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Genetics Mar 2017Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the... (Review)
Review
Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, has been the prominent model species: molecular variation in populations was first described in and most of the population genetics hypotheses were tested in species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data.
Topics: Animals; Drosophila; Genetics, Population; Genomic Instability; Genomics; Polymorphism, Genetic
PubMed: 28270526
DOI: 10.1534/genetics.116.196493 -
Heredity Jan 2017We describe the astonishing changes and progress that have occurred in the field of population genetics over the past 50 years, slightly longer than the time since the... (Review)
Review
We describe the astonishing changes and progress that have occurred in the field of population genetics over the past 50 years, slightly longer than the time since the first Population Genetics Group (PGG) meeting in January 1968. We review the major questions and controversies that have preoccupied population geneticists during this time (and were often hotly debated at PGG meetings). We show how theoretical and empirical work has combined to generate a highly productive interaction involving successive developments in the ability to characterise variability at the molecular level, to apply mathematical models to the interpretation of the data and to use the results to answer biologically important questions, even in nonmodel organisms. We also describe the changes from a field that was largely dominated by UK and North American biologists to a much more international one (with the PGG meetings having made important contributions to the increased number of population geneticists in several European countries). Although we concentrate on the earlier history of the field, because developments in recent years are more familiar to most contemporary researchers, we end with a brief outline of topics in which new understanding is still actively developing.
Topics: Evolution, Molecular; Genetic Drift; Genetics, Population; History, 20th Century; History, 21st Century; Linkage Disequilibrium; Models, Genetic; Mutation; Polymorphism, Genetic; Selection, Genetic; Sequence Analysis, DNA
PubMed: 27460498
DOI: 10.1038/hdy.2016.55 -
Nature Methods Sep 2020
Topics: Gene Library; Genetics, Population; Models, Genetic; Software
PubMed: 32873980
DOI: 10.1038/s41592-020-0951-4 -
BSCS Pamphlets
Topics: Genetics; Genetics, Population; Humans; Population
PubMed: 14254932
DOI: No ID Found -
Briefings in Bioinformatics May 2014Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on comparative data, today usually DNA sequences. These have become... (Review)
Review
Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on comparative data, today usually DNA sequences. These have become so plentiful that alignment-free sequence comparison is of growing importance in the race between scientists and sequencing machines. In phylogenetics, efficient distance computation is the major contribution of alignment-free methods. A distance measure should reflect the number of substitutions per site, which underlies classical alignment-based phylogeny reconstruction. Alignment-free distance measures are either based on word counts or on match lengths, and I apply examples of both approaches to simulated and real data to assess their accuracy and efficiency. While phylogeny reconstruction is based on the number of substitutions, in population genetics, the distribution of mutations along a sequence is also considered. This distribution can be explored by match lengths, thus opening the prospect of alignment-free population genomics.
Topics: Animals; Computational Biology; Evolution, Molecular; Genetics, Population; Genome, Mitochondrial; Humans; Models, Genetic; Mutation; Phylogeny; Recombination, Genetic; Selection, Genetic; Sequence Alignment; Sequence Analysis, DNA
PubMed: 24291823
DOI: 10.1093/bib/bbt083 -
Yi Chuan = Hereditas Aug 2016The genomes of more and more organisms have been sequenced due to the advances in next-generation sequencing technologies. As a powerful tool, computer simulators play a... (Review)
Review
The genomes of more and more organisms have been sequenced due to the advances in next-generation sequencing technologies. As a powerful tool, computer simulators play a critical role in studying the genome-wide DNA polymorphism pattern. Simulations can be performed both forwards-in-time and backwards-in-time, which complement each other and are suitable for meeting different needs, such as studying the effect of evolutionary dynamics, the estimation of parameters, and the validation of evolutionary hypotheses as well as new methods. In this review, we briefly introduced population genetics related theoretical framework and provided a detailed comparison of 32 simulators published over the last ten years. The future development of new simulators was also discussed.
Topics: Computer Simulation; Evolution, Molecular; Genetics, Population; High-Throughput Nucleotide Sequencing
PubMed: 27531609
DOI: 10.16288/j.yczz.16-100 -
Nature Ecology & Evolution Feb 2024
Topics: Genetics, Population; Phylogeny; Prokaryotic Cells
PubMed: 38177691
DOI: 10.1038/s41559-023-02276-6 -
Nature Microbiology Dec 2017
Topics: Genetics, Population; Prokaryotic Cells
PubMed: 29176697
DOI: 10.1038/s41564-017-0066-6 -
Parasite (Paris, France) Sep 2008Although parasitism is one of the most common lifestyles among eukaryotes, population genetics on parasites lag for behind those on free-living organisms. Yet, the... (Review)
Review
Although parasitism is one of the most common lifestyles among eukaryotes, population genetics on parasites lag for behind those on free-living organisms. Yet, the advent of molecular markers offers great tools for studying important processes, such as dispersal, mating systems, adaptation to host and speciation. Here we highlight some studies that used molecular markers to address questions about the population genetics of fungal (including oomycetes) plant pathogens. We conclude that population genetics approaches have provided tremendous insights into the biology of a few fungal parasites and warrant more wide use in phytopathology. However, theoretical advances are badly needed to best apply the existing methods. Fungi are of prime interest not only because they are major parasites of plants and animals, but they also constitute tractable and highly useful models for understanding evolutionary processes. We hope that the emerging field of fungal evolution will attract more evolutionary biologists in the near future.
Topics: Evolution, Molecular; Fungi; Gene Flow; Genetic Markers; Genetics, Population; Host-Pathogen Interactions; Molecular Epidemiology; Mycological Typing Techniques; Plant Diseases; Species Specificity
PubMed: 18814721
DOI: 10.1051/parasite/2008153449 -
Current Opinion in Genetics &... Dec 2006The number and frequency of susceptibility alleles for common diseases are important factors to consider in the efficient design of disease association studies. These... (Review)
Review
The number and frequency of susceptibility alleles for common diseases are important factors to consider in the efficient design of disease association studies. These quantities are the results of the joint effects of mutation, genetic drift and selection. Hence, population genetics models, informed by empirical knowledge about patterns of disease variation, can be used to make predictions about the allelic architecture of common disease susceptibility and to gain an overall understanding about the evolutionary origins of such diseases. Equilibrium models and empirical studies suggest a role for both rare and common variants. In addition, increasing evidence points to changes in selective pressures on susceptibility genes for common diseases; these findings are likely to form the basis for further modeling studies.
Topics: Genetic Predisposition to Disease; Genetics, Population; Humans; Models, Genetic; Mutation; Selection, Genetic
PubMed: 17055247
DOI: 10.1016/j.gde.2006.10.002