The present study represents the first one that comprehensively characterizes the karyotype of TCR. In general, previous homologies of HSA and TCR chromosomes could be confirmed . However, in this study, homologous regions for TCR chromosomes 4, 10, 11, 14, 17, 18 and 21 (that were not studied before)  were specifically aligned to their HSA-homologous. In contrast to  NOR was mapped here to the fusion points of HSA 14 and HSA 15, i.e. TCR 5 and not TCR 15. In our two studied individuals derived from Thailand, no differences in TCR 1 banding pattern were seen, which is in accordance with the literature .
For the first time, the exact breakpoints could be determined for the extremely rearranged karyotype of TCR, in comparison to HSA. In fact, 69 evolutionary conserved breakpoints were determined in a male TCR and confirmed in a female individual, excluding Y1 and Y2 chromosomes, obviously.
In this study no special attention was given to the centromeric regions of TCR, i.e. they were not detailed characterized as in other studies e.g. by  or . However, a first impression is provided in which centromeres kept their positions during evolution from common ancestors to HSA and TCR and were neo-centromeres (Table 1), i.e. ~50% of them stayed at the same positions and ~50% moved either in one of the two species or in both. As expected from the literature , even the centromeric regions that kept their positions did not have the identical alphoid sequences in HSA and TCR.
Previous studies in human chromosomal rearrangements revealed that the majority of them (70-88%) are found in G-light sub-bands . In contrast only 37 (45.5%) of the 69 evolutionary conserved breakpoints of TCR were located in GTG-light bands (Table 2). However, 70% of the here observed TCR breakpoints colocalized with human fragile sites  supporting their potential role in the “Fragile Breakage Model”  and in the formation of evolutionary chromosomal rearrangements [21–26] (Table 2).
Concerning evolution it is interesting to report that in TCR and in HLA 11 evolutionary conserved breakpoints are identical and 15 more are most likely in concordance to each other. Even more interesting, 6 identical and 2 most likely identical evolutionary conserved breakpoints were identified in TCR and in GGO (Table 2). These findings need to be confirmed in further studies by locus-specific probes, and if confirmed, they will be very useful for the reconstruction of a common ancestral karyotype. Compared to the postulated Hominidea ancestral karyotype proposed by , only four chromosomes remained unchanged in TCR, i.e. chromosomes 4, 7, 11 and X, eleven chromosomes underwent only intrachromosomal changes like inversions (TCR 2, 3, 10, 12, 13, 14, 17, 18, 19, 20, 21) and two TCR chromosomes resulted from a fusion of ancestral chromosomes (TCR 5 and 15).
Interestingly, the regions between TCR 1 and TCR Y1 and TCR Y2 being homologous to HSA 5 were shown to be subject to different evolutionary conserved rearrangements. Broadly speaking, TCR Y1 is homologous to TCR 1p and TCR Y2 to TCR 1q. However, each arm of chromosome TCR 1 underwent a further paracentric inversion, most likely being important to separate the sex chromosomes from the chromosome 1 during meiosis. Thus, a XY1Y2 sex chromosome system is present in TCR, and not an X1X2Y1Y2 system as initially suggested . However, as in TCR from Indonesia, two other forms of TCR 1 chromosome could be found . Therefore, the existence of an X1X2Y1Y2 system cannot be completely excluded by this study.
The sex determination system in mammals is usually highly conserved as XY-system. However, multiple sex chromosome systems, like the one present in TCR and few other apes [27, 28] are exceptionally found in some species of e.g. the orders Insectivora, Chiroptera, Artiodactyla, Rodentia , and in marsupials . In general, constitutional Y-chromosome / autosome translocations in human appear de novo and have a deleterious effect and, although the infertility is the only common feature, other clinical symptoms can also be observed depending on the involved breakpoints . In such cases, the infertility is thought to be a result of disruption of the sex vesicle during meiosis . From this point of view it is hard to imagine conditions which are in favor of developing a multiple sex- from an XY-chromosome system. On the other hand, in population genetic models of Y-autosome and X-autosome rearrangements the population can gain a selective advantage under a wide range of conditions. If they can invade the population, Y-autosome rearrangements always spread to fixation, whereas X-autosome rearrangements may be maintained as stable polymorphisms” . The XY1Y2 sex chromosome system observed in TCR fits well into the suggestions of  that (i) female meiotic drive is the major contribution to the evolution of neo-sex chromosomes and (ii) that “in mammals, the XY1Y2 sex chromosome system is more prevalent in species with karyotypes of more biarmed chromosomes” rather than in species with acrocentric chromosomes. Research on meiotic behavior of such sex systems is scarce; however, one study on Bolivian owl monkey (Aotus spec.) showed that no XY pairing was observable but the Y-chromosomes formed trivalents with an autosome during gametogenesis .