If every single human alive was
exclusively descended from two people who lived around 6000 years ago, we would
not expect the data from population genetics to show that the human population
was never smaller than a few thousand individuals. Nor would we expect to see
coalescent times for human genes in the hundreds of thousands of years. This is
however exactly what we see, and it completely falsifies the anti-evolutionist
position that the entire human race descended from six individuals
approximately 4500 years ago and propagated away from Mt Ararat. What we see
continues to show an African origin for the human race. As always, the problem
here is simply one of choosing from an avalanche of papers that show this fact.
Minimum human population has been never smaller than a few thousand
In
2006, Liu et al noted that both fossil and genetic data supported “a recent
single origin of modern humans in East Africa”[1] but
noted that apart from this basic fact, there were difficulties in clarifying
details of this. They analysed 52 human populations, and stated their data
“suggest an initial expansion of modern humans ∼56,000 years ago from a small
founding population of ∼1,000 effective individuals.”
Five
years later, Li and Durban, using whole genome sequence data from Europeans,
African, and East Asian individuals, stated that the genomic evidence showed a
marked bottleneck in European and Asian populations between 20-40 thousand
years ago of around 1200, and a less marked bottleneck in African populations
around 50,000 years ago of around 5700.[2] This
pattern of a less marked bottleneck in African populations as compared with
non-African populations is reflected in other studies. It is also worth noting
that these bottleneck sizes are in the thousands, not 2-6 individuals.
Population size
estimate from autosomal (a) and X chromosome data (b). Source: Nature (2011) 475:493-496
The 1000
Genomes Project Consortium published in 2015 their report[3]
announcing the completion of their project in which they reconstructed the
genomes of 2504 people from 26 populations (Africa, East Asia, Europe, South
Asia, and the Americas). Some of the salient points:
·
Individuals from African ancestry populations
harbour the greatest numbers of variant sites, as predicted by the out-of-Africa
model of human origins
·
The human race has a shared demographic history
for all humans beyond ~150,000 to 200,000 years ago
·
European, Asian, and American populations
experienced a bottleneck ~15,000 to 20,000 years ago, while the African
population experienced a bottleneck of lower severity at the same time of
around 4250 individuals
Median PSMC curve for each population. Source: Nature (2015) 526:68-74
Stephan Schiffels and Richard
Durban published a paper in Nature Genetics reporting on a new method which
allows geneticists to examine genetic history more recent than around 20,000 –
30,000 years ago. In applying their technique to genomic data from nine
populations, Shiffels and Durban found evidence for separation of the ancestors
of non-Africans from African Yoruban ancestors well before 50,000 years ago.
Their method also showed a non-African bottleneck (again, not 6 or 2 people!)
and a less marked bottleneck in the African population, just as the 1000
Genomes Project Consortium showed:
We find that
all non-African populations that we analysed show a remarkably similar history
of population decline from 200kya until about 50kya, consistent with a single
non-African ancestral population that underwent a bottleneck at the time of the
exodus from Africa around 40-60kya. The prior separation of non-African and
African ancestral population size estimates begins much earlier at 150-200kya,
clearly preceding this bottleneck, as already observed using PSMC. We will
quantify this further below by directly estimating the relative cross
coalescence rate over time. In contrast, we see only a mild bottleneck in the
African population histories with an extended period of relatively constant
population size more recently than 100kya. Between 30kya and 10kya we see
similar expansions in population size for the CEU, TSI, GIH, and CHB
populations.[4]
Source:
Nature Genetics (2014) 46:919-925
The Simons
Genome Diversity Project[5] has
analysed 300 genomes from 142 populations, and likewise has shown that the human
population has never been as small as 2-6 people. Specifically, the authors
noted:
- The population (not individual) ancestral to all modern humans began developing substructure at least 200,000 years ago, with substantive separation of non-African and southern African populations around 131,000 years ago, and substantive separation of non-African and central African populations around 112,000 years ago
- Non-African population sub-structure dates around 50,000 years ago, consistent with the archaeological evidence for modern human dispersal into Europe and Asia around this time.
- Minimum human population sizes never dropped below a few thousand people.
Source: Nature (2016) 538:201-206
Mallick et al caution that the
date estimates do not take into account uncertainty about the human mutation
rate on which their work (and that of the others cited earlier) depends; this
could by 30% higher or lower than the value used. However, this does not allow
YECs a way out of this data for two reasons. The first is that increased
mutation rates result in data that conflict with known archaeological data. As
Schiffels and Durban note:
Our results
are scaled to real times using a mutation rate of 1.25×10−8 per
nucleotide per generation, as proposed recently and supported by several direct
mutation studies. Using a value of 2.5×10−8 as was common previously
would halve the times. This would bring the midpoint of the out-of-Africa
separation to an uncomfortably recent 30-40kya, but more concerningly it would bring
the separation of Native American ancestors (MXL) from East-Asian populations
to 5-10kya, inconsistent with the paleontological record.[6]
(Emphasis mine)
The second reason is that there
exists an alternative method utilising linkage disequilibrium, which allows us
to calculate minimum effective population sizes that is independent of the
mutation rate.[7]
In 2007, Tenesa et al published the first genome-wide estimate of the effective
population size by using linkage disequilibrium methods, and arrived at
effective population sizes of ~3100 from Eurasian data and ~7500 from African,
“consistent with the
out-of-Africa theory of ancestral human population expansion and concurrent bottlenecks.”[8]
Source: ” Genome Res.
