That special creationists in our community still deny the fact of common descent despite the powerful witness to this fact from the genomics data is a testament both to how poorly informed their anti-evolution arguments are, and the degree to which their adherence to fundamentalist distortions of the creation narratives blinds them to this evidence. I've outlined this evidence many times before, but in order to make this series self-contained, I will go through the main lines of evidence in the following posts.
Genomic Evidence for Common Descent – Synteny and Chromosomal Fusion
Twenty years ago, careful examination of human chromosome 2 showed that it was the result of an ancient telomere to telomere fusion:
Twenty years ago, careful examination of human chromosome 2 showed that it was the result of an ancient telomere to telomere fusion:
The inverted arrangement of the 1TAGGG array and the adjacent sequences, which are similar to sequences found at present-day human telomeres, is precisely that predicted for a head-to-head telomeric fusion of two chromosomes...These data provide strong evidence that the inverted repeats in c8.1 arose from the head-to-head fusion of ancestral telomeres.[1]
One year later, further research showed
evidence[2] of an
ancient centromere in human chromosome 2, giving us evidence of both
centromeric and telomeric remnant DNA which is what one would expect if human
chromosome 2 was the product of a fusion event. This is no longer controversial
in molecular biology. For example, a decade ago, researchers investigating the
structure and evolution of human chromosome two noted in passing:
Humans have 46 chromosomes, whereas chimpanzee, gorilla, and orangutan have 48. This major karyotypic difference was caused by the fusion of two ancestral chromosomes to form human chromosome 2 and subsequent inactivation of one of the two original centromeres (Yunis and Prakash 1982). As a result of this fusion, sequences that once resided near the ends of the ancestral chromosomes are now located in the middle of chromosome 2, near the borders of bands 2q13 and 2q14.1. For brevity, we refer henceforth to the region surrounding the fusion as 2qFus. Two head-to-head arrays of degenerate telomere repeats are found at this site; their head-to-head orientation indicates that chromosome 2resulted from a telomere to telomere fusion. (Emphasis mine).[3]
The evidence is unambiguous and
irrefutable. Human chromosome 2 is the product of an ancient fusion of two
ape-like chromosomes, as evidenced by the telomeric and centromeric remnant in
the chromosome. That
chromosome 2 owes its origin to a fusion event is no longer in doubt. Recent
papers on the subject tend to concentrate the specific details of when and how
the fusion event took place. For example, Ventura et al in a 2012 paper
in Genome Research proposed a model for how the fusion event occurred,
and a scenario for the evolutionary history not only of human chromosome 2, but
the two chromosomes that in chimps and gorillas did not fuse.[4]
Do
we know the exact details of the fusion event and the evolutionary history of
chromosome 2 and the unfused homologous chromosomes in chimps and apes? No, but
we have a good idea of how it could have happened. Are we in doubt that a
fusion event occurred? Not al all. The evidence is unambiguous and irrefutable.
Human chromosome 2 is the product of an ancient fusion of two ape-like
chromosomes, as evidenced by the telomeric and centromeric remnant in the
chromosome.
Genomic Evidence for Common Descent – Pseudogenes
The first – and arguably most
famous example – is that of the GULO-P pseudogene which in humans, chimpanzees,
orangutans and macaques[5] is
broken in exactly the same was. (For those interested in the details, the 164
nucleotide sequence of exon X shared a single nucleotide deletion). While
guinea pigs also have a non-functional GULO gene, this was inactivated in a
completely different way[6] and therefore represents a separate
pseudogenisation event. The GULO pseudogene in humans, apes and old world
monkeys is broken in exactly the same way, consistent with the incapacitation
of GULO in the common ancestor of these primates.
After a gene is rendered
non-functional, it becomes selectively neutral, which means that it is free to
acquire random mutations. If we look at all the species that have the same pseudogene
in common, those that share a recent common ancestor should differ by fewer
random mutations. Conversely, those that have a distant common ancestor will
have had more time to accumulate random mutations, and therefore will be less
similar. By creating a family tree based on this mutation data, we should be
able to create a tree roughly consistent with the expected evolutionary tree.
This is exactly what we see when we look at the GULO data in primates:
The primate data clusters closely
together, with humans and chimpanzees closest of all. Rodents cluster closely
together, with guinea pigs clustering closely with the rodents. This is exactly
what we’d expect if common descent was true. Special creation simply has no
credible answer. Remember, when we look at the primate data, we’re looking at
random mutations in a non-functional gene. The creationist either has to assume
that this occurred purely by chance; the odds of which are so remote as to be
practically impossible or answer:
- Why did
God create primates with a broken vitamin C synthesis system, leaving
others with the ability to synthesise vitamin C
- Why did
God create humans, apes and old world monkeys (which according to
evolutionary biology form a clade, or group of organisms sharing a common
ancestor) with a GULO pseudogene broken in exactly the same way?
