On May 2, 2008, at 5:02 PM, Gregory Arago wrote:
> "The current view is not a founder pair but a founder small
> population in the 10K range." - TG
> Is this consistent with the idea of 'polygenism,' even if it doesn't
> address the 'multiregional hypothesis'? Does it not contradict the
> idea of 'monogenism'?
>
> Can you forgive my SoS question: whose view is the 'current view'
> and the 'present notion'? Is this what 'normal science' says? (And
> for a non-NS) Which fields does the 'current view' mainly draw upon?
>
> It seems to me that David C.'s post carefully left open more than
> one option, which I quite appreciate, not being a 'scientist' in a
> field that speaks about bottlenecks (though 'probka' means
> 'bottleneck/traffic jam' in Russian) or near extinction events. The
> consequences of a 'founder small population' instead of a 'founder
> pair' in sociology is significant, though not commonly discussed in
> the literature.
>
All of this goes back to a very simple observation. The genetic
diversity of people of African descent have greater genetic diversity
than those who aren't. It gets a lot more complicated than this but
there are basically two ways you can get this, bottlenecks and founder
effects. When a population suddenly gets smaller in a bottleneck its
genetic diversity also goes down. Likewise, when there is colonization
the same happens. Out-of-Africa holds to a multiple founder effects
and Multi-Regional-Evolution to bottlenecks. Another difference
between the two approaches is MRE claims there is admixture of
"modern" humans with Neanderthal, the evidence being some
commonalities in the microcephalin gene in MtDNA found in fossilized
Neanderthal. OOA says there is little or no admixture but that the
Eurasia population were replaced by African ones. Both approaches give
you dates and population sizes. NONE of the options or suboptions give
you monogenism. That's why I prefer Adam and Eve in the ANE because
both it and its alternative have the same theological problems. Note:
the theological problems caused by evolution are still there even when
you restrict yourself to genetics and so-called microevolution. David
C's point was there are problems with uncalibrated molecular clocks
giving accurate dates. Both sides agree with the size of the original
population Terry quoted. More on this later.
What we have here is a classic stage two science with two conflicting
theories fighting for dominance. We are, however, on the cusp of stage
three here and that is a very interesting story. Note what does not
happen where both sides don't talk to each other, just publish in the
popular literature and produce no falsifiable hypotheses like ID.
Given the time frame is roughly the same as ID, this will give us a
good comparison/contrast between the scientific approach and the ID
approach. David C. mentioned the issue with molecular clocks and this
reflects the battle between the paleontologists and the molecular
biologists on how things are dated. This is also moving from stage two
to stage three. The answer is to do both mirroring the massive success
of the neo-darwinian synthesis. This has of late produced some very
fruitful results. For example, we are getting the same answer out of
both fields of the what and when concerning the speciation of mammals.
We are even getting confirming evidence from ancient biological
materials. Collagen from T Rex confirmed what the paleontologists have
been telling us that dinosaurs are birds. The other thing that makes
it much easier is since the human genome was produced five years ago
the technology has taken off like a rocket -- and ID still produces no
research. I would submit the fundamental difference between science
now and fifty years ago is not a difference in the philosophy of
science but rather the technology of science.
Paul Harvey voice: "And now for the resssst of the story. Page two."
In 2004, Osbjorn M. Pearson wrote "Has the Combination of Genetic and
Fossil Evidence Solved the Riddle of Modern Human
Origins?" [Evolutionary Anthropology 13:145-159 (2004)]. This was when
the debate between OOA and MRE was in the second stage, trench warfare
stage. By combining the genetic and archeological data the balance was
tipping to the OOA side. Pearson said:
> Debate over the origin of modern humans continues without a clear
> end in sight. Currently, the genetic and fossil evidence is still
> used to support two different interpretations of the origin of
> modern humans. Some researchers claim that the genetic evidence is
> compatible with either an Out-of-Africa or a Multiregional model,
> while other scientists argue that the evidence supports only a
> Multiregional model of evolution. I argue that the fossil record and
> archeological evidence constrain interpretation of the genetic
> evidence and imply that very little, if any, admixture with Eurasian
> archaic hominins such as the Neanderthals occurred during the spread
> of modern humans out of Africa.
