A5021476604- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Genetic and phenotypic traits in livestock
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Protist diversity and phylogeny
- Chromosomal and Genetic Variations
- Microbial Community Ecology and Physiology
- Animal Behavior and Reproduction
- Genetic Associations and Epidemiology
- Fish Ecology and Management Studies
- Genetics and Plant Breeding
- Wheat and Barley Genetics and Pathology
- Plant Taxonomy and Phylogenetics
- Mathematical and Theoretical Epidemiology and Ecology Models
- Reproductive Biology and Fertility
- Evolutionary Algorithms and Applications
- Hormonal Regulation and Hypertension
- Microbial Metabolic Engineering and Bioproduction
- Physiological and biochemical adaptations
- Blood properties and coagulation
- COVID-19 epidemiological studies
- Ophthalmology and Eye Disorders
- Blood Coagulation and Thrombosis Mechanisms
- Ovarian function and disorders
University of North Carolina at Chapel Hill
2023-2025
Ambedkar University Delhi
2024
Arizona State University
2019-2023
Indiana University Bloomington
2014-2023
The question of the relative evolutionary roles adaptive and nonadaptive processes has been a central debate in population genetics for nearly century. While advances have made theoretical development underlying models, statistical methods estimating their parameters from large-scale genomic data, framework an appropriate null model remains elusive. A incorporating known to be constant operation, genetic drift (as modulated by demographic history population) purifying selection, is lacking....
The field of population genomics has grown rapidly in response to the recent advent affordable, large-scale sequencing technologies. As opposed situation during majority 20th century, which development theoretical and statistical genetic insights outpaced generation data they could be applied, genomic are now being produced at a far greater rate than can meaningfully analyzed interpreted. With this wealth come tendency focus on fitting specific (and often rather idiosyncratic) models data,...
The Paramecium aurelia complex is a group of 15 species that share at least three past whole-genome duplications (WGDs). macronuclear genome sequences P. biaurelia and sexaurelia are presented compared to the published sequence tetraurelia . Levels duplicate-gene retention from recent WGD differ by >10% across species, with losing significantly more genes than or In addition, historically high rates gene conversion have homogenized paralogs, probably extending paralogs’ lifetimes....
Current procedures for inferring population history generally assume complete neutrality-that is, they neglect both direct selection and the effects of on linked sites. We here examine how presence purifying background may bias demographic inference by evaluating two commonly-used methods (MSMC fastsimcoal2), specifically studying underlying shape distribution fitness fraction directly selected sites interact with parameter estimation. The results show that, even after masking functional...
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.
Abstract In the companion paper to this, we examined consequences for patterns of linkage disequilibrium “gene” model fitness, which postulates that effects recessive or partially deleterious mutations located at different sites within a gene fail complement each other. Here, examine genetic and inbreeding loads, using both analytical simulation methods, contrast it with frequently used “sites” allows allelic complementation. We show results in slightly lower load, but much smaller than...
Abstract Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages. The redundancy created by WGDs typically results in a phase massive loss. However, some WGD–derived paralogs are maintained over long evolutionary periods, and relative contributions different selective pressures to their maintenance still debated. Previous studies revealed history three successive lineage ciliate Paramecium tetraurelia two its sister species from aurelia complex. Here, we...
Abstract Building evolutionarily appropriate baseline models for natural populations is not only important answering fundamental questions in population genetics—including quantifying the relative contributions of adaptive versus nonadaptive processes—but also essential identifying candidate loci experiencing relatively rare and episodic forms selection (e.g., positive or balancing selection). Here, a model was developed human West African ancestry, Yoruba, comprising processes constantly...
The detection of selective sweeps from population genomic data often relies on the premise that beneficial mutations in question have fixed very near sampling time. As it has been previously shown power to detect a sweep is strongly dependent time since fixation as well strength selection, naturally case strong, recent leave strongest signatures. However, biological reality enter populations at rate, one partially determines mean wait between events and hence their age distribution. An...
