Recovery success of seven focal genes, with comparison of <i>de novo</i> and reference-based assemblies.

<p>For protein-coding genes, values in cells are the fractional recovery of the query sequence (for <i>de novo</i> assemblies) or reference sequence (for reference-based assemblies). Cells are shaded in a gray-scale ramp with black recovery of 100% of the fragment length and white 0%. For ribosomal genes, values in cells are the fractional recovery of the query sequence (for <i>de novo</i> assemblies), and for reference-based assemblies, values in cells represent the percentage recovery of the assembly relative to the <i>de novo</i> assembly (as opposed to the query or reference sequence). Values less than 1.0 indicate that some bases were missing from the reference-based assembly. A comparison of the <i>de novo</i> assembly sequence to the reference sequence shows that those missing regions are very different between the museum sample and the reference, and thus that region of the reference-based assembly failed. If there are no base differences between the reference-based and the <i>de novo</i> assemblies, the cell is colored using a blue ramp, with pure blue indicating 100% recovery. If there are base differences, the cell is colored red, with the number of base differences shown in parentheses. An asterisk (*) indicates that the sequence so marked is not in the predicted place in the maximum likelihood tree including the DeNovo, FarRef, and NearRef sequences; two asterisks (**) indicates that this placement failure is supported by a bootstrap value of over 50%. “-”indicates that no attempt was made to find this fragment in the assemblies. Four specimens with less than 34 million reads have specimen abbreviation and age shown in gray.