Data from: Polygenic adaptation: from sweeps to subtle frequency shifts
| Main Authors: | Höllinger, Ilse, Pennings, Pleuni S., Hermisson, Joachim |
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| Format: | info dataset Journal |
| Terbitan: |
, 2019
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/4986176 |
Daftar Isi:
- 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.
- 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