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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 -
Animal Genetics Dec 2023Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised... (Review)
Review
Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised by the rapid spread of an advantageous genetic variant through a population and hence play an important role in shaping evolution and research on genetic diversity. The process by which a beneficial allele arises and becomes fixed in a population, leading to a increase in the frequency of other linked alleles, is known as genetic hitchhiking or genetic draft. Kimura's neutral theory and hitchhiking theory are complementary, with Kimura's neutral evolution as the 'null model' and positive selection as the 'signal'. Both are widely accepted in evolution, especially with genomics enabling precise measurements. Significant advances in genomic technologies, such as next-generation sequencing, high-density SNP arrays and powerful bioinformatics tools, have made it possible to systematically investigate selection signatures in a variety of species. Although the history of selection signatures is relatively recent, progress has been made in the last two decades, owing to the increasing availability of large-scale genomic data and the development of computational methods. In this review, we embark on a journey through the history of research on selective sweeps, ranging from early theoretical work to recent empirical studies that utilise genomic data.
Topics: Animals; Selection, Genetic; Models, Genetic; Alleles; Computational Biology; Genomics; Genetics, Population
PubMed: 37710403
DOI: 10.1111/age.13355 -
Reports on Progress in Physics.... Apr 2023This review is about statistical genetics, an interdisciplinary topic between statistical physics and population biology. The focus is on the phase of(QLE). Our goals... (Review)
Review
This review is about statistical genetics, an interdisciplinary topic between statistical physics and population biology. The focus is on the phase of(QLE). Our goals here are to clarify under which conditions the QLE phase can be expected to hold in population biology and how the stability of the QLE phase is lost. The QLE state, which has many similarities to a thermal equilibrium state in statistical mechanics, was discovered by M Kimura for a two-locus two-allele model, and was extended and generalized to the global genome scale by&. What we will refer to as the Kimura-Neher-Shraiman theory describes a population evolving due to the mutations, recombination, natural selection and possibly genetic drift. A QLE phase exists at sufficiently high recombination rate () and/or mutation rateswith respect to selection strength. We show how in QLE it is possible to infer the epistatic parameters of the fitness function from the knowledge of the (dynamical) distribution of genotypes in a population. We further consider the breakdown of the QLE regime for high enough selection strength. We review recent results for the selection-mutation and selection-recombination dynamics. Finally, we identify and characterize a new phase which we call the non-random coexistence where variability persists in the population without either fixating or disappearing.
Topics: Linkage Disequilibrium; Models, Genetic; Selection, Genetic; Mutation; Genotype; Genetics, Population
PubMed: 36944245
DOI: 10.1088/1361-6633/acc5fa -
Genome Biology and Evolution Feb 2023Population genetics is transitioning into a data-driven discipline thanks to the availability of large-scale genomic data and the need to study increasingly complex...
Population genetics is transitioning into a data-driven discipline thanks to the availability of large-scale genomic data and the need to study increasingly complex evolutionary scenarios. With likelihood and Bayesian approaches becoming either intractable or computationally unfeasible, machine learning, and in particular deep learning, algorithms are emerging as popular techniques for population genetic inferences. These approaches rely on algorithms that learn non-linear relationships between the input data and the model parameters being estimated through representation learning from training data sets. Deep learning algorithms currently employed in the field comprise discriminative and generative models with fully connected, convolutional, or recurrent layers. Additionally, a wide range of powerful simulators to generate training data under complex scenarios are now available. The application of deep learning to empirical data sets mostly replicates previous findings of demography reconstruction and signals of natural selection in model organisms. To showcase the feasibility of deep learning to tackle new challenges, we designed a branched architecture to detect signals of recent balancing selection from temporal haplotypic data, which exhibited good predictive performance on simulated data. Investigations on the interpretability of neural networks, their robustness to uncertain training data, and creative representation of population genetic data, will provide further opportunities for technological advancements in the field.
