DOI: 10.5061/dryad.7n6vg10
title: Data from: Polygenic adaptation: from sweeps to subtle frequency shifts

description: Evolutionary theory has produced two conflicting paradigms for the
 adaptation of a polygenic trait. While population genetics views
 adaptation as a sequence of selective sweeps at single loci underlying the
 trait, quantitative genetics posits a collective response, where
 phenotypic adaptation results from subtle allele frequency shifts at many
 loci. Yet, a synthesis of these views is largely missing and the
 population genetic factors that favor each scenario are not well
 understood. Here, we study the architecture of adaptation of a binary
 polygenic trait (such as resistance) with negative epistasis among the
 loci of its basis. The genetic structure of this trait allows for a full
 range of potential architectures of adaptation, ranging from sweeps to
 small frequency shifts. By combining computer simulations and a newly
 devised analytical framework based on Yule branching processes, we gain a
 detailed understanding of the adaptation dynamics for this trait. Our key
 analytical result is an expression for the joint distribution of mutant
 alleles at the end of the adaptive phase. This distribution characterizes
 the polygenic pattern of adaptation at the underlying genotype when
 phenotypic adaptation has been accomplished. We find that a single
 compound parameter, the population-scaled background mutation rate
 $\Theta_{bg}$, explains the main differences among these patterns. For a
 focal locus, $\Theta_{bg}$ measures the mutation rate at all redundant
 loci in its genetic background that offer alternative ways for adaptation.
 For adaptation starting from mutation-selection-drift balance, we observe
 different patterns in three parameter regions. Adaptation proceeds by
 sweeps for small $\Theta_{bg} \lesssim 0.1$, while small polygenic allele
 frequency shifts require large $\Theta_{bg} \gtrsim 100$. In the large
 intermediate regime, we observe a heterogeneous pattern of partial sweeps
 at several interacting loci.
description: Simulation Package for
 Polygenic AdaptationIn the simulation
 package we provide two different simulation programs. They track allele
 frequency changes of a polygenic, binary trait with complete or relaxed
 redundancy within the genetic basis of the trait. These programs are given
 in the scripts folder. The output of the simulations will be written to
 the output folder. Simulation code is devided in several parts: (1) R
 file: ParameterInput.r Here all parameters can be entered. (2) C++
 Methods: - PolygenAdaptation_RedundantTrait.cpp polygenic adaptation of a
 binary trait with complete redundancy within its genetic basis, linkage
 equilibrium between the loci, haploid individuals -
 PolygenAdaptation_RelaxedRedundancyTrait.cpp polygenic adaptation with
 relaxed redundancy, linkage equilibrium between the loci, haploid
 individuals (3) There are four additinal files (2 of each), - WriteFile*.r
 are needed to create a correctly readable output- into .json and .csv
 files.- RunSample*.r defines the class Run, which corresponds to one
 replicateDryad_Repository_Code.zipData for FiguresThis folder contains simulation data and summary statistics underlying the presented Figures in our manuscript. Hoellinger, Pennings, Hermisson: Polygenic Adaptation: From Sweeps to Subtle Frequency Shifts, 2019.Dryad_PLOS_Genetics_Figure_Data_FINAL.zip