A5088743128- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Aquatic Ecosystems and Phytoplankton Dynamics
- Plant and animal studies
- Insect-Plant Interactions and Control
- Cancer Genomics and Diagnostics
- Protist diversity and phylogeny
- Animal Virus Infections Studies
- Viral gastroenteritis research and epidemiology
- Fish Ecology and Management Studies
- Insect symbiosis and bacterial influences
- DNA Repair Mechanisms
- Genetic and phenotypic traits in livestock
- CRISPR and Genetic Engineering
- Wheat and Barley Genetics and Pathology
- Plant Virus Research Studies
- Legume Nitrogen Fixing Symbiosis
- Ecology and Vegetation Dynamics Studies
- Plant Pathogenic Bacteria Studies
- Genetic Mapping and Diversity in Plants and Animals
- Genetics and Plant Breeding
- Bacteriophages and microbial interactions
- Virus-based gene therapy research
- Microbial Community Ecology and Physiology
National Pork Board
2021
Arizona State University
2018
Indiana University Bloomington
2012-2017
Mutation dictates the tempo and mode of evolution, like all traits, mutation rate is subject to evolutionary modification. Here, we report refined estimates for a prokaryote with an exceptionally small genome unicellular eukaryote large genome. Combined prior results, these provide basis potentially unifying explanation wide range in rates that exists among organisms. Natural selection appears reduce species level scales negatively both effective population size ( N e ), which imposes drift...
Significance Drawing from whole-genome sequences of multiple genotypes, this study documents the molecular-genetic consequences loss recombination in a microcrustacean, demonstrating that heterozygosity via gene conversion-like processes is dramatically more powerful force than accumulation new mutations.
Despite the general assumption that site-specific mutation rates are independent of local sequence context, a growing body evidence suggests otherwise. To further examine context-dependent patterns mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR–) mutation–accumulation (MA) lines gram-positive model organism Bacillus subtilis. We then analyzed>7,500 base-substitution across B. subtilis, Escherichia coli, Mesoplasma florum WT MMR– MA...
Knowledge of the genome-wide rate and spectrum mutations is necessary to understand origin disease genetic variation driving all evolutionary processes. Here, we provide a analysis obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. can be propagated ameiotically while maintaining naturally heterozygous, diploid genome, allowing capture full genomic changes arise...
Abstract Mutations are the ultimate source of variation used for evolutionary adaptation, while also being predominantly deleterious and a genetic disorders. Understanding rate insertion-deletion mutations (indels) is essential to understanding processes, especially in coding regions, where such can disrupt production proteins. Using direct estimates indel rates from 14 phylogenetically diverse eukaryotic bacterial species, along with measures standing we obtain results that imply an inverse...
Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact effective population size on genome evolution. For this purpose, we present a high quality assembly Daphnia pulex (PA42), and compare first sequenced species (TCO), which was derived an isolate >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at gene level, average amino acid sequence identity 98.8 >60% orthologous proteins identical....
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...
Deinococcus bacteria are extremely resistant to radiation, oxidation, and desiccation. Resilience these factors has been suggested be due enhanced damage prevention repair mechanisms, as well highly efficient antioxidant protection systems. Here, using mutation-accumulation experiments, we find that the GC-rich radiodurans an overall background genomic mutation rate similar of E. coli, but differs in spectrum, with A/T G/C (based on a total count 88 A:T→G:C transitions 82 A:T→C:G...
Significance We have investigated multiple aspects of the Euplotes - Polynucleobacter system, which provides a unique opportunity for study an obligate symbiont with closely related free-living organism that itself possesses peculiarly reduced genome and metabolism. confirmed robustness generality patterns in evolution bacterial symbionts’ genome, adding at same time new elements hypotheses concerning reduction both symbiotic bacteria. argue this system will provide exceptionally useful...
High levels of genetic diversity exist among natural isolates the bacterium Pseudomonas fluorescens, and are especially elevated around replication terminus genome, where strain-specific genes found. In an effort to understand role variation in evolution Pseudomonas, we analyzed 31,106 base substitutions from 45 mutation accumulation lines P. fluorescens ATCC948, naturally deficient for mismatch repair, yielding a base-substitution rate 2.34 × 10−8 per site generation (SE: 0.01 10−8)...
Hybridization plays a potentially important role in the origin of obligate parthenogenesis (OP) many organisms. However, it remains controversial whether hybridization directly triggers transition from sexual reproduction to asexuality or hybrid genetic background enables asexual species persist. Furthermore, we know little about specific elements divergent, yet still hybridizing lineages responsible for this and how these are further spread create other OP lineages. In study, address...
Abstract Genetic linkage maps are critical for assembling draft genomes to a meaningful chromosome level and deciphering the genomic underpinnings of biological traits. The estimates recombination rates derived from genetic also play an important role in understanding multiple aspects evolution such as nucleotide substitution patterns accumulation deleterious mutations. In this study, we developed high-throughput experimental approach that combines fluorescence-activated cell sorting,...
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...
Mutations contribute to genetic variation in all living systems. Thus, precise estimates of mutation rates and spectra across a diversity organisms are required for full comprehension evolution. Here, mutation-accumulation (MA) assay was carried out on the endosymbiotic bacterium Teredinibacter turnerae. After ∼3,025 generations, base-pair substitutions (BPSs) insertion–deletion (indel) events were characterized by whole-genome sequencing analysis 47 independent MA lines, yielding BPS rate...
Porcine reproductive and respiratory syndrome (PRRS) continues to represent a significant cost the swine industry efforts are focused on prevention mitigation of losses across production phases. Herein describes PRRS modified-live virus (MLV) vaccinated breeding herd that changed commercial MLV vaccines improve post-weaning performance. Two whole-herd vaccinations with new vaccine, administered 4 weeks apart, occurred without disruptions limited changes in diagnostic results. Replacement...
ABSTRACT Population structure can be described by genotypic correlation coefficients between groups of individuals, the most basic which are pair-wise 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 them population-genomic data. Simulations is nearly unbiased, even at 3× coverage, errors...