Abstract Human cytomegalovirus (HCMV) represents a major threat to human health, contributing both birth defects in neonates as well organ transplant failure and opportunistic infections immunocompromised individuals. HCMV exhibits considerable interhost intrahost diversity, which likely influences the pathogenicity of virus. Therefore, understanding relative contributions various evolutionary forces shaping patterns variation is critical importance mechanistically clinically. Herein, we...
Abstract Population structure can be described by genotypic-correlation coefficients between groups of individuals, the most basic which are pairwise relatedness any two individuals. There nine in general model, and we show that these reduced to seven for biallelic loci. Although all estimated from pedigrees, six have been beyond empirical reach. We provide a numerical optimization procedure estimates population-genomic data. Simulations is nearly unbiased, even at 3× coverage, errors five...
The ability to accurately identify and quantify genetic signatures associated with soft selective sweeps based on patterns of nucleotide variation has remained controversial. We here provide counter viewpoints recent publications in PLOS Genetics that have argued not only for the statistical identifiability sweeps, but also their pervasive evolutionary role both Drosophila HIV populations. present evidence these claims owe a lack consideration competing models, unjustified interpretations...
Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such for unicellular eukaryotes prompted us assess in Paramecium, one the most well-studied ciliate genera. Paramecium aurelia complex consists ∼15 morphologically indistinguishable species that diverged subsequent two rounds whole-genome duplications (WGDs, as long 320 MYA) possess extremely streamlined genomes. We examine patterns both...
Abstract Whole-genome duplications (WGDs) have occurred in many eukaryotic lineages. However, the underlying evolutionary forces and molecular mechanisms responsible for long-term retention of gene duplicates created by WGDs are not well understood. We employ a population-genomic approach to understand selective acting on paralogs investigate ongoing duplicate-gene loss multiple species Paramecium that share an ancient WGD. show mutations abolish protein function more likely be segregating...
A widely used model of the effects mutations on fitness (the "sites" model) assumes that heterozygous recessive or partially deleterious at different sites in a gene complement each other, similarly to genes. However, general lack complementation between major effect allelic suggests an alternative possibility, which we term "gene" model. This pair trans behave effectively as homozygotes, so fitnesses heterozygotes are lower than those cis heterozygotes. We examine properties two models,...
The evolution of mitochondrial genomes and their population-genetic environment among unicellular eukaryotes are understudied. Ciliate exhibit a unique combination characteristics, including linear organization the presence multiple genes with no known function or detectable homologs in other eukaryotes. Here we study variation ciliate both within across 13 highly diverged Paramecium species, species from P. aurelia complex, four outgroup species: caudatum, multimicronucleatum, two strains...
Abstract It has previously been shown that, conditional on its fixation, the time to fixation of a semi-dominant deleterious autosomal mutation in randomly mating population is same as that an advantageous mutation. This result implies mutations could generate selective sweep-like effects. Although their probabilities greatly differ, much larger input relative beneficial suggests this phenomenon be important. We here examine how mildly affects levels and patterns polymorphism at linked...
ABSTRACT The accurate estimation of the distribution fitness effects (DFE) new mutations is critical for population genetic inference but remains a challenging task. While various methods have been developed DFE using site frequency spectrum putatively neutral and selected sites, their applicability in species with diverse life history traits complex demographic scenarios not well understood. Selfing common among eukaryotic can lead to decreased effective recombination rates, increasing...
Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection sweeps can produce genomic signatures at linked sites that mimic or mask signals associated with historical population size change. While theoretical biases introduced by effects have been well established, it unclear whether ancestral recombination graph (ARG)-based approaches...
Abstract Whole-Genome Duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages. The redundancy created by WGDs typically results in a phase massive loss. However, some WGD-derived paralogs are maintained over long evolutionary periods and relative contributions different selective pressures to their maintenance is still debated. Previous studies revealed history three successive lineage ciliate Paramecium tetraurelia two its sister species from P. aurelia complex....