Herv evolution

I have found the following references so far. Can Cornelius explain to
us how science explains what he considers a refutation of common descent?

Pim

Evidence from DNA sequencing studies strongly indicated that humans and
chimpanzees are more closely related to each other than either is to
gorillas [1-4]. However, precise details of the nature of the
evolutionary separation of the lineage leading to humans from those
leading to the African great apes have remained uncertain. The unique
insertion sites of endogenous retroviruses, like those of other
transposable genetic elements, should be useful for resolving
phylogenetic relationships among closely related species. We identified
a human endogenous retrovirus K (HERV-K) provirus that is present at the
orthologous position in the gorilla and chimpanzee genomes, but not in
the human genome. Humans contain an intact preintegration site at this
locus. These observations provide very strong evidence that, for some
fraction of the genome, chimpanzees, bonobos, and gorillas are more
closely related to each other than they are to humans. They also show
that HERV-K replicated as a virus and reinfected the germline of the
common ancestor of the four modern species during the period of time
when the lineages were separating and demonstrate the utility of using
HERV-K to trace human evolution.

Current Biology A HERV-K provirus in chimpanzees, bonobos and gorillas,
but not humans
Volume 11, Issue 10, 15 May 2001, Pages 779-783

Few human endogenous retroviruses (HERVs) have been extensively studied
in non-human primates. Such investigations have demonstrated that
several element classes are primate unique, contain members with
important biological function, are conserved in specific primate
lineages, and have in some cases expanded in copy number. We have
examined multiple sub-families of all major groups of HERVs using a DNA
microarray based on the reverse transcriptase (RT) domain of the viral
polymerase gene (/pol/). The microarray was used to investigate the
distribution of HERVs in non-human primates with particular focus on the
differences between New World monkeys (NWMs) and other anthropoids. This
is the first study examining most HERV families in multiple non-human
primate DNAs using a uniform and sensitive method and suggests that
major differences exist between primate groups. The results indicate
that a major invasion and expansion of /pol/ containing HERVs occurred
after the platyrrhine (NWM) lineage separated from the catarrhines (Old
World Monkeys and apes).

Virology The distribution of pol containing human endogenous
retroviruses in non-human primates
Volume 334, Issue 2 , 10 April 2005, Pages 203-213

Retroviral infections of the germline have the potential to episodically
alter gene function and genome structure during the course of evolution.
Horizontal transmissions between species have been proposed, but little
evidence exists for such events in the human/great ape lineage of
evolution. Based on analysis of finished BAC chimpanzee genome sequence,
we characterize a retroviral element (/Pan troglodytes/ endogenous
retrovirus 1 [PTERV1]) that has become integrated in the germline of
African great ape and Old World monkey species but is absent from humans
and Asian ape genomes. We unambiguously map 287 retroviral integration
sites and determine that approximately 95.8% of the insertions occur at
non-orthologous regions between closely related species. Phylogenetic
analysis of the endogenous retrovirus reveals that the gorilla and
chimpanzee elements share a monophyletic origin with a subset of the Old
World monkey retroviral elements, but that the average sequence
divergence exceeds neutral expectation for a strictly nuclear inherited
DNA molecule. Within the chimpanzee, there is a significant integration
bias against genes, with only 14 of these insertions mapping within
intronic regions. Six out of ten of these genes, for which there are
expression data, show significant differences in transcript expression
between human and chimpanzee. Our data are consistent with a retroviral
infection that bombarded the genomes of chimpanzees and gorillas
independently and concurrently, 3–4 million years ago. We speculate on
the potential impact of such recent events on the evolution of humans
and great apes.

Lineage-Specific Expansions of Retroviral Insertions within the Genomes
of African Great Apes but Not Humans and Orangutans Volume 3 | Issue 4 |
APRIL 2005 Plos Biology

BACKGROUND: Endogenous retroviruses contribute to the evolution of the
host genome and can be associated with disease. Human endogenous
retrovirus K (HERV-K) is related to the mouse mammary tumor virus and is
present in the genomes of humans, apes and cercopithecoids (Old World
monkeys). It is unknown how long ago in primate evolution the
full-length HERV-K proviruses that are in the human genome today were
formed. RESULTS: Ten full-length HERV-K proviruses were cloned from the
human genome. Using provirus-specific probes, eight of the ten were
found to be present in a genetically diverse set of humans but not in
other extant hominoids. Intact preintegration sites for each of these
eight proviruses were present in the apes. A ninth provirus was detected
in the human, chimpanzee, bonobo and gorilla genomes, but not in the
orang-utan genome. The tenth was found only in humans, chimpanzees and
bonobos. Complete sequencing of six of the human-specific proviruses
showed that full-length open reading frames for the retroviral protein
precursors Gag-Pro-Pol or Env were each present in multiple proviruses.
CONCLUSIONS: At least eight full-length HERV-K genomes that are in the
human germline today integrated after humans diverged from chimpanzees.
All of the viral open reading frames and cis-acting sequences necessary
for HERV-K replication must have been intact during the recent time when
these proviruses formed. Multiple full-length open reading frames for
all HERV-K proteins are present in the human genome today.

Curr Biol. 1999 Aug 26;9(16):861-8.
Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans.
Barbulescu M, Turner G, Seaman MI, Deinard AS, Kidd KK, Lenz J.

There are 60 articles which cite this one... Ouch I'd say this is merely
a minor puzzle hardly something worth the claim that it falsified common
descent.

Which is of course understandable given the vaste amount of evidence
supporting common descent.

Not to mention the lack of any competing scientific hypothesis.
Received on Thu Oct 6 22:50:50 2005