SUPPLEMENTAL FILE SF1
(Refer to Supplemental table ST1, ST4 and ST5)

Chromosomal flow changes from Hominoidea ancestor to Hylobatidae ancestor
(click to enlarge each Figure)

The 9 slides of Supplemental File 1 report the flow of chromosomal changes from the Hominoidea ancestor (ANC in the slides, as reconstructed in Figure 4) to the Hylobatidae ancestor (HyA, as shown in Figure 3). HyA chromosomes which are derived from different segments of the same ancestral Hominoidea chromosome(s) are grouped in the same slide. The present interpretation was compared with literature data [essentially  (Muller et al. 2003) and (Nie et al. 2001)], which were based on reciprocal painting experiments. This latter approach can easily miss small chromosomal fragments or marker order arrangement, that can be crucial in suggesting alternative interpretations of the flow of rearrangements. The Figures are based on extensive FISH experiments, providing detailed information on marker position and reciprocal arrangement, and orientation of syntney  blocks in NLE (Roberto et al. 2007) and HLA (present paper). H. hoolock was characterized only by reciprocal painting (Nie et al. 2001). A detailed analysis of this species by high-resolution BAC-FISH would be helpful to further refine  hypothetical reconstructions of the chromosome configuration of the HyA. Some Figures are self-explanatory because the rearrangements are relatively simple, and no comment is added.

Green hatched boxes include chromosomes involved in the rearrangement; blue dotted boxes contain intermediate chromosomes, while red boxes indicate the final chromosomal form. Red numbers internal to chromosomes indicate the human chromosome corresponding to that region. Numbers followed by a letter on the right of chromosomes indicate a specific human BAC as reported in both ST1 and ST5 Supplemental Tables. The numbers on the right of the final Hylobatidae ancestor chromosome (HyA) represent arbitrarily chosen points useful in indicating its composition, as reported in ST4 Supplemental Table. Usually they correspond to a BAC. When found at the borders of the synteny blocks they identify two BACs facing each other following a rearrangement. The symbol :: (double dots) indicates breakage and reunion. NEC stands for new evolutionary centromere.    = Inactivated centromere

The Hylobatidae Ancestral Kayotype (HyAK) is depicted in Fig.3.

References:
- Misceo, D., Cardone, M.F., Carbone, L., D'Addabbo, P., de Jong, P.J., Rocchi, M., and Archidiacono, N. 2005.
Evolutionary history of chromosome 20. Mol. Biol. Evol. 22: 360-366.
- Muller, S., Hollatz, M., and Wienberg, J. 2003.
Chromosomal phylogeny and evolution of gibbons (Hylobatidae). Hum. Genet. 113: 493-501.
- Nie, W., Rens, W., Wang, J., and Yang, F. 2001.
Conserved chromosome segments in Hylobates hoolock revealed by human and H. leucogenys paint probes. Cytogenet. Cell Genet. 92: 248-253.
- Roberto, R., Capozzi, O., Wilson, R.K., Mardis, E.R., Lomiento, M., Tuzun, E., Cheng, Z., Mootnick, A.R., Archidiacono, N., Rocchi, M. et al. 2007.
Molecular refinement of gibbon genome rearrangement. Genome Res. 17: 249-257.

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