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\begin{document}

\title{Fishing for DNA? Designing baits for population genetics in target
enrichment experiments: guidelines, considerations and the new tool
supeRbaits}



\author[1]{Belen Jimenez Mena}%
\author[1]{Hugo Flávio}%
\author[1]{Romina Henriques}%
\author[1]{Alice Manuzzi}%
\author[2]{Miguel Ramos}%
\author[1]{Dorte Meldrup}%
\author[3]{Janette Edson}%
\author[4]{Snaebjorn Palsson}%
\author[4]{Guðbjörg Ásta  Ólafsdóttir}%
\author[3]{Jennifer Ovenden}%
\author[1]{Einar Nielsen}%
\affil[1]{Technical University of Denmark}%
\affil[2]{University of Porto}%
\affil[3]{The University of Queensland}%
\affil[4]{University of Iceland}%


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  \date{May 25, 2024}


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\begin{abstract}
Targeted sequencing is an increasingly popular Next Generation
Sequencing (NGS) approach for studying populations, through focusing
sequencing efforts on specific parts of the genome of a species of
interest. Methodologies and tools for designing targeted baits are
scarce but in high demand. Here, we present specific guidelines and
considerations for designing capture sequencing experiments for
population genetics for both neutral genomic regions and regions subject
to selection. We describe the bait design process for three diverse fish
species: Atlantic salmon, Atlantic cod and tiger shark, which was
carried out in our research group, and provide an evaluation of the
performance of our approach across both historical and modern samples.
The workflow used for designing these three bait sets has been
implemented in the R-package supeRbaits, which encompass our
considerations and guidelines for bait design to benefit researchers and
practitioners. The supeRbaits R package is user-friendly and versatile.
It is written in C++ and implemented in R. supeRbaits and its manual are
available from Github: https://github.com/BelenJM/supeRbaits%
\end{abstract}%



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