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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 -
The Yale Journal of Biology and Medicine Dec 2018Humans are responsible for a cataclysm of species extinction that will change the world as we see it, and will adversely affect human health and wellbeing. We need to... (Review)
Review
Humans are responsible for a cataclysm of species extinction that will change the world as we see it, and will adversely affect human health and wellbeing. We need to understand at individual and societal levels why species conservation is important. Accepting the premise that species have value, we need to next consider the mechanisms underlying species extinction and what we can do to reverse the process. One of the last stages of species extinction is the reduction of a species to a few populations of relatively few individuals, a scenario that leads invariably to inbreeding and its adverse consequences, inbreeding depression. Inbreeding depression can be so severe that populations become at risk of extinction not only because of the expression of harmful recessive alleles (alleles having no phenotypic effect when in the heterozygous condition, ., Aa, where is the recessive allele), but also because of their inability to respond genetically with sufficient speed to adapt to changing environmental conditions. However, new conservation approaches based on foundational quantitative and population genetic theory advocate for active genetic management of fragmented populations by facilitating gene movements between populations, ., admixture, or genetic rescue. Why species conservation is critical, the genetic consequences of small population size that often lead to extinction, and possible solutions to the problem of small population size are discussed and presented.
Topics: Animals; Biodiversity; Ecosystem; Genetics, Population; Humans; Inbreeding
PubMed: 30588214
DOI: No ID Found -
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 -
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 -
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 -
Nature Genetics May 2011Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding... (Comparative Study)
Comparative Study
Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. The amounts of raw data produced are prodigious, and many computational steps are required to translate this output into high-quality variant calls. We present a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs. Our process includes (i) initial read mapping; (ii) local realignment around indels; (iii) base quality score recalibration; (iv) SNP discovery and genotyping to find all potential variants; and (v) machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies. We here discuss the application of these tools, instantiated in the Genome Analysis Toolkit, to deep whole-genome, whole-exome capture and multi-sample low-pass (∼4×) 1000 Genomes Project datasets.
Topics: Data Interpretation, Statistical; Databases, Nucleic Acid; Exons; Genetic Variation; Genetics, Population; Genome, Human; Genotype; Humans; Polymorphism, Single Nucleotide; Sequence Alignment; Sequence Analysis, DNA; Software
PubMed: 21478889
DOI: 10.1038/ng.806 -
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 -
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 -
Heredity Oct 2016
Topics: Animals; Ecology; Evolution, Molecular; Genetics, Population; Linkage Disequilibrium; Models, Genetic; Polymorphism, Single Nucleotide; Population Density
PubMed: 27553454
DOI: 10.1038/hdy.2016.75 -
BSCS Pamphlets
Topics: Genetics; Genetics, Population; Humans; Population
PubMed: 14254932
DOI: No ID Found