2021
DOI: 10.1101/2021.07.21.453231
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Modelling the spatiotemporal spread of beneficial alleles using ancient genomes

Abstract: Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regi… Show more

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Cited by 4 publications
(6 citation statements)
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References 93 publications
(161 reference statements)
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“…This means that positively selected loci, and genomic regions in linkage disequilibrium with them, are expected to have more descendant lineages which can explore space and travel faster than neutral ones. This result is similar to Fisher’s travelling wave model, where the velocity of spread is proportional to the square root of the selection coefficient (Fisher 1937; Muktupavela et al 2021; Steiner and Novembre 2022). For the purpose of inference, we often assume that the coalescent branching process and geographic location are independent (although this is not the case, see Wilkins and Wakeley 2002).…”
Section: Discussionsupporting
confidence: 80%
“…This means that positively selected loci, and genomic regions in linkage disequilibrium with them, are expected to have more descendant lineages which can explore space and travel faster than neutral ones. This result is similar to Fisher’s travelling wave model, where the velocity of spread is proportional to the square root of the selection coefficient (Fisher 1937; Muktupavela et al 2021; Steiner and Novembre 2022). For the purpose of inference, we often assume that the coalescent branching process and geographic location are independent (although this is not the case, see Wilkins and Wakeley 2002).…”
Section: Discussionsupporting
confidence: 80%
“…In the realm of population genetics, the model continues to be studied theoretically—for example, a recent extension to address finite population size shows that the speed of spread for an adaptive allele is dependent on population density as well as dispersal and selection, with the wave of advance result corresponding to the maximal speed under infinite population size [ 28 ]. The wave of advance model has only occasionally been applied to empirical data (with relevant examples being [ 32 37 ]).…”
Section: Population Genetic Models For the Spatial Spread Of Advantag...mentioning
confidence: 99%
“…Moving forward, we expect that the slendr framework will become a useful tool for comparing and benchmarking inference methods for modeling spatial genomic processes (Peter and Slatkin, 2013; Petkova, Novembre and Stephens, 2016; Marcus et al ., 2021; Muktupavela et al ., 2021). It will also enable the development of new approaches to spatial problems in population genomics.…”
Section: Discussionmentioning
confidence: 99%