DOI: 10.5061/dryad.k0p2ngfdj
title: Data from: Critical role of insertion preference for invasion trajectory of transposons

description: It is unclear how mobile DNA sequences (transposable elements, hereafter
 TEs) invade eukaryotic genomes and reach stable copy numbers, as
 transposition can decrease host fitness. This challenge is particularly
 stark early in the invasion of a TE family at which point hosts may lack
 the specialized machinery to repress the spread of these TEs. One
 possibility (in addition to the evolution of host regulation of TEs), is
 that TE families may evolve to preferentially insert into chromosomal
 regions that are less likely to impact host fitness. This may allow the
 mean TE copy number to grow while minimizing the risk for host population
 extinction. To test this, we constructed simulations to explore how the
 transposition probability and insertion preference of a TE family
 influence the evolution of mean TE copy number and host population size,
 allowing for extinction. We find that the effect of a TE family’s
 insertion preference depends on a host’s ability to regulate this TE
 family. Without host repression, a neutral insertion preference increases
 the frequency of and decreases the time to population extinction. With
 host repression, a preference for neutral insertions minimizes the
 cumulative deleterious load, increases population fitness, and,
 ultimately, avoids triggering an extinction vortex.
description: We use a non-Wright-Fisher framework in SLiM 3 (Haller and Messer
 2019) to explore how transposition probability and insertion preference
 influence the evolution of mean TE copy number and host population size .
 We consider a naïve diploid population that gains a single copy of a TE in
 the genome of a single individual (analogous to horizontal transfer). This
 TE belongs to a unique family with an assigned transposition probability
 and range of fitness effects for novel insertions that represent insertion
 preference. We generated 6 distinct models to explore this question that
 incorporate distinct biological features including host repression,
 non-autonomous TEs, and random excision of TEs. The table below highlights
 the differences between these models. Simulation results are stored in
 this data respository with a specific file for each model. The scripts for
 all simulations, job submissions, and figure visualizations can be found
 on GitHub: https://github.com/mam737/InsertionPreference_TEs.   Model Number of Chromosomes Recombination Rate Excision Non-Autonomous Elements Transposition Regulation 1 Five 1 x 10<sup>-5</sup> No No No 2 Five 1 x 10<sup>-5</sup> No No Yes 3 One 1 x 10<sup>-8</sup> No No No 4 One 1 x 10<sup>-8</sup> Yes No No 5 One 1 x 10<sup>-8</sup> No Yes No 6 One 1 x 10<sup>-8</sup> Yes Yes No
description: All data files included with submission are text files and can be
 opened with any text editor. There is a compressed (.tar.gz) file for each
 distinct model that houses its respective simulation results. Once
 unzipped, each folder will contain a series of subdirectories named after
 the specific parameter combination used to generate them. There are at
 most 169 unique parameter combinations, and, for each parameter
 combination, at most 100 technical replicates. Due to computational
 constraints, some models have fewer parameter combinations and some
 parameter combinations have fewer technical replicates. Please refer to
 the manuscript for specific details.