A5082225594- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- Legume Nitrogen Fixing Symbiosis
- Genetic Mapping and Diversity in Plants and Animals
- Genetic diversity and population structure
- Agronomic Practices and Intercropping Systems
- Diet, Metabolism, and Disease
- Forensic and Genetic Research
- Banana Cultivation and Research
- Diabetes and associated disorders
- Coastal wetland ecosystem dynamics
- Plant nutrient uptake and metabolism
- Influenza Virus Research Studies
- DNA Repair Mechanisms
- Pleistocene-Era Hominins and Archaeology
- Genomics and Rare Diseases
- Nematode management and characterization studies
- Forensic Anthropology and Bioarchaeology Studies
- Mitochondrial Function and Pathology
- Cancer Genomics and Diagnostics
- Genetic and phenotypic traits in livestock
- Primate Behavior and Ecology
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Chromatin Dynamics
- Chromosomal and Genetic Variations
University of California, Los Angeles
2020-2025
Illumina (United States)
2023
Aarhus University
2018-2022
Columbia University
2021-2022
City University of Seattle
2021
Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer this as species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show is distinct entity, well separated from other genus. Its sister taxon R. anhuiense. constructed phylogeny based on concatenated of 120 universal (core) genes, calculated pairwise average nucleotide identity (ANI) between all genomes. From...
In most mammals and likely throughout vertebrates, the gene PRDM9 specifies locations of meiotic double strand breaks; in mice humans at least, it also aids their repair. For both roles, many molecular partners remain unknown. Here, we take a phylogenetic approach to identify genes that may be interacting with by leveraging fact arose before origin vertebrates but was lost times, either partially or entirely-and it, its role recombination. As first step, characterize domain composition...
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...
The X chromosome in non-African humans shows less diversity and Neanderthal introgression than expected from neutral evolution. Analyzing 162 human male chromosomes worldwide, we identified fourteen chromosomal regions where nearly identical haplotypes spanning several hundred kilobases are found at high frequencies non-Africans. Genetic drift alone cannot explain the existence of these haplotypes, which must have been associated with strong positive selection partial selective sweeps....
Rhizobia supply legumes with fixed nitrogen using a set of symbiosis genes. These can cross rhizobium species boundaries, but it is unclear how many other genes show similar mobility. Here, we investigate inter-species introgression de novo assembly 196 Rhizobium leguminosarum sv. trifolii genomes. The strains constituted five-species complex, and calculated scores based on gene-tree traversal to identify 171 that frequently boundaries. Rather than relying the gene order single reference...
Abstract The presence and impact of recessive lethal mutations have been widely documented in diploid outcrossing species. However, precise estimates the proportion new that are remain limited. Here, we evaluate performance Fit∂a∂i, a commonly used method for inferring distribution fitness effects (DFE), mutations. Using simulations, demonstrate both additive cases, inference deleterious nonlethal portion DFE is minimally affected by small (<10%) Additionally, while Fit∂a∂i cannot...
Selection is a fundamental evolutionary force that shapes patterns of genetic variation across species. However, simulations incorporating realistic selection along heterogeneous genomes in complex demographic histories are challenging, limiting our ability to benchmark statistical methods aimed at detecting and explore theoretical predictions. stdpopsim community-maintained simulation library already provides an extensive catalog species-specific population models. Here we present major...
Abstract Homologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations readily creating new combinations alleles. Here, we investigate how proportion amino acid substitutions fixed adaptive evolution (α) depends on rate in bacteria. We analyze 3,086 core protein-coding sequences from 196 genomes belonging five closely related species genus Rhizobium. These genes are found all do not display any signs introgression...
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...
Abstract Background Gene transfer between bacterial species is an important mechanism for adaptation. For example, sets of genes that confer the ability to form nitrogen-fixing root nodules on host plants have frequently moved Rhizobium species. It not clear, though, whether such exceptional, or if frequent inter-species introgression typical. To address this, we sequenced genomes 196 isolates leguminosarum complex obtained from white clover ( Trifolium repens ). Results Core gene phylogeny...
Abstract The presence and impact of recessive lethal mutations has been widely documented in diploid outcrossing species. However, precise estimates different species the proportion that are remain limited. Here, we attempt to quantify fraction new using Fit ∂ a i, commonly-used method for inferring distribution fitness effects (DFE) site frequency spectrum. Using simulations, demonstrate i cannot accurately estimate mutations, as expected given assumes all additive by default. Consistent...
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 data sets 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...
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 data sets 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...
Abstract The X chromosome in non-African human populations shows less diversity and Neanderthal introgression than expected under the standard neutral model. We analyzed 162 chromosomes from males worldwide discovered 14 chromosomal regions where haplotypes of several hundred kilobases rapidly rose to high frequencies non-Africans. These observations cannot be explained by genetic drift realistic demographic scenarios are only consistent with partial selective sweeps produced strong...
Abstract 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 data sets 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...
Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer this as species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show is distinct entity, well separated from other genus. Its sister taxon R. anhuiense. constructed phylogeny based on concatenated of 120 universal (core) genes, calculated pairwise average nucleotide identity (ANI) between all genomes. From...
Abstract The X chromosome in non-African populations has less diversity and Neanderthal introgression than expected. We analyzed across the globe discovered seventeen chromosomal regions, where haplotypes of several hundred kilobases have recently reached high frequencies only. selective sweeps must occurred more 45,000 years ago because ancient Ust’-Ishim male also carries its expected proportion these haplotypes. Surprisingly, swept are entirely devoid introgression, which implies that a...
Abstract Homologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations readily creating new combinations alleles. Here, we investigate how proportion amino acid substitutions fixed adaptive evolution ( α ) depends on rate in bacteria. We analyze 3086 core protein-coding sequences from 196 genomes belonging five closely-related species genus Rhizobium . These genes are found all do not display any signs introgression...