(2007) 17: 520-526
That this evidence is robust, and
overwhelmingly argues against monogenism is not seriously doubted outside of a
tiny fringe of Christian fundamentalists. As the geneticist Dennis Venema
notes, in a 2010 paper in Perspectives on
Science and Christian Faith:
Studies based on SNP/LD approaches have now estimated
ancestral population dynamics for various human groups over time in more detail
than is possible with mutation-based estimates. African groups have a higher
effective population size (~7,000) than do non-African groups (~3,000) over the
last 200,000 years. This approach, though based on methods and assumptions
independent of previous work, nonetheless continues to support the conclusion that humans, as a species, are descended from an
ancestral population of at least several thousand individuals. More
importantly, the scalability of this approach reveals that there was no
significant change in human population size at the time modern humans appeared
in the fossil record (~200,000 years ago), or at the time of significant
cultural and religious development at ~50,000 years ago.
Taken individually and collectively, population
genomics studies strongly suggest that our lineage has not experienced an extreme population bottleneck in the last nine
million years or more (and thus not in any hominid, nor even an
australopithecine species), and that any bottlenecks our lineage did experience
were a reduction only to a population of several thousand breeding individuals.
As such, the hypothesis that humans are
genetically derived from a single ancestral pair in the recent past has no
support from a genomics perspective, and, indeed, is counter to a large
body of evidence.[9]
(Emphasis mine)
Long coalescent times
for genes: more evidence against monogenism
The
coalescent time for a particular collection of variant forms of a particular
gene is the time (known as Tmrca
in the literature) that has passed since the existence of the most recent
common ancestor for that collection of genes.[10] Needless to say, we would not expect to see Tmrca for genes older than around 6000
years if we were descended exclusively from two people who lived around 6000
years ago.
What are the coalescent times for
human genes? Space precludes a complete listing given that there are
approximately 20,000 protein-coding genes, but what the literature shows is that
the Tmrca for many genes and
genetic elements are far older than 6000 years; we are
talking hundreds of thousands of years, and in some cases well over one million
years. (Given that the oldest Homo
sapiens fossil is around 200,000 years old, these Tmrca data alone are enough to show that our ancestry
stretches well into the remote past). Laurent Excoffier[11]
summarises a number of sequence studies, and shows the Tmrca values for them. Values range from 39,000 years to around
1.78 million years:
It hardly needs to be pointed out that no one
is interpreting this data as supporting universal recent human descent from six
people who lived 4500 years ago, dispersing from Mt Ararat.
Human-Ape common
ancestry from ERVs drives the nail in the coffin of monogenism
I’ve
often referred to the evidence for human-ape common ancestry (which alone
falsifies monogenism), so I don’t want to go into detail. The argument here is
simple and elegant: if we see exactly the same ‘genetic error’ in exactly the
same place in the genomes of humans and apes, the odds of the same mistake
occurring purely by chance are billions to one against. When we have many such
errors, the odds are so small as to be effectively zero. The ‘genetic errors’ include
broken genes (pseudogenes), mobile genetic parasitic DNA (retrotransposons)
that simply copy and paste themselves randomly throughout the genome, and
endogenous retroviral elements, which are evidence of past retroviral infection
that has integrated into the host germline.
