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Methods in Molecular Biology (Clifton,... 2017Haplotypes, as they specify linkage patterns between individual nucleotide variants, confer critical information for understanding the genetics of human diseases....
Haplotypes, as they specify linkage patterns between individual nucleotide variants, confer critical information for understanding the genetics of human diseases. However, haplotype information is not directly obtainable from high-throughput genotyping platforms. In this chapter, we introduce four representative methods to reconstruct haplotypes from unphased genotype data, two of them are for unrelated individuals and the other two are for families.
Topics: Female; Genetic Predisposition to Disease; Genetics, Population; Genotype; Genotyping Techniques; Haplotypes; Humans; Linkage Disequilibrium; Male; Pedigree; Software
PubMed: 28980260
DOI: 10.1007/978-1-4939-7274-6_23 -
Genes Jan 2022True truffle ( spp.) is one group of ascomycetes with great economic importance. During the last 30 years, numerous fine-scale population genetics studies were conducted... (Review)
Review
True truffle ( spp.) is one group of ascomycetes with great economic importance. During the last 30 years, numerous fine-scale population genetics studies were conducted on different truffle species, aiming to answer several key questions regarding their life cycles; these questions are important for their cultivation. It is now evident that truffles are heterothallic, but with a prevalent haploid lifestyle. Strains forming ectomycorrhizas and germinating ascospores act as maternal and paternal partners respectively. At the same time, a number of large-scale studies were carried out, highlighting the influences of the last glaciation and river isolations on the genetic structure of truffles. A retreat to southern refugia during glaciation, and a northward expansion post glaciation, were revealed in all studied European truffles. The Mediterranean Sea, acting as a barrier, has led to the existence of several refugia in different peninsulas for a single species. Similarly, large rivers in southwestern China act as physical barriers to gene flow for truffles in this region. Further studies can pay special attention to population genetics of species with a wide distribution range, such as , and the correlation between truffle genetic structure and the community composition of truffle-associated bacteria.
Topics: Ascomycota; Genetics, Population; Life Cycle Stages; Phylogeography; Species Specificity
PubMed: 35052485
DOI: 10.3390/genes13010145 -
Molecular Biology and Evolution May 2024This perspective article offers a meditation on FST and other quantities developed by Sewall Wright to describe the population structure, defined as any departure from...
This perspective article offers a meditation on FST and other quantities developed by Sewall Wright to describe the population structure, defined as any departure from reproduction through random union of gametes. Concepts related to the F-statistics draw from studies of the partitioning of variation, identity coefficients, and diversity measures. Relationships between the first two approaches have recently been clarified and unified. This essay addresses the third pillar of the discussion: Nei's GST and related measures. A hierarchy of probabilities of identity-by-state provides a description of the relationships among levels of a structured population with respect to genetic diversity. Explicit expressions for the identity-by-state probabilities are determined for models of structured populations undergoing regular inbreeding and recurrent mutation. Levels of genetic diversity within and between subpopulations reflect mutation as well as migration. Accordingly, indices of the population structure are inherently locus-specific, contrary to the intentions of Wright. Some implications of this locus-specificity are explored.
Topics: Models, Genetic; Genetic Variation; Genetics, Population; Mutation; Inbreeding
PubMed: 38696269
DOI: 10.1093/molbev/msae083 -
The Journal of Heredity Mar 2018Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has... (Review)
Review
Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has seriously lagged behind that of diploids. This is unfortunate since the analysis of polyploid genetic data-and the interpretation of the results-requires even more scrutiny than with diploid data. This is because of several polyploidy-specific complications in segregation and genotyping such as tetrasomy, double reduction, and missing dosage information. Here, we review the theoretical and statistical aspects of the population genetics of polyploids. We discuss several widely used types of inferences, including genetic diversity, Hardy-Weinberg equilibrium, population differentiation, genetic distance, and detecting population structure. For each, we point out how the statistical approach, expected result, and interpretation differ between different ploidy levels. We also discuss for each type of inference what biases may arise from the polyploid-specific complications and how these biases can be overcome. From our overview, it is clear that the statistical toolbox that is available for the analysis of genetic data is flexible and still expanding. Modern sequencing techniques will soon be able to overcome some of the current limitations to the analysis of polyploid data, though the techniques are lagging behind those available for diploids. Furthermore, the availability of more data may aggravate the biases that can arise, and increase the risk of false inferences. Therefore, simulations such as we used throughout this review are an important tool to verify the results of analyses of polyploid genetic data.