...
> First, the effective population size of [approximately] 10,000
> individuals for our species would have to have arisen from a
> bottleneck or series of bottlenecks long before the origin of modern
> humans ... [RDB Note: this is what Terry quoted. This will come back
> again so keep your eye on the ball.]
...
> Future discoveries in genetic patterns or the genetic basis of
> “modern” traits should help to narrow down even further the
> possibilities with respect to exactly what happened with the origin
> of modern humans. There is reason for optimism that these
> discoveries will be made soon. [RDB Note: He was right.]
Fast forward to 2008.
Weaver and Roseman, New Developments in the Genetic Evidence for
Modern Human Origins, Evolutionary Anthropology 17:69–80 (2008)
> The genetic evidence for modern human origins was reviewed recently
> in Evolutionary Anthropology by Pearson, so our goal is to highlight
> new developments rather than attempt a comprehensive review. For
> years, polarized Multiregional and Out-of-Africa models for modern
> human origins were debated vigorously, but today there is
> substantial agreement among specialists. One area of broad consensus
> is that Africa or, more accurately, sub-Saharan Africa, played a
> predominant role in the origins of modern humans. This view is found
> even among researchers who argue against complete replacement of
> nonmodern Eurasians. The importance of Africa is clear not only from
> genetics, but also from the fossil record. On the other hand, most
> researchers also agree that, at least in principle, modern humans
> and nonmodern Eurasians, such as Neandertals, could have interbred
> with each other. The fossil record suggests that Neandertals and
> modern humans constituted independent evolutionary lineages, but
> their recent common ancestry leaves open the possibility of
> admixture. The open question is whether there is any evidence of
> admixture.
>
What brought about the consensus? A better technique using short
tandem repeat analysis (STR) rather than single nucleotide
polymorphisms (SNP) was done. This produces much less ascertainment
bias and thus allows us to do within-population variation on the
global STR dataset. If you look at just the difference in genetic
diversity between African and other locations this can be explained
via multiregionalism with isolation by distance which is an
equilibrium model. But, looking at in-population gives us greater
precision. When looking at this there is a straight line relationship
for every population with the diversity with distance from East
Africa. In other words, we have a smoking gun for OOA. The farther you
are from Africa the later the founder arrives and the further you are
away from equilibrium. Isolation by distance has no such preference to
the direction of the distance.
Late last year a Bayesian analysis was done on 50 independent
autosomal noncoding loci with six different models (African
Replacement, Assimilation, Multiregional with instantaneous
(bottleneck) and exponential growth). [Fagundes et al, Statistical
evaluation of alternative models of human evolution, PNAS 104:45,
17614-17619 (2007)] The winning model based on posterior
probabilities was the African Replacement Model with Exponential
Growth (AFREG). After the model was determined, 5,000,000 different
simulations under an approximate Bayesian computation (ABC) framework
were done to get the parameters. Did you keep your eye on the ball and
remember Terry's population size number? Note what came out as the
ancient African population (12722). Also note that census populations
(what we normally think of populations) can and often are quite larger
than the effective number of diploid individuals.
Table 1. Demographic and historical parameters estimated under the
favored AFREG model
Parameters†
Median‡ 95% HPD§
Speciation time for modern human, yr (TMH) 141,455 103,535–185,642
Exit out of Africa, yr (TAS) 51,102
40,135–70,937
Colonization of the Americas, yr (TAM) 10,280 7,647–15,945
Size of archaic African population (NA-AF) 12,772 6,604–20,211
Bottleneck size during speciation (NbMH) 600 76–1,620
Bottleneck size when leaving Africa (NbAS) 462 64–1,224
Bottleneck size when leaving Asia (NbAM) 452 71–1,280
† Population sizes are given in effective number of diploid
individuals.
‡ Median value of the marginal posterior density.
§ The 95% highest posterior density interval.
