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I understand that if I typeset using Lualatex or Xelatex, and include the following in the preamble:

\usepackage{fontspec}
\setmainfont{XYZ}

Then system-wide non-latex fonts can be used (substituted for XYZ in the above).

My question is, by using fontspec, does this mean that ligatures and kerning, that make LaTeX document otherwise of a higher 'typeset' quality would be essentially discarded for the convenience of getting access to a larger number of fonts?

Does this mean that in the above, one is essentially settling for 2nd best?

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    No: a modern opentype font has many ligatures and font shaping possibilities specified within the font. In addition if you also want classic TeX convenience ligatures such as -- to ndash you can use \setmainfont[Ligatures=TeX]{XYZ} – David Carlisle Dec 2 '13 at 0:29
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    If you choose a font that doesn't have ligatures, you're not going to get ligatures. See the manual for more information about which ligatures you might want to use if the font has them. What are the other 'subtleties'? – jon Dec 2 '13 at 0:31
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    OpenType font files -- which I assume you're interested in -- generally include detailed kerning tables, and fontspec (and a subsidiary package called luaotfload) will make use of these tables if they're present. In addition, it is possible to set up so-called "feature files" that override and/or augment the settings shipped with the font family. – Mico Dec 2 '13 at 10:30
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A modern opentype font has many ligatures and font shaping possibilities specified within the font. In addition if you also want classic TeX convenience ligatures such as -- to ndash you can use

\setmainfont[Ligatures=TeX]{XYZ}

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