- Why did
God then insert random mutations into this broken pseudogene in such a way
as to allow one to construct an evolutionary family tree that agrees with
the conventional evolutionary tree derived from morphological data?
This is why the biochemist and
intelligent design advocate Michael Behe admitted that the GULO data is
powerful evidence for common descent:
When two lineages share what appears to be an arbitrary genetic accident, the case for common descent becomes compelling, just as the case for plagiarism becomes overpowering when one writer makes the same unusual misspellings of another, within a copy of the same words. That sort of evidence is seen in the genomes of humans and chimpanzees. For examples, both humans and chimps have a broken copy of a gene that in other mammals helps make vitamin C As a result, neither humans nor chimps can make their own vitamin C.
[…]
The same mistakes in the same gene in the same positions of both human and chimp DNA. If a common ancestor first sustained the mutational mistakes and subsequently gave rise to these two modern species, that would very readily account for both why both species have them how. It's hard to imagine how there could be stronger evidence for common ancestry of chimps and humans[7]. (Emphasis mine)
The enzyme cytochrome P450 C21 is
of critical importance in the biosynthesis of steroid hormones. Humans have
both a working copy of the CYP21 gene (which has eight exons), as well as a
pseudogene, which is damaged in three main ways:
- An eight
base pair deletion in exon 3 of the gene
- A one
base pair substitution at codon 318 of exon 8
- A single
nucleotide insertion in exon 7
Kawaguchi et al analysed the DNA
of humans, orangutans, chimpanzees and gorillas to clarify how and when the
defects in the CYP21 pseudogene occurred:
The primary purpose of this study has been to determine the evolutionary origins of the three defects characterizing the human CYP21P gene. The study shows that the 8-bp deletion in exon 3 is present in the chimpanzee but not in the gorilla or orangutan genes, whereas the T insertion in exon 7 and the substitution generating the stop codon in exon 8 are restricted to human genes.[8]
In other words, the 8 base pair
deletion occurred in a common ancestor of humans and chimpanzees, while the
substitution and insertion occurred after the human-chimpanzee speciation
event:
Our results are consistent with this scenario: the 8-bp deletion apparently occurred after the gorilla lineage split off but before the chimpanzee and human lineages separated from each other. We can thus date the occurrence of the 8-bp deletion rather precisely within a relatively short period of some 6 Myr ago. The deletion was followed, in the human lineage, by the two other defective mutations.[9]
Again, recall our analogy of
multiple examination papers with the same wrong errors and the same mistakes in
the wrong answers, down to the same spelling errors. No one would seriously
advance multiple independent errors as a valid explanation. Rather, they'd
conclude that copying had occurred. The same applies here. When we have
identical errors in the CYP21 pseudogene of chimpanzees and humans, it
stretches credibility to assume that:
- Purely
by chance, chimpanzees and humans both have a CYP21 pseudogene which arose
via a duplication event
- Purely
by chance, they both acquired the same eight base pair deletion
- Common descent, with the duplication event occurring in a species ancestral to human and chimpanzee which was then passed down to chimpanzee and human lineages is the only credible explanation.
Similar examples abound, as cell biologist and cancer researcher Graeme Finlay in a 2003 paper summarising the genomic evidence for common descent notes:
Our genome contains 6,000 to 10,000 derelict genes or gene fragments (pseudogenes) that no longer produce functional proteins (Figure 2). Some are disabled versions of genes which remain functional in other species. Others are inactive copies or duplicated fragments of functional genes. Each pseudogene is unique. It is the product of a random, unrepeatable originating event (or series of events) that occurred during the history from which humanity arose. Pseudogenes therefore provide unambiguous evidence for the animal ancestry of humans.[10]
Genomic Evidence for Common Descent – Retrotransposons
Retrotransposons are a class of
genetic element that copy and paste themselves throughout the genome; unlike
DNA transposons, they copy themselves into an RNA intermediate which is
inserted randomly into the genome via the process of reverse transcription.
They can be co-opted by the host genome to perform a useful function, but
generally, their benefit at best is neutral, and sometimes can be deleterious.
