Thursday 2 February 2012

Does the Chromosome 2 Fusion Evidence Prove Our Shared Ancestry With Chimpanzees?

Those of you who follow discussions surrounding evolution and intelligent design will doubtless have heard of the argument for human-chimp shared ancestry based on evidence for a fusion event with respect to chromosome 2. This argument is put forward quite famously by Brown University biologist Ken Miller in this video:

Briefly, the chromosomal fusion argument for human-chimp common descent begins with the observation that humans possess 23 pairs of chromosomes, whereas apes possess 24 pairs, thus allowing one to predict that -- evolution being true -- a chromosomal fusion must have taken place at some point in our lineage. And, indeed, this is what we observe. Chromosome 2 possesses two centromeres. It also possesses a section where there are two telomeres in the middle of the chromosome, which are oriented in such a way so as to suggest that the ends of the two chromosomes were fused together. Every telomere in human and great-ape chromosomes has the six base-pair sequence TTAGGG repeated over and over approximately fifty to one hundred times in tandem. Such telomeric repetitive units, when they are found not in the telomeres at the end of the chromosome, but rather in the middle of the chromosome (perhaps near the centromere), are referred to in the literature as "interstitial telomeric sequences" (or ITS's). At the supposed fusion site in chromosome 2, the sequence in the upper strand abruptly changes from TTAGGG repeats to CCCTAA repeats (the complementary sequence of the inversion). This is taken to indicate that the DNA in a telomere of one chromosome and the DNA in a telomere of the other chromosome broke and subsequently the two chromosomes fused at the broken ends. This site is referred to in the literature as 2q13 ("2" referring to the chromosome number, "q" referring to the long arm, and "13" referring to the position on the arm).

Furthermore, chromosomal centromeres possess a characteristic DNA called alpha satellite sequences. Secondary alpha satellite DNA (over and above that which is associated with the active centromere), which has been found in the case of chromosome 2 (see Avarello et al. 1992), is taken as further evidence for this fusion event.

But just how sound is this argument?

For one thing, there are, in fact, plausible alternative explanations for this observation. For example, envision a scenario where our genus Homo, originally possessing 48 chromosomes, underwent a chromosomal fusion event within its own independent lineage. Sure, the banding patterns of chromosome 2 are similar to two of the autosomes in the chimpanzee lineage. But then we are only coming back to the argument from similarity, which supports common descent no more than it suggests common design.

Secondly, some of the arguments for supposing that chromosome 2 did indeed arise from a fusion event have been significantly weakened in recent years. One very interesting peer-reviewed paper, appearing in the journal Cytogenetic and Genome Research in 2009, by Farre, Ponsa and Bosch, reported:

Although their function has not yet been clearly elucidated, interstitial telomeric sequences (ITSs) have been cytogenetically associated with chromosomal reorganizations, fragile sites, and recombination hotspots. In this paper, we show that ITSs are not located at the exact evolutionary breakpoints of the inversions between human and chimpanzee and between human and rhesus macaque chromosomes. We proved that ITSs are not signs of repair in the breakpoints of the chromosome reorganizations analyzed. We found ITSs in the region (0.7-2.7 Mb) flanking one of the two breakpoints in all the inversions assessed. The presence of ITSs in those locations is not by chance. They are short (up to 7.83 repeats) and almost perfect (82.5-97.1% matches). The ITSs are conserved in the species compared, showing that they were present before the reorganizations occurred.
So, what is the significance of the cited paper? Though there are many documented instances of these interstitial telomeric sequences in the genomes of humans and chimps, the 2q13 interstitial telomeric sequence is the only one that is able to be associated with an evolutionary breakage point or fusion. The other ones fail to line up with primate chromosomal breakpoints.

As the authors of the paper note,

The availability of complete genome sequences (Hubbard et al., 2007) offers the opportunity to characterize the regions flanking the breakpoints of chromosomal reorganizations at the molecular level. However, to our knowledge, only the head-to-head ITS located in the human 2q13 region, which is a relic of an ancient telomere-telomere fusion, is precisely associated with an evolutionary breakpoint (Ijdo et al., 1991). Here, we used bioinformatic tools to analyze, in the current genome releases, the presence of short ITSs in the chromosomal inversions that do not involve terminal regions and that occurred between human and chimpanzee and between human and rhesus macaque during evolution."
The pro-ID evolutionary biologist Richard Sternberg has also briefly weighed in on the paper here. Sternberg notes,
How, precisely, are miles and miles of TTAGGG of significance? From the standpoint of chromosome architecture, the repetitive elements en masse have the propensity to form complicated topologies such as quadruplex DNA. These sequences or, rather, topographies are also bound by a host of chromatin proteins and particular RNAs to generate a unique "suborganelle" -- for the lack of better term -- at each end. As a matter of fact, the chromatin organization of telomeres can silence genes and has been linked to epigenetic modes of inheritance in yeast and fruit flies. Furthermore, different classes of transcripts emanate from telomeres and their flanking repetitive DNA regions, which are involved in various and sundry cellular and developmental operations.


ITSs reflect sites where TTAGGG repeats have been added to chromosomes by telomerases, that these repeats are moreover engineered -- literally synthesized by the telomerase machinery, that ITSs have a telomere-like chromatin organization and are associated with distinct sets of proteins, and that many have been linked to roles such a recombination hotspots.

Thus, the take-home message is this: To make much of the 2q13 interstitial telomeric sequence and portray it as typical of what is observed in chimp and human genomes may be considered careful cherry-picking of data.

And what about the secondary alpha satellite sequences found in chromosome 2? Is that not best understood as a genetic residue from a previously functioning centromere on a separate chromosome? Perhaps. But the situation is not quite as clear as is often made out. Neo-centromeres, for example, are rare events which result in the formation of a new centromere (see, for example, Warburton 2004). One suggestion, however, that the additional centromere in chromosome 2 did not arise by this process is the fact that neo-centromeres are usually not associated with the characteristic centromeric repetitive alpha-satellite DNA. But these neo-centromeres are poorly understood, and it may come to pass that a mechanism is discovered that can make these neo-centromeres full of alpha-satellite DNA.

One particularly interesting study, from Baldini et al. (1993), reported the presence of secondary alpha satellite DNA on human chromosome 9! To further complicate matters, Luke and Verma (1995) subsequently reported on the occurrence of secondary alpha satellite DNA in all primates. In 1997, a research group published another interesting study (Samonte et al., 1997). These researchers hybridized twenty-one different chromosome-specific human alpha satellite DNA probes to the full complement of chromosomes from the chimpanzee, gorilla and the orangutan. They reported that most of the human probes failed to hybridize to the equivalent ape chromosome. Instead, they gave positive signals on non-corresponding chromosomes. Thus, they concluded, alpha satellite DNA sequences show little conservation in primate lineages.

In summary, the argument for human-chimp common ancestry, based on the chromosome 2 fusion evidence, is inconclusive. Given the sheer lack of a viable naturalistic mechanism to account for the evolution of life on earth, I am inclined to be rather skeptical of the claims of common descent -- particularly in its universal sense.

This article was excerpted from a longer article on Evolution News & Views.

1 comment:

  1. I know this is an old post, but I was hoping you could clarify your position. I struggle to see how you can make the claim of cherry picking when the fusion site is the only ITS in a head-to-head configuration, and it is an order of magnitude longer (~800bp) than the longest of these short ITSs ("up to 7.83 repeats" = 47bp).


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