Rewriting Human History and Empowering Indigenous Communities with Genome Editing Tools.

Appropriate empirical-based evidence and detailed theoretical considerations should be used for evolutionary explanations of phenotypic variation observed in the field of human population genetics (especially Indigenous populations). Investigators within the population genetics community frequently overlook the importance of these criteria when associating observed phenotypic variation with evolutionary explanations. A functional investigation of population-specific variation using cutting-edge genome editing tools has the potential to empower the population genetics community by holding "just-so" evolutionary explanations accountable. Here, we detail currently available precision genome editing tools and methods, with a particular emphasis on base editing, that can be applied to functionally investigate population-specific point mutations. We use the recent identification of thrifty mutations in the CREBRF gene as an example of the current dire need for an alliance between the fields of population genetics and genome editing

Coalescence 2.0: a multiple branching of recent theoretical developments and their applications

Population genetics theory has laid the foundations for genomics analyses including the recent burst in genome scans for selection and statistical inference of past demographic events in many prokaryote, animal and plant species. Identifying SNPs under natural selection and underpinning species adaptation relies on disentangling the respective contribution of random processes (mutation, drift, migration) from that of selection on nucleotide variability. Most theory and statistical tests have been developed using the Kingman coalescent theory based on the Wright-Fisher population model. However, these theoretical models rely on biological and life-history assumptions which may be violated in many prokaryote, fungal, animal or plant species. Recent theoretical developments of the so called multiple merger coalescent models are reviewed here ({\Lambda}-coalescent, beta-coalescent, Bolthausen-Snitzman, {\Xi}-coalescent). We explicit how these new models take into account various pervasive ecological and biological characteristics, life history traits or life cycles which were not accounted in previous theories such as 1) the skew in offspring production typical of marine species, 2) fast adapting microparasites (virus, bacteria and fungi) exhibiting large variation in population sizes during epidemics, 3) the peculiar life cycles of fungi and bacteria alternating sexual and asexual cycles, and 4) the high rates of extinction-recolonization in spatially structured populations. We finally discuss the relevance of multiple merger models for the detection of SNPs under selection in these species, for population genomics of very large sample size and advocate to potentially examine the conclusion of previous population genetics studies.Comment: 3 Figure

Genes in the postgenomic era

We outline three very different concepts of the gene - 'instrumental', 'nominal', and 'postgenomic'. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype

Implications of fisheries during the spawning season for the sustainable management and recovery of depleted fish stocks: a conceptual framework

Fishing during the spawning season may negatively affects the reproductive potential and reproductive dynamics of exploited fish stocks due to a variety of mechanisms such as the disturbance of the natural spawning behaviour, effects on the age, size and sex composition of the spawning population and effects on the population genetics. The effect may differ between species in relation to the spawning strategy and population dynamic characteristics. Based on first principles of reproductive biology, population biology and fishing methods, a theoretical framework is developed on the effects of fishing during the spawning period. This framework is used to structure a review of the available scientific evidence. Implications of the findings on the recovery of depleted fish stocks and the sustainability of exploitation will be discussed and illustrated for a selection of North Sea fish stocks (flatfish, roundfish and pelagic)

The theoretical approach to population genetics

Population genetics is the study of gene variation within or between populations. It deals with the allele frequencies in a given population and the forces, which might change this. Such forces, which are known to alter and change the allele frequency are mutation, naturalselection, and genetic drift, among others. Understanding population genetics is aimed at those who have at least an intermediate knowledge of the natural sciences and a basic understanding of mathematics

Populations in statistical genetic modelling and inference

What is a population? This review considers how a population may be defined in terms of understanding the structure of the underlying genetics of the individuals involved. The main approach is to consider statistically identifiable groups of randomly mating individuals, which is well defined in theory for any type of (sexual) organism. We discuss generative models using drift, admixture and spatial structure, and the ancestral recombination graph. These are contrasted with statistical models for inference, principle component analysis and other `non-parametric' methods. The relationships between these approaches are explored with both simulated and real-data examples. The state-of-the-art practical software tools are discussed and contrasted. We conclude that populations are a useful theoretical construct that can be well defined in theory and often approximately exist in practice