As Robert Trivers and Austin Burt note:
Due to their abundance, transposable elements are almost guaranteed to have profound effects on their hosts. About half of our own genome is derived from transposable elements. And, in addition to transposition itself, these elements can cause a bewildering array of chromosomal rearrangements. As with other types of mutations, some fraction of these insertions and rearrangements will be beneficial to the host and positively selected. Transposable elements may thus be important sources of mutation that would not occur by other means. And transposable elements can also be domesticated (rarely) by the host-as we shall see, just such an event was critical to the evolution of the vertebrate immune system. These beneficial effects notwithstanding, transposable elements are still best considered as parasites, not as host adaptations or mutualists.[11] (Emphasis mine)
Parasite is an excellent word to
use to describe these transposable elements. Ignoring the tiny fraction that
has been co-opted, almost all of the retrotransposon complement is largely dead
metabolic weight. They are also directly linked to genetic disease[12],[13],[14],[15] a point
that respected evolutionary biologist John Avise notes:
Mobile elements have the potential to cause human diseases by several mechanisms. When a mobile element inserts into a host genome, it normally does so at random with respect to whether or not its impact at the landing site will harm the host. If it happens to land in an exon, it can disrupt the reading frame of a functional gene with disastrous consequences. If it jumps into an intron or an intron-exon boundary, it may cause problems by altering how a gene product is spliced during RNA processing. If it inserts into a gene’s regulatory region, it can also cause serious mischief. The potential for harm by such insertional mutagenesis is great. It has been estimated, for example, that an L1 or Alu mobile element newly inserts somewhere in the genome in about 1–2% and 5%, respectively, of human births. Another problem is that when a mobile element lands in a functional gene, genetic instabilities are sometimes observed that result in deleted portions of the recipient locus. Several genetic disorders have been traced to genomic deletions associated with de novo insertions of mobile elements. Finally, mobile elements (or their immobile descendents that previously accumulated in the human genome) can also cause genomic disruptions via non-allelic homologous recombination. Serious metabolic disorders can result.[16]
While this does not prove common
descent (though it completely overturns any argument that retrotransposons were
specially created parts of the human genome), the presence of shared
retrotransposons at identical sections of genomes in related species confirms
common descent. A classic example is a study that confirmed hippos and whales
share a common ancestor, using retrotransposon data:
Analysis of the KM14, HIP4, HIP24, and AF loci show that hippopotamuses and cetaceans form a monophyletic group that excludes ruminants. In each case, the CHR-1 SINE was inserted into the genome of a common ancestor of these species, as confirmed by hybridization experiments with probes specific for CHR-1 and its flanking region...On closer examination, it was revealed that the CHR-1 SINE was integrated into a common ancestor of hippopotamuses and whales…(indicating a sister-group relationship between these taxa), whereas a MER unit was integrated into the genome of a common ancestor of ruminants only.[17]
The presence of identical
retrotransposons at the same place in the genomes of related species is prima
facie evidence for common descent. As mentioned, these are mobile genetic
elements that are copied from elsewhere and insert themselves randomly into
other places in the genome. The odds of the same SINE or LINE inserting at the
same place in the genomes of related species is vanishingly small, making
common descent the only credible explanation for the pattern of retrotransposon
distribution seen. As Nikaido et al point out:
SINES and LINEs are virtually unique and irreversible mutations...which is well documented with primate Alu (SINE) sequences. During the last 10 years, one of us (N.O.) has studied several hundred SINE loci, but he has never observed any occurrence of independent SINE insertions among species at identical genomic positions (i.e., between the same two nucleotides). Because the probability that a SINE / LINE will be lost once it has been inserted into the genome is extremely small, and the probability that the same SINE / LINE will be inserted independently into an identical region in the genomes of two different taxa is also very small, the probability that homoplasy will obscure phylogenetic relationships is, for all practical purposes, zero...Therefore, one can reconstruct phylogenetic trees with high confidence by considering multiple independent SINE / LINE insertion events that define given nodes in a tree.[18] (Emphasis mine)
As the presence of
retrotransposons in the genome is evidence of prior copying and pasting of that
genetic element, if we see the same retrotransposon in exactly the same place
in the genome of two related species, then we have two options:
- Purely
by chance, the same retrotransposon inserted itself into exactly the same
place in human and ape genomes
- The
retrotransposon was first inserted in the genome of the common ancestor of
human and ape, and then inherited by the descendant species.
