Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks

Genetics
Lynsey BunnefeldKonrad Lohse

Abstract

The advent of the genomic era has necessitated the development of methods capable of analyzing large volumes of genomic data efficiently. Being able to reliably identify bottlenecks--extreme population size changes of short duration--not only is interesting in the context of speciation and extinction but also matters (as a null model) when inferring selection. Bottlenecks can be detected in polymorphism data via their distorting effect on the shape of the underlying genealogy. Here, we use the generating function of genealogies to derive the probability of mutational configurations in short sequence blocks under a simple bottleneck model. Given a large number of nonrecombining blocks, we can compute maximum-likelihood estimates of the time and strength of the bottleneck. Our method relies on a simple summary of the joint distribution of polymorphic sites. We extend the site frequency spectrum by counting mutations in frequency classes in short sequence blocks. Using linkage information over short distances in this way gives greater power to detect bottlenecks than the site frequency spectrum and potentially opens up a wide range of demographic histories to blockwise inference. Finally, we apply our method to genomic data from a...Continue Reading

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Citations

Jul 4, 2017·ELife·Daniel B Weissman, Oskar Hallatschek
Oct 29, 2017·Proceedings of the National Academy of Sciences of the United States of America·Andrea BenazzoGiorgio Bertorelle
Dec 31, 2015·Genetics·Konrad LohseNicholas H Barton
Apr 18, 2017·Genetics·Aaron P Ragsdale, Ryan N Gutenkunst
Jun 28, 2018·Proceedings of the National Academy of Sciences of the United States of America·Lynsey BunnefeldKonrad Lohse
Aug 3, 2019·Nature Communications·Alexander MackintoshKonrad Lohse
Sep 13, 2017·G3 : Genes - Genomes - Genetics·Annabel C BeichmanKirk E Lohmueller
Jul 27, 2018·Theoretical Population Biology·Raazesh Sainudiin, Amandine Véber
Jul 13, 2021·Molecular Ecology·William WaltonKonrad Lohse
Sep 6, 2021·Molecular Ecology·Rebecca S TaylorPaul J Wilson

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Software Mentioned

msHOT
SAMtools
Mathematica
ms
MUCH

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