Table 1. Specimens subjected to 454-FLX pyrosequencing, number of reads and ratio of endogenous and contaminant sequences obtained.

Specimen	N reads	% endogenous seqs	% human seqs
Neandertal	155,676	0.32% (N = 503)	*
Neolithic	168,998	0.66% (N = 1,117)	*
Lynx	361,151	0.11% (N = 414)	1.4% (N = 5,078)
Myotragus	96,357	0.27% (N = 260)	0.35% (N = 337)

*: in the case of human samples, it is impossible to discern a priori which sequences are endogenous and which are human contaminants. However, we have mitochondrial DNA estimates of the maximum potential contamination <1% in the Neandertal sample and <5% in the Neolithic sample.