Originally posted by UTEOTW:
The next subject to look at is retroviral DNA insertions.
"Constructing primate phylogenies from ancient retrovirus sequences," Welkin E. Johnson and John M. Coffin,
Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, Issue 18, 10254-10260, August 31, 1999.
Here, about a dozen different retroviral DNA inserts are used to construct the evolutionary tree of human and the other apes and primates. See the following chart to see how closely the different inserts match.
http://www.pnas.org/content/vol96/issue18/images/large/pq1892815002.jpeg
</font><blockquote>quote:</font><hr />The genomes of modern humans are riddled with thousands of endogenous retroviruses (HERVs), the proviral remnants of ancient viral infections of the primate lineage. Most HERVs are nonfunctional, selectively neutral loci. This fact, coupled with their sheer abundance in primate genomes, makes HERVs ideal for exploitation as phylogenetic markers.
...
Endogenous retrovirus loci provide no less than three sources of phylogenetic signal, which can be used in complementary fashion to obtain much more information than simple distance estimates of homologous sequences. First, the distribution of provirus-containing loci among taxa dates the insertion.
Given the size of vertebrate genomes (>1 × 109 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14). Furthermore, integrated proviruses are extremely stable: there is no mechanism for removing proviruses precisely from the genome, without leaving behind a solo LTR or deleting chromosomal DNA. The distribution of an ERV among related species also reflects the age of the provirus: older loci are found among widely divergent species, whereas younger proviruses are limited to more closely related species. In theory, the species distribution of a set of known integration sites can be used to construct phylogenetic trees in a manner similar to restriction fragment length polymorphism (RFLP) analysis.