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American Journal of Human Genetics Feb 2023It has been 15 years since the advent of the genome-wide association study (GWAS) era. Here, we review how this experimental design has realized its promise by... (Review)
Review
It has been 15 years since the advent of the genome-wide association study (GWAS) era. Here, we review how this experimental design has realized its promise by facilitating an impressive range of discoveries with remarkable impact on multiple fields, including population genetics, complex trait genetics, epidemiology, social science, and medicine. We predict that the emergence of large-scale biobanks will continue to expand to more diverse populations and capture more of the allele frequency spectrum through whole-genome sequencing, which will further improve our ability to investigate the causes and consequences of human genetic variation for complex traits and diseases.
Topics: Humans; Genome-Wide Association Study; Gene Frequency; Genetics, Population; Multifactorial Inheritance; Polymorphism, Single Nucleotide
PubMed: 36634672
DOI: 10.1016/j.ajhg.2022.12.011 -
Genes Oct 2021The pig (Sus scrofa) is the most popular large farm animal in the world [...].
The pig (Sus scrofa) is the most popular large farm animal in the world [...].
Topics: Animals; Genetic Association Studies; Genetics, Population; Genomics; Sequence Analysis, RNA; Sus scrofa
PubMed: 34828298
DOI: 10.3390/genes12111692 -
Human Genetics Feb 2021We present selected topics of population genetics and molecular phylogeny. As several excellent review articles have been published and generally focus on European and... (Review)
Review
We present selected topics of population genetics and molecular phylogeny. As several excellent review articles have been published and generally focus on European and American scientists, here, we emphasize contributions by Japanese researchers. Our review may also be seen as a belated 50-year celebration of Motoo Kimura's early seminal paper on the molecular clock, published in 1968.
Topics: Genetics, Population; Humans; Phylogeny
PubMed: 32683493
DOI: 10.1007/s00439-020-02208-5 -
European Journal of Human Genetics :... Nov 2021
Topics: Genetic Testing; Genetics, Population; Genome-Wide Association Study; Genotyping Techniques; Humans
PubMed: 34616014
DOI: 10.1038/s41431-021-00979-7 -
Nature Ecology & Evolution Aug 2022Populations of cancer cells are subject to the same core evolutionary processes as asexually reproducing, unicellular organisms. Transmissible cancers are particularly... (Review)
Review
Populations of cancer cells are subject to the same core evolutionary processes as asexually reproducing, unicellular organisms. Transmissible cancers are particularly striking examples of these processes. These unusual cancers are clonal lineages that can spread through populations via physical transfer of living cancer cells from one host individual to another, and they have achieved long-term success in the colonization of at least eight different host species. Population genetic theory provides a useful framework for understanding the shift from a multicellular sexual animal into a unicellular asexual clone and its long-term effects on the genomes of these cancers. In this Review, we consider recent findings from transmissible cancer research with the goals of developing an evolutionarily informed perspective on transmissible cancers, examining possible implications for their long-term fate and identifying areas for future research on these exceptional lineages.
Topics: Animals; Biological Evolution; Genetics, Population; Genome; Neoplasms; Population Dynamics
PubMed: 35879542
DOI: 10.1038/s41559-022-01790-3 -
Trends in Microbiology Sep 2022Biofilms are communities of bacteria forming high-density sessile colonies. Such a lifestyle comes associated with costs and benefits: while the growth rate of biofilms... (Review)
Review
Biofilms are communities of bacteria forming high-density sessile colonies. Such a lifestyle comes associated with costs and benefits: while the growth rate of biofilms is often lower than that of their free-living counterparts, this cost is readily repaid once the colony is subjected to antibiotics. Biofilms can grow in antibiotic concentrations a thousand times higher than planktonic bacteria. While numerous mechanisms have been proposed to explain biofilm recalcitrance towards antibiotics, little is yet known about their effect on the evolution of resistance. We synthesize the current understanding of biofilm recalcitrance from a pharmacodynamic and a population genetics perspective. Using the pharmacodynamic framework, we discuss the effects of various mechanisms and show that biofilms can either promote or impede resistance evolution.
Topics: Anti-Bacterial Agents; Bacteria; Biofilms; Drug Resistance, Microbial; Genetics, Population; Microbial Sensitivity Tests; Plankton
PubMed: 35337697
DOI: 10.1016/j.tim.2022.02.005 -
BMC Genetics Oct 2020
Topics: Congresses as Topic; Genetics, Population; Humans; Moscow
PubMed: 33092531
DOI: 10.1186/s12863-020-00906-7 -
Proceedings of the National Academy of... Mar 2022SignificanceMany microbial populations proliferate in small channels. In such environments, reproducing cells organize in parallel lanes. Reproducing cells shift these...
SignificanceMany microbial populations proliferate in small channels. In such environments, reproducing cells organize in parallel lanes. Reproducing cells shift these lanes, potentially expelling other cells from the channel. In this paper, we combine theory and experiments to understand how these dynamics affects the diversity of a microbial population. We theoretically predict that genetic diversity is quickly lost along lanes of cells. Our experiments confirm that a population of proliferating in a microchannel organizes into lanes of genetically identical cells within a few generations. Our findings elucidate the effect of lane formation on populations evolution, with potential applications ranging from microbial ecology in soil to dynamics of epithelial tissues in higher organisms.
Topics: Escherichia coli; Genetics, Population; Soil
PubMed: 35302890
DOI: 10.1073/pnas.2120821119 -
Journal of Human Genetics Jan 2021Uniform manifold approximation and projection (UMAP) has been rapidly adopted by the population genetics community to study population structure. It has become common in... (Review)
Review
Uniform manifold approximation and projection (UMAP) has been rapidly adopted by the population genetics community to study population structure. It has become common in visualizing the ancestral composition of human genetic datasets, as well as searching for unique clusters of data, and for identifying geographic patterns. Here we give an overview of applications of UMAP in population genetics, provide recommendations for best practices, and offer insights on optimal uses for the technique.
Topics: Computational Biology; Gene Frequency; Genetic Variation; Genetics, Population; Genome, Human; Genomics; Genotype; HLA Antigens; Human Genome Project; Humans
PubMed: 33057159
DOI: 10.1038/s10038-020-00851-4 -
Genes Nov 2022The Roma are a group of populations with a common origin that share the Romani identity and cultural heritage. Their genetic history has been inferred through multiple... (Review)
Review
The Roma are a group of populations with a common origin that share the Romani identity and cultural heritage. Their genetic history has been inferred through multiple studies based on uniparental and autosomal markers, and current genomic data have provided novel insights into their genetic background. This review was prompted by two factors: (i) new developments to estimate the genetic structure of the Roma at a fine-scale resolution have precisely identified the ancestral components and traced migrations that were previously documented only in historical sources, clarifying and solving debates on the origins and the diaspora of the Roma; (ii) while there has been an effort to review the health determinants of the Roma, the increasing literature on their population genetics has not been subjected to a dedicated review in the last two decades. We believe that a summary on the state of the art will benefit both the public and scholars that are approaching the subject.
Topics: Humans; Roma; Haplotypes; Genetics, Population; Human Migration
PubMed: 36360305
DOI: 10.3390/genes13112068