What about the admixture of humans and Neanderthal? Currently there
isn't enough information to prove or exclude it. We are still in stage
2 there. Given the speed at which the genetic technology is moving I
would not be surprised to be at stage 3 soon. This is a rather easy
prediction to make. (Just don't force me to pick which one is right. :-)
Rich Blinne
Member ASA
P.S. I am including the glossary from the 2008 Evolutionary
Anthropology article to explain the terms used in this post:
Admixture—transfer of genes between two populations that had
previously been isolated from each other.
Ancient DNA—a DNA sequence retrieved from a biological sample of a
dead organism, often coming from an extinct taxon.
Ascertainment bias—genetic loci are usually discovered by finding
differences among individuals in a small sample, then typed for a
larger sample. This nonrandom discovery process often biases estimates
of population genetic parameters such as measures of
within-population genetic diversity, among-population differentiation,
linkage disequilibrium, and tests for departures from mutation-drift-
equilibrium. The only way to eliminate ascertainment bias is to
completely resequence all the individuals in the study; that is, the
discovery sample is the same as the study sample.
Autosomal locus—a position on one of the paired (non-sex) chromosomes.
Bottleneck—a sharp contraction followed by a recovery in population
size.
Census population size—the actual number of individuals in a
population.
Coalescence time—the time in the past when all DNA sequences in a
sample shared a last common ancestor (time to the most recent common
ancestor).
Directional natural selection— when natural selection favors a
phenotype that differs from the population mean, resulting in a shift
of the mean.
Effective population size—a population genetics parameter that equals
the number of breeding individuals in an idealized population
that would have as much genetic drift as is in the actual population.
Founder effect—when a small subset of a population moves to a new
geographic region, its genetic diversity is lower than and is often
unrepresentative of the original population. A founder effect produces
a genetic signature similar to a bottleneck.
Gene flow—transfer of genes between populations by migration of
individuals between the populations and subsequent mating.
Gene tree—a tree that shows the evolutionary relationships among a
sample of DNA sequences.
Genetic distance—a statistic that reflects some aspect of genetic
variation between two populations, sometimes standardized by the
variation found within them.
Genetic drift—chance genetic changes in a population due to finite
size.
Genetic locus—a particular position in the genome.
Haplotype—the presence of particular nucleotides over a stretch of
DNA that tend to be inherited together.
Isolation by distance—an equilibrium model that predicts a positive
relationship between genetic and geographic distance. This
relationship occurs because individuals tend to migrate short
distances to find mates and because long-range migrations are rare.
Linkage disequilibrium—deviation from a random association of the
nucleotides present at a set of genetic loci.
Microsatellite—a rapidly evolving block of DNA in which a simple DNA
sequence is repeated multiple
times and individuals vary in their number of repeats.
Mitochondrial DNA—a short DNA molecule that is found outside of the
cell nucleus. It traces maternal lines of descent because it is
inherited only from the mother.
Mutation-drift-equilibrium—a population is said to be at mutation-
drift-equilibrium when a balance (equilibrium) has been reached
between the genetic variation introduced by mutation and that lost by
genetic drift.
Negative natural selection— when natural selection acts to remove low-
frequency novel genotypes from a population.
Nuclear DNA—the bulk of an individual’s DNA, which is found within
the cell nucleus.
Population subdivision or structure—a population is said to be
subdivided or structured when it is divided into a set of local groups
and there is nonrandom mating across groups.
Population tree—a tree that shows the evolutionary relationships
among a set of populations.
Positive natural selection— when natural selection acts to shift low-
frequency novel genotypes to high frequency or fixation within a
population.
Purifying natural selection— another term for negative natural
selection.
Range expansion—an increase in the geographic range occupied by a
population or species. Range expansions are often linked with
increases in population size.
Short tandem repeat (STR)— another term for a microsatellite.
Single nucleotide polymorphism (SNP)—a position in the genome where
individuals differ with regard to which nucleotide is pre-
sent.
Stabilizing natural selection— when natural selection favors the mean
phenotype, preventing a shift of the mean.
Y-chromosome—a sex chromosome that is paired with the X chromosome in
males, whereas females have two X chromosomes. The
nonrecombining portion traces paternal lines of descent.
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Received on Sun May 4 20:55:18 2008
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