-Trees) capable revealing...
Abstract Real geography is continuous, but standard models in population genetics are based on discrete, well-mixed populations. As a result, many methods of analyzing genetic data assume that samples random draw from population, applied to clustered populations structured clinally over space. Here, we use simulations living continuous study the impacts dispersal and sampling strategy summary statistics, demographic inference, genome-wide association studies (GWAS). We find most common...
Abstract Characterizing the nature of adaptive process at genetic level is a central goal for population genetics. In particular, we know little about sources substitution or number variants currently segregating in nature. Historically, geneticists have focused attention on hard-sweep model adaptation which de novo beneficial mutation arises and rapidly fixes population. Recently more has been given to soft-sweep models, alleles that were previously neutral, nearly so, drift until such time...
Here we describe discoal, a coalescent simulator able to generate population samples that include selective sweeps in feature-rich, flexible manner. discoal can perform simulations conditioning on the fixation of an allele due drift or either hard soft sweeps-even those occurring large genetic distance away from simulated locus. simulate with recurrent mutation adaptive allele, recombination, and gene conversion, under non-equilibrium demographic histories without specifying frequency...