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. 2014 May 8;31(8):2108–2123. doi: 10.1093/molbev/msu155

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© The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Fig. 1. — (A) Possible variant sites within a four-way alignment of the orthologous and gametologous sequences from human and chimpanzee sex chromosomes. Different types of sites are shown: C, C-site or conversion site; N, N-site or nonconversion site; S, S-site (or Singleton); M, multiple mutation site; W, other complex site. Invariant sites are not shown. Classification according to Kijima and Innan (2010). (B) Different molecular mechanisms for the formation of variable sites. A type-S site may arise if a mutation occurs in one sex chromosome after human–chimpanzee speciation, whereas an N-site may be generated by a mutation occurring before speciation. If a gene conversion event involves a type-N nucleotide, it generates an S-site, whereas a conversion of an S-site may generate a C-nucleotide or an invariant site depending on the direction of conversion. M- and W-sites may arise only with multiple mutational events.