Topics: Animals; Cluster Analysis; Gene Frequency; Genetic Variation; Genetics, Population; Heterozygote; Models, Genetic; Multivariate Analysis; Polyploidy; Reproduction
PubMed: 29385510
DOI: 10.1093/jhered/esy006 -
Genes Nov 2020Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of... (Review)
Review
Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and pottery manufacturing (2500 BCE-150 CE), which led to the rise of several cultures connected by commerce and farming. Hence, Mesoamericans probably carried an invaluable genetic diversity partly lost during the Spanish conquest and the subsequent colonial period. Mesoamerican ancient DNA (aDNA) research has mainly focused on the study of mitochondrial DNA in the Basin of Mexico and the Yucatán Peninsula and its nearby territories, particularly during the Postclassic period (900-1519 CE). Despite limitations associated with the poor preservation of samples in tropical areas, recent methodological improvements pave the way for a deeper analysis of Mesoamerica. Here, we review how aDNA research has helped discern population dynamics patterns in the pre-Columbian Mesoamerican context, how it supports archaeological, linguistic, and anthropological conclusions, and finally, how it offers new working hypotheses.
Topics: Archaeology; Central America; DNA, Ancient; Genetics, Population; History, Ancient; Humans; Population Dynamics
PubMed: 33202852
DOI: 10.3390/genes11111346 -
Biological Reviews of the Cambridge... Aug 2016The notion that natural selection is a process of fitness maximization gets a bad press in population genetics, yet in other areas of biology the view that organisms... (Review)
Review
The notion that natural selection is a process of fitness maximization gets a bad press in population genetics, yet in other areas of biology the view that organisms behave as if attempting to maximize their fitness remains widespread. Here I critically appraise the prospects for reconciliation. I first distinguish four varieties of fitness maximization. I then examine two recent developments that may appear to vindicate at least one of these varieties. The first is the 'new' interpretation of Fisher's fundamental theorem of natural selection, on which the theorem is exactly true for any evolving population that satisfies some minimal assumptions. The second is the Formal Darwinism project, which forges links between gene frequency change and optimal strategy choice. In both cases, I argue that the results fail to establish a biologically significant maximization principle. I conclude that it may be a mistake to look for universal maximization principles justified by theory alone. A more promising approach may be to find maximization principles that apply conditionally and to show that the conditions were satisfied in the evolution of particular traits.
Topics: Biological Evolution; Gene Frequency; Genetics, Population; Models, Genetic; Phenotype; Selection, Genetic
PubMed: 25899152
DOI: 10.1111/brv.12190 -
Molecular Ecology Resources Sep 2015Linkage disequilibrium (LD, association of allelic states across loci) is poorly understood by many evolutionary biologists, but as technology for multilocus sampling...
Linkage disequilibrium (LD, association of allelic states across loci) is poorly understood by many evolutionary biologists, but as technology for multilocus sampling improves, we ignore LD at our peril. If we sample variation at 10 loci in an organism with 20 chromosomes, we can reasonably treat them as 10 'independent witnesses' of the evolutionary process. If instead, we sample variation at 1000 loci, many are bound to be close together on a chromosome. With only one or two crossovers per meiosis, associations between close neighbours decay so slowly that even LD created far in the past will not have dissipated, so we cannot treat the 1000 loci as independent witnesses (Barton ). This means that as marker density on genomes increases classic analyses assuming independent loci become mired in the problem of overconfidence: if 1000 independent witnesses are assumed, and that number should be much lower, any conclusion will be overconfident. This is of special concern because our literature suffers from a strong publication bias towards confident answers, even when they turn out to be wrong (Knowles ). In contrast, analyses that take into account associations across loci both control for overconfidence and can inform us about LD generating events far in the past, for example human/Neanderthal admixture (Fu et al. ). With increased marker density, biologists must increase their awareness of LD and, in this issue of Molecular Ecology Resources, Kemppainen et al. () make software available that can only help in this process: LDna allows patterns of LD in a data set to be explored using tools borrowed from network analysis. This has great potential, but realizing that potential requires understanding LD.
