How to deal with hyphens in .bib files?

The dash character in the line

title = {{A Quantitative Survey of Local Adaptation and Fitness Trade‐Offs}},

is indeed not a "simple" dash (ASCII code 45), but a unicode-encoded character (code U+2010).

Observe that this is a LaTeX issue, not a BibTeX issue.

You can do several things. E.g.,

• Do a global search of ‐ (U+2010) and replace all instances with - (U+0045).

• Switch to a TeX engine and a font family that can handle the character U+2010 directly. In the following example, LuaLaTeX and the EB Garamond font are used.

% !TEX TS-program = lualatex
\documentclass{article}

\usepackage{filecontents}
\begin{filecontents}{mybib.bib}
@article{Hereford2009,
author  = {Hereford, Joe},
doi     = {10.1086/597611},
file    = {:Users/remi/Documents/Biologie/Literature/BackgroundSelection/597611.pdf:pdf},
issn    = {0003-0147},
journal = {The American Naturalist},
keywords= {adaptation,genetic drift,genotype-by-environment interaction,local,natural selection,population divergence,reciprocal},
number  = {5},
pages   = {579--588},
title   = {{A Quantitative Survey of Local Adaptation and Fitness Trade‐Offs}},
url     = {http://www.jstor.org/stable/10.1086/597611},
volume  = {173},
year    = {2009}
}
\end{filecontents}

\usepackage{natbib}
\bibliographystyle{apalike} % choose your bibliography style

\usepackage{fontspec}
\setmainfont{EB Garamond}

\begin{document}
\nocite{*}
\bibliography{mybib}
\end{document}

I can reproduce the faulty output if I have \usepackage[applemac]{inputenc} in my document.

\begin{filecontents*}{\jobname.bib}
@article{Hereford2009,
author = {Hereford, Joe},
doi = {10.1086/597611},
file = {:Users/remi/Documents/Biologie/Literature/BackgroundSelection/597611.pdf:pdf},
issn = {0003-0147},
journal = {The American Naturalist},
keywords = {adaptation,genetic drift,genotype-by-environment interaction,local,natural selection,population divergence,reciprocal},
number = {5},
pages = {579--588},
title = {{A Quantitative Survey of Local Adaptation and Fitness Trade‐Offs}},
url = {http://www.jstor.org/stable/10.1086/597611},
volume = {173},
year = {2009}
}
\end{filecontents*}

\documentclass{article}
\usepackage[T1]{fontenc}
\usepackage[applemac]{inputenc}

\begin{document}

\cite{Hereford2009}

\bibliographystyle{plain}

\bibliography{\jobname}

\end{document}

If I change this to

\begin{filecontents*}{\jobname.bib}
@article{Hereford2009,
author = {Hereford, Joe},
doi = {10.1086/597611},
file = {:Users/remi/Documents/Biologie/Literature/BackgroundSelection/597611.pdf:pdf},
issn = {0003-0147},
journal = {The American Naturalist},
keywords = {adaptation,genetic drift,genotype-by-environment interaction,local,natural selection,population divergence,reciprocal},
number = {5},
pages = {579--588},
title = {{A Quantitative Survey of Local Adaptation and Fitness Trade‐Offs}},
url = {http://www.jstor.org/stable/10.1086/597611},
volume = {173},
year = {2009}
}
\end{filecontents*}

\documentclass{article}
\usepackage[T1]{fontenc}
\usepackage[utf8,applemac]{inputenc}

\DeclareUnicodeCharacter{2010}{-}

\begin{document}

\cite{Hereford2009}

\bibliographystyle{plain}

\inputencoding{utf8}
\bibliography{\jobname}
\inputencoding{applemac} % just in case something follows

\end{document}

I get correct output.

It's best if you start using UTF-8 for all of your documents.