One
of my favourite papers is a seminal 1999 PNAS paper from two world-renown
virologists, Welkin Johnson and John Coffin that employed endogenous retroviral
data in humans and apes to construct a robust evolutionary family tree that was
consistent with existing evolutionary trees. The existence of the same ERV
elements at exactly the same place in human and ape DNA is best explained by a
retroviral infection of a common ancestor of human and ape that became fixed in
the common ancestor DNA, and passed down both lines like other genetic data. As
the authors note:
Given the
size of vertebrate genomes (>1 × 109 bp) and the random nature of
retroviral integration, multiple integrations (and subsequent fixation) of ERV
loci at precisely the same location are highly unlikely. 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. 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.[12]
(Emphasis mine)
The results, as I noted before,
showed that the pattern of retroviral insertion gave evolutionary trees
consistent with consensus trees:
The HERVs
analyzed above include six unlinked loci, representing five unrelated HERV
sequence families. Except where noted, these sequences gave trees that were consistent
with the well established phylogeny of the old world primates,
including OWMs, apes, and humans.[13]
(Emphasis mine)
I’m not the only one to be
impressed by this evidence (or this paper). New Zealand cell biologist and
cancer researcher (and Christian) Graeme Finlay, in his book “Human Evolution: Genes, Genealogies and
Phylogenies” (2013: Cambridge University Press) notes:
A 1982 study prepared
the way (as far as I was concerned!) for the surprising answer [of when such
retroviral DNA first entered the human genome]. A length of cloned human
chromosomal DNA had been mapped on the basis of restriction enzyme-cutting sites
(that provide sequence landmarks along the DNA). An equivalent piece of DNA
cloned from the chimpanzee showed almost the same restriction enzyme-mapping sites,
indicating that these lengths of cloned DNA were from the corresponding parts
of the two genomes. But what is remarkable was that each of these segments of
DNA overlapped the sequence of an ERV. This finding implied that the ERV in
each of the two genomes was inserted at the same location. If indeed it was the
same insert (same class of ERV, inserted in precisely the same site with the
same target-site duplication, and lying in the same direction), then we would
have to conclude that both species are descendants of the single progenitor in
which this unique insert event occurred. This remarkable conclusion, reflecting
the way in which shared proviruses establish the monoclonality of tumours, was
forced on me by every instinct inculcated by cell biological experience.
But was the ERV
indeed the same one in both species? The definitive answer could only come from
DNA sequencing studies, and this pioneering work preceded the high-throughput sequencing
revolution. DNA sequencing had not been performed on these cloned lengths of
human and chimp genome. The answer was not available. However, this research
held out the tantalising prospect that the sequencing of ERV integration sites
in related species might provide the definitive answer to the question of
whether humans and chimps are monoclonal (as a cell biologist might express
it). The word monophyletic applies
more appropriately to multiple species descended from one ancestor. The
distribution of ERVs in the DNA of primate species could provide the ultimate
statement on common descent.
Work published in
1999 [the Johnson and Coffin paper] settled the question of whether shared ERVs
could demonstrate human and chimp descent from a common ancestor. This seminal
study identified those primate species in which each of six ERVs was present –
and defined insertion sites at single-base resolution. The data confirmed that
each of these ERVs is shared by humans and chimps. Indeed, each ERV is shared
not only by humans and chimps, but also by gorillas and more distantly related
primate species. [14]
This is of necessity a short review of the
evidence against monogenism, but is more than enough for the honest,
disinterested reader to see that the human population has never been as small
as two people.
References
[1]
Liu H et al “A Geographically Explicit Genetic Model of Worldwide
Human-Settlement History” Am. J. Hum.
Genet (2006) 79:230-237
[2]
Li H., Durbin R “Inference of human population population history from
individual whole-genome sequences.” Nature
(2011) 475:493-496
[3]
The 1000 Genomes Project Consortium “A global reference for human genetic
variation” Nature (2015) 526:68-74
[4]
Schiffels S., Durban R “Inferring human population size and separation history
from multiple genome sequences” Nature
Genetics (2014) 46:919-925
[5]
Mallick S et al “The Simons Genome Diversity Project: 300 genomes from 142
diverse populations” Nature (2016) 538:201-206
[6]
Schiffels and Durban, p 206
[7]
Geneticist Dennis Venema pre-empts this creationist attempt to evade the power
of this evidence for minimum population sizes, “Ah, you might say, these studies require an
estimate of mutation frequencies from the distant past. What if the mutation
frequency once was much higher than it is now? Couldn’t that explain the data
we see now and still preserve an original founding couple? Aside from the
problems this sort of mutation rate would present to any species, we have other
ways of measuring ancestral population sizes that do not depend on mutation
frequency. These methods thus provide an independent way to check our results
using allele diversity alone.” Venema, Dennis R.; McKnight, Scott. Adam
and the Genome: Reading Scripture after Genetic Science. Brazos Press,
2017. p48-49.
[8]
Temesa et al
“Recent human effective population size estimated from
linkage disequilibrium” Genome Res.
(2007) 17: 520-526
[9]
Venema D “Genesis and the
Genome: Genomics Evidence for Human-Ape Common Ancestry and Ancestral Hominid
Population Sizes” Perspectives on Science
and Christian Faith (2010) 62:166-178
[10]
Rosenberg A.A., and Feldman M.W. “The relationship between coalescence times
and population divergence times” in Slatkin M, Veuille M (Eds) “Modern
Developments in Theoretical Population Genetics” (2002: Oxford University
Press)
[11] Excoffier L “Human demographic history: refining the
recent African origin model” Curr Opin
Genet Dev (2002) 12:675–682
[12]
Johnson
W.E., Coffin J.M. “Constructing primate phylogenies from ancient retrovirus
sequences” Proc Natl Acad Sci USA. (1999)
96:10254-10260
[13]
ibid, p 10259