Topics: Deep Learning; Bayes Theorem; Neural Networks, Computer; Algorithms; Genetics, Population
PubMed: 36683406
DOI: 10.1093/gbe/evad008 -
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 -
Biological Reviews of the Cambridge... Dec 2021Dominance is a basic property of inheritance systems describing the link between a diploid genotype at a single locus and the resulting phenotype. Models for the... (Review)
Review
Dominance is a basic property of inheritance systems describing the link between a diploid genotype at a single locus and the resulting phenotype. Models for the evolution of dominance have long been framed as an opposition between the irreconcilable views of Fisher in 1928 supporting the role of largely elusive dominance modifiers and Wright in 1929, who viewed dominance as an emerging property of the structure of enzymatic pathways. Recent theoretical and empirical advances however suggest that these opposing views can be reconciled, notably using models investigating the regulation of gene expression and developmental processes. In this more comprehensive framework, phenotypic dominance emerges from departures from linearity between any levels of integration in the genotype-to-phenotype map. Here, we review how these different models illuminate the emergence and evolution of dominance. We then detail recent empirical studies shedding new light on the diversity of molecular and physiological mechanisms underlying dominance and its evolution. By reconciling population genetics and functional biology, we hope our review will facilitate cross-talk among research fields in the integrative study of dominance evolution.
Topics: Genes, Dominant; Genetics, Population; Genotype; Models, Genetic; Phenotype
PubMed: 34382317
DOI: 10.1111/brv.12786 -
Trends in Ecology & Evolution Sep 2020Genetic redundancy has been defined in many different ways at different levels of biological organization. Here, we briefly review the general concept of redundancy and... (Review)
Review
Genetic redundancy has been defined in many different ways at different levels of biological organization. Here, we briefly review the general concept of redundancy and focus on the evolutionary importance of redundancy in terms of the number of genotypes that give rise to the same phenotype. We discuss the challenges in determining redundancy empirically, with published experimental examples, and demonstrate the use of the C-score metric to quantify redundancy in evolution studies. We contrast the implicit assumptions of redundancy in quantitative versus population genetic models, show how this contributes to signatures of allele frequency shifts, and highlight how the rapid accumulation of genome-wide association data provides an avenue for further understanding the prevalence and role of redundancy in evolution.
Topics: Biological Evolution; Evolution, Molecular; Genetics, Population; Genome; Genome-Wide Association Study; Genotype; Models, Genetic; Multigene Family; Phenotype; Selection, Genetic
PubMed: 32439075
DOI: 10.1016/j.tree.2020.04.009 -
Annual Review of Genomics and Human... Aug 2020Nervous systems allow animals to acutely respond and behaviorally adapt to changes and recurring patterns in their environment at multiple timescales-from milliseconds... (Review)
Review
Nervous systems allow animals to acutely respond and behaviorally adapt to changes and recurring patterns in their environment at multiple timescales-from milliseconds to years. Behavior is further shaped at intergenerational timescales by genetic variation, drift, and selection. This sophistication and flexibility of behavior makes it challenging to measure behavior consistently in individual subjects and to compare it across individuals. In spite of these challenges, careful behavioral observations in nature and controlled measurements in the laboratory, combined with modern technologies and powerful genetic approaches, have led to important discoveries about the way genetic variation shapes behavior. A critical mass of genes whose variation is known to modulate behavior in nature is finally accumulating, allowing us to recognize emerging patterns. In this review, we first discuss genetic mapping approaches useful for studying behavior. We then survey how variation acts at different levels-in environmental sensation, in internal neuronal circuits, and outside the nervous system altogether-and then discuss the sources and types of molecular variation linked to behavior and the mechanisms that shape such variation. We end by discussing remaining questions in the field.
Topics: Evolution, Molecular; Genetics, Behavioral; Genetics, Population; Humans; Polymorphism, Genetic; Selection, Genetic
PubMed: 32283949
DOI: 10.1146/annurev-genom-111219-080427 -
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