Topics: Computational Biology; Genetics, Population; Linkage Disequilibrium; Software
PubMed: 26261040
DOI: 10.1111/1755-0998.12424 -
Social Science & Medicine (1982) Jun 2016The concept of geneticization belongs to a style of thinking within the social sciences that refers to wide-ranging processes and consequences of genetic knowledge.... (Review)
Review
The concept of geneticization belongs to a style of thinking within the social sciences that refers to wide-ranging processes and consequences of genetic knowledge. Lippman's original use of the term was political, anticipating the onerous consequences of genetic reductionism and determinism, while more recent engagements emphasise the productivity and heterogeneity of genetic concepts, practices and technologies. This paper reconstructs the geneticization concept, tracing it back to early political critiques of medicine. The argument is made that geneticization belongs to a style of constructionist thinking that obscures and exaggerates the essentializing effects of genetic knowledge. Following Hacking's advice, we need a more literal sense of construction in terms of 'assembly' to give a clearer account of the relationship between processes and products. Using the 'assemblage' concept to explore the social ontology of genetics, the paper reviews three areas of the empirical literature on geneticization - disease classification, clinical practice and biosociality - to show that a new style of thinking has appeared within the social sciences. In the final assessment, the conditions that gave rise to geneticization are now obsolete. While it may serve as a useful ritual of debate, conceptually geneticization offers a limited account of the heterogeneity of socio-technical change.
Topics: Genetics, Population; Humans; Philosophy, Medical; Social Sciences
PubMed: 27191974
DOI: 10.1016/j.socscimed.2016.05.011 -
Journal of Molecular Evolution Jan 2020Between the 1930s and 1950s, scientists developed key principles of population genetics to try and explain the aging process. Almost a century later, these aging... (Review)
Review
Between the 1930s and 1950s, scientists developed key principles of population genetics to try and explain the aging process. Almost a century later, these aging theories, including antagonistic pleiotropy and mutation accumulation, have been experimentally validated in animals. Although the theories have been much harder to test in humans despite research dating back to the 1970s, recent research is closing this evidence gap. Here we examine the strength of evidence for antagonistic pleiotropy in humans, one of the leading evolutionary explanations for the retention of genetic risk variation for non-communicable diseases. We discuss the analytical tools and types of data that are used to test for patterns of antagonistic pleiotropy and provide a primer of evolutionary theory on types of selection as a guide for understanding this mechanism and how it may manifest in other diseases. We find an abundance of non-experimental evidence for antagonistic pleiotropy in many diseases. In some cases, several studies have independently found corroborating evidence for this mechanism in the same or related sets of diseases including cancer and neurodegenerative diseases. Recent studies also suggest antagonistic pleiotropy may be involved in cardiovascular disease and diabetes. There are also compelling examples of disease risk variants that confer fitness benefits ranging from resistance to other diseases or survival in extreme environments. This provides increasingly strong support for the theory that antagonistic pleiotropic variants have enabled improved fitness but have been traded for higher burden of disease later in life. Future research in this field is required to better understand how this mechanism influences contemporary disease and possible consequences for their treatment.
Topics: Biological Evolution; Disease; Evolution, Molecular; Genetic Pleiotropy; Genetics, Population; Humans; Mutation; Selection, Genetic
PubMed: 31863128
DOI: 10.1007/s00239-019-09923-2 -
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