The odds of independent identical
retrotransposon insertion at identical places in human and ape genomes is
remote. If we have an example where seven retrotransposons are found in exactly
the same places in human and chimpanzee genomes, then the chances are so remote
as to be impossible. This is exactly what we have found. In the alpha
haemoglobin cluster of humans and chimpanzees. Researchers have found that
"[i]n each case, with the exception of minor sequence differences, the
identical Alu repeat is located at identical sites in the human and chimpanzee
genomes."[19] In
fact, by looking for the presence of retrotransposons in primate genomic data,
we have been able to construct a reliable evolutionary family tree that is
consistent with the accepted tree based on morphological data.
The use of the unique pattern of
retrotransposon data has real-world applications in allowing researchers to
identify - for example - what sort of primates a carnivore eats based on the
genetic material detected in its faeces. It also allows accurate identification
of products seized in the illegal wildlife trade.[20] It is
also worth noting that this approach can be used to identify humans.[21] Special
creationists who accept the result of a paternity test should, to be
consistent, accept this technique when it confirms common descent of humans and
apes.
Genomic Evidence for Common Descent – ERVs
Arguably the most compelling
evidence for common descent comes from endogenous retroviral elements, which
are the remnants of retroviral infection that has integrated into the germline
and has been passed down like other genetic material.
While
pseudogenes and retrotransposons are 'indigenous' to the species in question
for want of a better term, ERV data is unarguably alien, presence of an ancient
retroviral infection that became integrated into the germ line of the animal,
and passed down the generations. Therefore, the presence of identical
retroviral elements at the same position in human and ape genomes strongly
suggests infection and integration of the retroviral element in a species
ancestral to human and ape.
Common
descent would predict that if a species was infected by a retrovirus which
became fixed in the genome, all the descendant species should also inherit this
ERV. The probability that multiple species have independently been infected by
the same retrovirus at the same point in their genomes is quite remote. The
respected virologist John Coffin notes:
“Because the site of integration in the genome, which comprises some three billion base pairs in humans, is essentially random, the presence of an ancient provirus at exactly the same position in different, but related, species cannot occur by chance, but must be a consequence of integration into the DNA of a common ancestor of all the species that contain it. It evolution of retroviruses follows, therefore, that we can infer what viruses were present millions of years ago by examining the distribution of endogenous proviruses in modern species.” [22]
ERV elements differ from
pseudogenes and retrotransposons in that they have three sources of information
that allow evolutionary family trees to be constructed:
- The distribution of ERVs among related species
- Accumulated mutations in ERVs, allowing an
estimate of genetic distance
- Sequence divergence between the LTRs at each end of the ERV, which is a source of information unique to endogenous retroviruses.
The odds of this distribution of
ERV elements occurring by chance is remote. The vertebrate genome is huge, and
retroviral integration is random, making the odds of identical ERV integration
at the same place in multiple genomes 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.[23]
The second point has been
addressed previously, and need not be covered again. The final point is one
unique to ERVs. At each end of the ERV is a sequence known as a LTR, or Long
Terminal Repeat. The mechanics of reverse transcription mean that both LTRs
will be identical when the ERV integrates into the genome. Johnson and Coffin
note:
Furthermore, both clusters are predicted to have similar branching patterns as determined by the phylogenetic history of the host species, with similar branch lengths. Thus, each tree displays two estimates of host phylogeny, both of which are derived from the evolution of an initially identical sequence. As we shall see, deviation of actual trees from this prediction provides a powerful means of testing the assumptions and detecting events other than neutral accumulation of mutations in the evolutionary history of a species.[24]
Johnson and Coffin looked at the
distribution of ERVs in the primate genetic material analysed, and found:
Three of the loci, HERV-KC4, HERV-KHML6.17, and RTVL-Ia, were detectable in the genomes of OWMs and hominoids, but not New World monkeys, and therefore integrated into the germ line of a common ancestor of the Old World lineages. HERV-K18, RTVL-Ha, and RTVL-Hb were found exclusively in humans, gorillas, chimpanzees, and bonobos, and thus are consistent with a gorilla/chimpanzee/human clade. None of the loci was detected in New World monkeys.[25]
This is perfectly explained by
common descent. To reiterate 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.”
Johnson and Coffin found many loci shared by these primate species, some shared
only by humans, chimps, bonobos and gorillas, some shared only by old world
monkeys and hominoids (humans and great apes). This data is consistent with an
evolutionary origin of these species, but impossible to explain by special
creation.
