"The conclusion follows that human ancestral populations could
never have been smaller than two or three thousand individuals at any
time over the last several million years. This conclusion might be
strengthened by taking into account that extensive polymorphisms exist
at other HLA loci (and at other genes as well). For example, 63 primate
alleles are known of the DRB1 gene, 17 of them in humans. As many as 14
DRB1 human alleles predate the origin of Homo erectus, 9 alleles predate
the divergence of the human and chimpanzee lineages, and 7 alleles
predate the divergence of the human and orangutan lineages. Another
instance is the occurrence of multiallelic polymorphisms in the [beta]-
globin family that yield at least 17 haplotypes, the coalescence of
which goes back to 450,000 years B.P. or earlier and would be consistent
with an effective population of 10,000 individuals through that time
span."~Francisco J. Ayala, Ananias Escalante, Colm O'hUigin and Jan
Klein, "Molecular Genetics of Speciation and Human Origins," Proc. Natl.
Acad. Sci, USA, 91:pp6787-6794, July 1994, p. 6791.
Obviously, if this is true, a recent origin of Adam is ruled out. This
would rule out all young earth views and the views of Hugh Ross. But
even my view has difficulty with this data and I am looking for a
solution.
They also say,
"If we assume a mean population size of 10 5 individuals and a
long-term generation time of 15 years, the expected coalescence for
neutral alleles is 6 Myr, which is much less than the 30 Myr coalescence
of the DRB1 alleles. Although the coalescence estimate has a large
variance, it seems that either our ancestral population was even larger
than 10 5 or, as assumed, balancing selection accounts for the long
term persistence of the MHC polymorphisms. "(Ibid. p. 6790)
While the 6 Myr figure would fit with what I have suggested as the means
and time of Adam's origin, the 30 Myr time frame wouldn't. As I understand
it, this conclusion is apparently based on the idea the similarity of MHC
genes between various primates are too similar to have been derived
independently and balancing selection lengthens the time of the
coalescence. Thus the polymorphism has been evolving from prior to the
advent of the common ancestor of African apes and humans at 13 Myr ago.
But then I ran into this.
"Despite the long persistence time of alleles, each mammalian
order appears to have a different complement of DRB genes, Phylogenetic
trees based on complete coding sequences of DRB genes on exon 2 only
place all primate lineages on a single branch together, separate from
lineages in ungulates, rodents and carnivores. Thus in each order the
functional DRB lineages appear to be descended from a different single
gene. This observation places an upper age limit on allelic lineages of
about 90 MY although they may be considerably younger."~Colm O'hUigin,
"Quantifying the Degree of Convergence in Primate Mhc-DRB Genes,"
Immunological Reviews, 1995:143, p. 123-140, p. 124
which when combined with the following would seem to imply some cross-
order sharing of information.
cross species sharing of sequences? MHC data
"The relationship between alleles within and between species is
obscured by the frequenct similarities of portions of otherwise
dissimilar genes. Fig.2 illustrates the patchwork nature of the beta-l
domain of DRB genes. Allelic lineages differ from one another by the
presence and absence of distinctive motifs --short contiguous segments
characteristic for the particular lineage. Within a lineage the shared
motifs are frequently at the amino end of the beta-1 domain but the
motifs at the carboxy end do not appear to be lineage-specific and are
shared by diverse lineages. Motifs in the middle of the domain
similarly appear in a fashion which bears little relation to the
presumed phylogeny of the allelic lineages.
"The sharing of motifs between distantly related alleles makes the
evolutionary history of allelic lineages difficult to decipher,
especially given the short size of the second exon for which most
sequence data are available. Sequence exchange mechanisms including
recombination and gene conversion-like events have ben invoked to
account for the patchwork appearance of the beta-1 domain.
. . .
"In addition to their promiscuous distribution in a variety of
lineages, the motifs present a further puzzle in their apparent
persistence since the divergence of mammalian orders. Motifs
characteristic of particular primate lineages are found also in rodents
and ungulates. For example the motife 9EYSTS13 (the numbers indicate
the location of a motif in the beta-1 domain of the mature DRB protein
while amino acids are indicated in the international 1-letter code) is
characteristic of the primate DRB1*03 lineage and occurs in humans, apes
and monkeys, but is also found in the murine, bovine and equine DRB
genes. No primate lineage is thought to be sufficiently old to be
shared with other mammalian orders. It has therefore been suggested
that the motifs themselves represent recombinational unites, which have
persisted since before the separation of mammalian orders and have been
recombinationally propagated and grafted onto the newly emerging DRB
genes of each mammalian order. Lundberg & McDevitt (1992) argue that the
high degree of codon identity found in the DNA encoding similar murine
and human motifs can be best explained by direct descent of the motifs
from the common ancestor of primates and rodents."
"The DRB genes clearly present a pattern of motif sharing not
commonly found in the remainder of the genome. Whether the above
explanations are valid or not remains to be verified."~Colm O'hUigin,
"Quantifying the Degree of Convergence in Primate Mhc-DRB Genes,"
Immunological Reviews, 1995:143, p. 123-140, p. 126-127
My question is: Does the motif data imply some other mechanism for the
MHC polymorphism?
Also:
Why wouldn't the motifs be subjected to neutral drift or balancing
selection, and thus not be the same across the orders?
I noticed that the larger the effective population is, the smaller the
time required for coalescence. Thus, is there any set of assumptions which
would allow the MHC data to be explained staring from a single pair
growing to today's population over the past 6 MYR? Any hope for the
60,000 years of Hugh Ross?
Please be simple, remember I am just a geophysicist.
Note to Steve Clark: After tomorrow I will no longer be able to play the
one-armed man to Jim Bell's Dr. Kimball. :-)
glenn
Foundation,Fall and Flood
http://members.gnn.com/GRMorton/dmd.htm
Only 1 more day till I get this ^%$#&*@ cast off my arm