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Methods for Outbreaks Using Genomic Data
Published in Leonhard Held, Niel Hens, Philip O’Neill, Jacco Wallinga, Handbook of Infectious Disease Data Analysis, 2019
Don Klinkenberg, Caroline Colijn, Xavier Didelot
Ancestries in the Wright-Fisher model are described by a stochastic process starting at the tips and going backwards in time, generation by generation. The model assumes that each lineage in generation has a random parent in generation , independent of the parents of other lineages. As a consequence, if the population size in each generation is equal to , two lineages in generation g have the same parent in generation with probability , so the distribution of the number of generations back in time until two lineages share a most recent common ancestor (that the two lineages coalesce), is a geometric distribution with mean . To translate the number of generations to real time, the mean should be multiplied by the generation interval , resulting in the effective population size .
Mitochondrial DNAs and Phylogenetic Relationships
Published in S. K. Dutta, DNA Systematics, 2019
Following neutral gene theory, the long-term average of the rate of substitution of a base pair mutation in cell generations is equal to the rate of neutral base substitution. The influence of random genetic drift upon the rate of fixation, i.e., base pair substitution or loss in a population, together with the expectations of gene diversity within populations, is heavily dependent upon the effective population size, Neo, of organelle genes. This represents the long-term average of the number of organelle genes which contribute to subsequent generations. Neo is defined for the organelle genes as
Some Case Histories
Published in Jacques Derek Charlwood, The Ecology of Malaria Vectors, 2019
Historical fluctuations in effective population size (Ne) can be inferred from the genomes of extant individuals. From such data, a decline in the A. gambiae from Kenya was inferred to have occurred before the wide-scale use of nets for control. In Tanzania, a population decline was observed in the absence of any intervention and in Furvela a similar decline was seen (Figure 16.12).
From old markers to next generation: reconstructing the history of the peopling of Sardinia
Published in Annals of Human Biology, 2021
Carla Maria Calò, Giuseppe Vona, Renato Robledo, Paolo Francalacci
The maternally inherited mtDNA undergoes less severe genetic drift in respect to Y chromosomes because of a larger effective population size: in many human populations more females than males have offspring, but with a smaller number of children, whereas just a few males, if in dominant position, can potentially have a lot of descendants replacing other male haplotypes. The Sardinian mtDNA variability is rather consistent with the scenario observed for the Y chromosome. Indeed, the paper published by Olivieri et al. (2017) reporting the complete sequencing of more than 2,000 Sardinian mitogenomes, which includes the 1,200 individuals sampled for the Y chromosome analysis of Francalacci et al. (2013), shows that some rare maternal lineages (K1a2d and U5b1i1, which together comprise almost 3% of modern samples) might have been on the island already in pre-Neolithic times and possibly others that might have arrived at an early date but expanded during the early Neolithic period. Whereas U5b1i1 harbours deep ancestral roots in Palaeolithic western Europe and probably arrived on the island during the post LGM re-peopling of Europe, K1a2d is of Late Palaeolithic Near Eastern ancestry and entered Europe in the Late Glacial and postglacial periods anticipating the migration waves associated with the onset of farming (Olivieri et al. 2017).
Unusual β-Globin Haplotype Distribution in Newborns from Bengo, Angola
Published in Hemoglobin, 2019
Eliana Borges, Chissengo Tchonhi, Cátia S.B. Couto, Verónica Gomes, António Amorim, Maria João Prata, Miguel Brito
According to the available data on human societies, the ratio of male to female variance in reproductive success differs significantly with mating system, with polygynous societies showing significantly higher ratios than monogamous societies, meaning that the male mating success varies considerably more than the female mating success in a polygynous system [17]. Population genetics theory predicts that large variance in the reproductive success contributes to decrease the effective population size, to increase the inbreeding effective size (used to describe the average accumulation of identity by descent in a population), and consequently to reduce the observed heterozygosity in a population (reviewed in [18] but see also [19]). Furthermore, it is widely acknowledged that inbreeding increases the prevalence of autosomal recessive disorders in a population.
How have our clocks evolved? Adaptive and demographic history of the out-of-African dispersal told by polymorphic loci in circadian genes
Published in Chronobiology International, 2018
Arcady A. Putilov, Vladimir B. Dorokhov, Michael G. Poluektov
When alleles under selection increase in prevalence in a population, they leave distinctive genetics-based signatures (patterns of genetic variation) in DNA sequence. However, a great challenge for a search for such patterns is determining whether a given signature is due to selection or to the confounding effects of population demographic history that include bottlenecks (periods of reduced population size) and expansions (Kelley et al. 2006; Sabeti et al. 2006). Both the genetic bottleneck and the following rather rapid increase of effective population size had occurred on the way of out of Africa dispersal of the ancestors of the current Eurasians (Lippold et al. 2014). Consequently, the major purpose of the present analysis was to examine whether the expansion of human populations to higher latitudes of Eurasia led to latitude-driven shifts in allele frequency at some of polymorphic loci in circadian genes and whether such adaptive shifts might be distinguished from the shifts caused by the demographic changes in the Eurasian populations.