Most of the ERVs analysed
produced phylogenetic trees consistent with expectation. Their conclusions:
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… Phylogenetic analysis using HERV LTR sequences gives rise to trees with a predictable topology, on which is superimposed the phylogeny of the host taxa, and allows ready detection of conversion events.[26]
Other studies show that humans
and primates share ERVs in a way consistent with common descent.
Barbulescu et al showed that many human ERVs of the HERV-K class (present
in humans, apes and old world monkeys) are unique to humans:
Two proviruses, HERV-K105 and HERV-K110/HERV-K18 were detected in both humans and apes. HERV-K110 was present in humans, chimpanzees, bonobos and gorillas but not in the orangutan. Thus, this provirus formed after orangutans diverged from the lineage leading to gorillas, chimpanzees, bonobos and humans, but before the latter species separated from each other. HERV-K105 was detected in humans, chimpanzees and bonobos, but not in gorillas or the orang-utan. The preintegration site, however, could not be detected in gorillas or orang-utans using several different primers based on the human sequences that flank this provirus. It is therefore unclear from this analysis whether this provirus formed after gorillas diverged from the human–chimpanzee–bonobo lineage, or if it formed earlier but was subsequently deleted in one or more lineages leading to modern apes. It is clear that at least one full-length HERV-K provirus in the human genome today has persisted since before humans, chimpanzees, bonobos and gorillas separated during evolution, while at least eight formed after humans diverged from the extant apes.[27]
Belshaw et al, looking at the long-term
reinfection of the human genome by ERVs note that:
Within humans, the most recently active ERVs are members of the HERV-K (HML2) family. This family first integrated into the genome of the common ancestor of humans and Old World monkeys at least 30 million years ago, and it contains >12 elements that have integrated since the divergence of humans and chimpanzees, as well as at least two that are polymorphic among humans…This recent activity makes this family ideal for distinguishing between the alternative mechanisms of proliferation.[28]
The pattern of HERV-K elements,
shown below, demonstrates just how powerful the ERV evidence is in
demonstrating human-ape common ancestry, as well as confirming the standard
evolutionary history of primates. Again, ERVs are remnants of ancient
viral infection. They are not native to humans or primates, but bear witness to
ancient retroviral infection. The odds of multiple identical HERV elements
integrating into primate and human DNA in exactly the right places to simulate
common descent are so low as to be effectively zero.
This is exactly what we see when
we examine human and primate genomes - multiple ERVs inserting at the same
place in their respective genomes. More importantly, the pattern of insertion
of these ERVs matches the standard evolutionary family tree. Medstrand and
Mager[29]
examined the pattern of insertions of a particular class of endogenous
retroviruses, the HERV-K family. Thirty-seven ERV fragments were aligned into
clusters based on sequence divergence. When they compared this with primate
genomic data, they found that the clusters with greater divergence were also
found in Old World monkeys and apes, while those with a lesser amount of
divergence were found only among gorillas and chimpanzees. The cluster with the
least amount of divergence was found only in the human genome.
The pattern of HERV-K element
insertion shown above once again matches what common descent would predict:
In general, LTR sequences of clusters 1 to 5 were first identified in Old World monkey and gibbon DNAs, whereas LTRs of cluster 8 first appeared in DNAs of gorilla and chimpanzee. For example, the AF001550 LTR of cluster 3 is not present in Old World monkeys but is present in gibbon and all higher primates. In contrast, the AC003023 cluster 8 LTR is found only in chimpanzee and human, indicating a more recent integration, Initial results with primers flanking three of the integrated LTRs of cluster 9 resulted in the expected amplification products in human DNA but not in any of the other primate DNAs, To demonstrate that sequences of cluster 9 were unique to human DNA, primers flanking the other six identified LTRs of this cluster, including the full-length HERV-K10 element, were used in the amplification of primate DNA. Indeed, all were detected only in human DNA, indicating that sequences derived from this cluster integrated after the divergence of the human lineage from the great apes.[30]
It is this nesting of HERV
clusters, in a way according with what common descent predicts that makes this
powerful evidence for common descent. ERVs are evidence of ancient retroviral
infection, and the presence of the same ERV at the same place in related
species is as Coffin states prima facie evidence for an ancient retroviral infection
in the ancestor of both species. When we multiply the number of ERVs that have
integrated in the same place in many primate genomes, but do so in the pattern
above, the case for common descent based solely on ERV inclusions becomes
overwhelming.
This is only an overview of the
evidence for common descent from comparative genomics which is itself only one
of the many lines of evidence confirming common descent, but alone is enough to
show why common descent is not in doubt by the mainstream scientific community.
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