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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 -
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 -
Methods in Molecular Biology (Clifton,... 2018Genetic epidemiology is a discipline closely allied to traditional epidemiology that deals with the analysis of the familial distribution of traits. It emerged in the... (Review)
Review
Genetic epidemiology is a discipline closely allied to traditional epidemiology that deals with the analysis of the familial distribution of traits. It emerged in the mid-1980s bringing together approaches and techniques developed in mathematical and quantitative genetics, medical and population genetics, statistics and epidemiology. The purpose of this chapter is to familiarize the reader with key concepts in genetic epidemiology as applied at present to unveil the familial and genetic determinants of disease and the joint effects of genes and environmental exposures.
Topics: Gene-Environment Interaction; Genetic Association Studies; Genetic Predisposition to Disease; Genetic Variation; Genetics, Population; Humans; Inheritance Patterns; Molecular Epidemiology
PubMed: 29876888
DOI: 10.1007/978-1-4939-7868-7_2 -
Annual Review of Genomics and Human... 2015In this overview of my research, I have aimed to give the background as to how I came to be involved in my various areas of interest, with an emphasis on the early...
In this overview of my research, I have aimed to give the background as to how I came to be involved in my various areas of interest, with an emphasis on the early phases of my career, which largely determined my future directions. I had the enormous good fortune to have worked under two of the most outstanding scientists of the twentieth century, R.A. Fisher and Joshua Lederberg. From mathematics and statistics, I went to population genetics and the early use of computers for modeling and simulation. Molecular biology took me into the laboratory and eventually to somatic cell genetics and human gene mapping. One chance encounter led me into the HLA field and another led me into research on cancer, especially colorectal cancer. On the way, I became a champion of the Human Genome Project and of the need for scientists to help promote the public understanding of science.
Topics: Autoimmune Diseases; Biostatistics; Chromosome Mapping; Genetics, Population; HLA Antigens; History, 20th Century; History, 21st Century; Human Genome Project; Humans; Mathematics; Models, Theoretical; Molecular Biology; Neoplasms; Primula; United Kingdom
PubMed: 25939053
DOI: 10.1146/annurev-genom-090314-045856 -
Annual Review of Genetics Nov 2020Natural highly fecund populations abound. These range from viruses to gadids. Many highly fecund populations are economically important. Highly fecund populations... (Review)
Review
Natural highly fecund populations abound. These range from viruses to gadids. Many highly fecund populations are economically important. Highly fecund populations provide an important contrast to the low-fecundity organisms that have traditionally been applied in evolutionary studies. A key question regarding high fecundity is whether large numbers of offspring are produced on a regular basis, by few individuals each time, in a sweepstakes mode of reproduction. Such reproduction characteristics are not incorporated into the classical Wright-Fisher model, the standard reference model of population genetics, or similar types of models, in which each individual can produce only small numbers of offspring relative to the population size. The expected genomic footprints of population genetic models of sweepstakes reproduction are very different from those of the Wright-Fisher model. A key, immediate issue involves identifying the footprints of sweepstakes reproduction in genomic data. Whole-genome sequencing data can be used to distinguish the patterns made by sweepstakes reproduction from the patterns made by population growth in a population evolving according to the Wright-Fisher model (or similar models). If the hypothesis of sweepstakes reproduction cannot be rejected, then models of sweepstakes reproduction and associated multiple-merger coalescents will become at least as relevant as the Wright-Fisher model (or similar models) and the Kingman coalescent, the cornerstones of mathematical population genetics, in further discussions of evolutionary genomics of highly fecund populations.
Topics: Biological Evolution; Fertility; Genetics, Population; Genomics; Humans; Models, Genetic; Population Density; Population Growth; Reproduction
PubMed: 32870729
DOI: 10.1146/annurev-genet-021920-095932 -
Molecular Ecology Oct 2018The concept of kinship permeates many domains of fundamental and applied biology ranging from social evolution to conservation science to quantitative and human...
The concept of kinship permeates many domains of fundamental and applied biology ranging from social evolution to conservation science to quantitative and human genetics. Until recently, pedigrees were the gold standard to infer kinship, but the advent of next-generation sequencing and the availability of dense genetic markers in many species make it a good time to (re)evaluate the usefulness of genetic markers in this context. Using three published data sets where both pedigrees and markers are available, we evaluate two common and a new genetic estimator of kinship. We show discrepancies between pedigree values and marker estimates of kinship and explore via simulations the possible reasons for these. We find these discrepancies are attributable to two main sources: pedigree errors and heterogeneity in the origin of founders. We also show that our new marker-based kinship estimator has very good statistical properties and behaviour and is particularly well suited for situations where the source population is of small size, as will often be the case in conservation biology, and where high levels of kinship are expected, as is typical in social evolution studies.
Topics: Genetic Markers; Genetics, Population; Humans; Models, Genetic; Pedigree
PubMed: 30107060
DOI: 10.1111/mec.14833 -
Genome Biology and Evolution Apr 2023As the ancestral homeland of our species, Africa contains elevated levels of genetic diversity and substantial population structure. Importantly, African genomes are... (Review)
Review
As the ancestral homeland of our species, Africa contains elevated levels of genetic diversity and substantial population structure. Importantly, African genomes are heterogeneous: They contain mixtures of multiple ancestries, each of which have experienced different evolutionary histories. In this review, we view population genetics through the lens of admixture, highlighting how multiple demographic events have shaped African genomes. Each of these historical vignettes paints a recurring picture of population divergence followed by secondary contact. First, we give a brief overview of genetic variation in Africa and examine deep population structure within Africa, including the evidence of ancient introgression from archaic "ghost" populations. Second, we describe the genetic legacies of admixture events that have occurred during the past 10,000 years. This includes gene flow between different click-speaking Khoe-San populations, the stepwise spread of pastoralism from eastern to southern Africa, multiple migrations of Bantu speakers across the continent, as well as admixture from the Middle East and Europe into the Sahel region and North Africa. Furthermore, the genomic signatures of more recent admixture can be found in the Cape Peninsula and throughout the African diaspora. Third, we highlight how natural selection has shaped patterns of genetic variation across the continent, noting that gene flow provides a potent source of adaptive variation and that selective pressures vary across Africa. Finally, we explore the biomedical implications of population structure in Africa on health and disease and call for more ethically conducted studies of genetic variation in Africa.
Topics: Genetic Variation; Genetics, Population; Africa, Southern; Biological Evolution; Genome
PubMed: 36987563
DOI: 10.1093/gbe/evad054 -
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