EVOLUTIONARY HISTORIES OF DIFFERENT HERV FAMILIES
retroviruses arose from germ-line retroviral integrations at different times
during evolution. After their initial integrations, retroviral sequences are
transmitted vertically and they may proliferate by retrotransposition (or
re-infection). This intragenomic spread implies a process of co-evolution
between the endogenous retrovirus and the host genome. As shown in the examples
below, this process differs substantially from one HERV family to others.
We initially analyzed the
evolutionary history of ERV9 by using LTR sequences taken from the human
genome. We classified these insertions into 14 subfamilies based on several
characteristic nucleotide differences. The age of each subfamily was
approximately estimated based on the average sequence of its members from the
subfamily consensus sequence. Determination of the sequential order of
diagnostic substitutions led to the identification of four distinct lineages.
Strong evidence for mosaic evolution of some of these lineages is presented. We
conclude that ERV9 has been actively spreading within the genome of the lineage
leading to humans over a long period of primate evolution.
When we applied the same
methodology to study the evolutionary history of HERV-W, a totally different
picture appeared. Identification of shared diagnostic differences and
phylogenetic analyses revealed the existence of just three subfamilies. The
average divergence between sequences for each one of the subfamilies suggests
that most of the HERV-W elements were inserted within the genome during a short
period of time. Remarkably, each one of the subfamilies consists of two types
of insertions, the expected proviral sequences and other sequences with
structural features of processed retrogenes. In fact, the lower evolutionary
success of HERV-W in comparison with ERV9 might be related to the existence of a
considerable proportion of genomic RNA sequestered by the L1 machinery.
Although ERV9 has been
actively transposing during an extended period of primate evolution, it seems
that HERV-K represents the unique known case of endogenous retrovirus that
amplified in the human genome after the divergence of human and chimpanzee
lineages. Here, we also present comparative analyses about the youngest
insertions of ERV9 and HERV-K, suggesting again two contrasting histories.
While several lineages of HERV-K proviruses remained transpositionally active
after the humans/chimpanzee split, the last insertional events of ERV9 seems to
be due to the activity of only one active sequence.