Finally, the identification of specific marker chromosomes in certain karyomorphs, which could be tracked by unique morphologies, banding characteristics or repetitive DNAs
distribution patterns, could be informative with respect to the genomic rearrangements that occurred during the evolutionary history of Synbranchus and help understand
the phylogenetic relationships between the karyomorphs. Thus, karyomorphs A and B share the exclusive second metacentric pair containing one interstitial heterochromatic
block within the long arm and the first submetacentric pair containing two interstitial heterochromatic blocks within the long arm. Besides that, both had the same constant 18S rDNA sites-bearing chromosomes (pair 15). Marker chromosomes also confirm the proximity between karyomorphs C and E, which share the first subtelocentric pair containing one interstitial heterochromatic block within the long arm. Moreover, karyomorph C (Rio
Branco) and E have constant sites of 18S rDNA in this same pair. However, the presence of similar chromosomes in distinct lineages can be misleading; for example, a small
metacentric pair was identified in karyomorphs B, C, D,and E, although the origin of this pair in karyomorph B was independent of the others. Besides, the detection of
an additional 5S rDNA-bearing acrocentric pair observed in individuals belonging to karyomorph C-Rio Branco and some 18S rDNA chromosomal variants of karyomorphs
C-Cerrito and E, that evidence sinteny between both ribosomal sites also casts doubt on the real homology of the 5S rDNA-bearing chromosomes in all karyomorphs. Therefore, the nature of the homology between these specific chromosomes remains unclear, and it highlights the importance of phylogenetic and/or chromosome painting analyses to reduce possible misinterpretations of karyoevolution in organisms.