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\begin{document}

\title{The short-term, genome-wide effects of indirect selection deserve study:
a response to Charlesworth and Jensen (2022)}



\author[1]{Zachariah Gompert}%
\author[2]{Jeff Feder}%
\author[3]{Patrik Nosil}%
\affil[1]{Utah State University}%
\affil[2]{U. Notre Dame}%
\affil[3]{Affiliation not available}%


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  \date{May 15, 2024}


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\begin{abstract}
We recently published a paper quantifying the genome-wide consequences
of natural selection, including the effects of indirect selection due to
the correlation of genetic regions (neutral or selected) with directly
selected regions (Gompert et al. 2022). In their critique of our paper,
Charlesworth \& Jensen (2022) make two main points: (i) indirect
selection is equivalent to hitchhiking and thus well documented (i.e.,
our results are not novel), and (ii) that we do not demonstrate the
source of linkage disequilibrium (LD) between SNPs and the Mel-Stripe
locus in the Timema cristinae experiment we analyze. As we discuss in
detail below, neither of these are substantial criticisms of our work.%
\end{abstract}%



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