Some European urodeles have up to 10% of their genomes composed of a single class of satellite DNA. The satellite is a 32/33 bp sized, tandemly repeated fragment and is supposedly non-functional.
DNA-sequence analysis shows four types of satellites (1, 2, 3 and 4). Their repeat sequence is distinctly non-random as 1414 etc. and 2323 etc. Other combinations (ie. 12, 13, 24 and 34) appear absent or rare.
Phylogenetic analysis at the level of the satellite shows that the types are ordered in an (unrooted) network as 1-2-3-4. Phylogenetic analysis at the species level indicates that the 14 character state is derived and the 23 character state is ancestral. Both the 14 and 23 'supertypes' are old (estimated age 2-5 and ca. 10 million years, respectively).
One particular feature that existing supertypes have in common is a combined size of 65 bp, with some further non-random association of nucleotide character states at nine positions (out of 29 - ignoring the HaeIII restriction site used to generate the fragments).
I am searching for a mechanistic explanation for the existence of the 14 and 23 supertypes as might be suggested from conserved sequence information. I would appreciate receiving suggestions how to approach this problem. As a classical taxonomist I am unfamiliar with (the software in) this field.
J. W. (Pim) Arntzen
Universidade do Porto
Unidade de Genetica Animal e Conservacao
Campus Agrario de Vairao
Rua de Monte, Crasto, Vairao
4480 Vila do Conde