Supplementary Data Read Me File: 5-20-12

The supplementary data for the paper “An Alu-based phylogeny of gibbons (Hylobatidae) consists of one Word document, titled "Supplementary Table S1", one Excel spreadsheet, titled “Supplementary Tables S2 and S3.xlsx”, and one folder, titled “Supplementary Alignments”.

The Word document contains Table S1, which details the species, common and individual names, origins, and ID numbers for all DNA samples of all individuals used in our analyses.

The Excel spreadsheet contains two worksheets.  The first, titled “Table S2 – Loci & Primers” contains the locus IDs and corresponding forward and reverse primers for all informative loci used in the study.  The second worksheet, titled “Table S3 – Matrix” contains the character matrix used to produce the phylogenetic tree reported in the paper (Figure 4).

The folder (available for download here: http://batzerlab.lsu.edu/pub2012.html) contains all of the alignments for the informative loci used in the sequence analysis and primer design portions of the study.  The filename for each alignment is the same as the locus ID for each locus.  The top sequence in each alignment is always the Nomascus leucogenys leucogenys sequence we obtained from Ensemble.  Unless there was sequencing of the locus done in the Batzer Lab, the order of the sequences below the Ensemble sequence is always Human, Chimp, Orangutan (abbreviated Orang), and Rhesus.  There are instances in which Rhesus or Orangutan didn’t return results on BLAT, so in those cases that sequence was eliminated from the alignment.  In some of the alignments, instead of “Human”, “Chimp”, etc., the sequence names are instead the assemblies used to retrieve orthologous sequences with BLAT (e.g. H18…, PanTro…, etc.), but the order of the sequences from top to bottom remains the same.  Sequences obtained via DNA sequencing in the Batzer Lab are also included in their alignments.

Note that for locus HlM6B, only the 5' flanking was able to be matched on BLAT, so for the reverse primer, a primer was designed in a highly conserved portion of the 3' flanking that occurred in Human, Chimp, Orang, and Rhesus.  This reverse primer just happened to fall in a conserved spot in the gibbon sequence as well and we were able to amplify this locus in gibbons.