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What Separates Humans from Chimpanzees? (Part 1)
[This post is part of a series, What Separates Humans from the Animals?]
In a previous post in this series I explained that transposons are short stretches of DNA that make copies of themselves and insert back into the genome at a different place. Retrotransposons are very similar; the main difference between them is that regular transposons are directly copied as DNA, but retrotransposons are copied into RNA and then back into DNA, which then integrates into the genome. It may come as a surprise that retrotransposons make up about 42% of the human genome! (Regular transposons contribute another ~3%.)
There are several kinds of retrotransposons. Some are disabled viruses that are distantly related to HIV. Here we will focus on Alu elements, of which there are over 1 million copies in the human genome (or about 10% of the genome). Alu elements are only found in primate genomes, but they don't code for any proteins. A mere ~300 base pairs (i.e. DNA 'letters'), they depend entirely on proteins produced by the cell and other retrotransposons, for their replication. When new Alu copies integrate into the genome of a germline cell, the Alu element becomes part of the DNA that is passed on to that person's descendants. In humans they sometimes cause genetic diseases when they integrate into--and thus disrupt--a functional gene.
Scientists have found that Alu elements make great genetic markers, and the reason is pretty simple: for any stretch of DNA that has an Alu element, the ancestral state can be inferred to be the same stretch without the Alu. As an analogy, consider a document that has been photocopied repeatedly and distributed throughout an office. If you compare two copies--one with a nice big coffee stain, and one without--you know that the clean copy is descended from a copy that pre-dates the coffee-stained one. The same reasoning applies here. Further, the chances of two Alu elements independently inserting into the exact same place are low, and it is rare (but not impossible) for an Alu element to be precisely removed. 
When Alu elements are copied, mutations can occur which are then propagated to subsequent copies. For this reason, Alu elements can be grouped into families based on sequence differences [1]. Salem et al. compared Alu elements of a particular family in the genomes of humans, chimpanzees, bonobos (pygmy chimpanzees), orangutans, siamangs, green monkeys, and owl monkeys. More specifically, they looked for Alu elements that were located in the same place in the genome of different species. Their overall finding is summarized in Figure 3 of their paper.
Figure 3. Primate relationships reconstructed by using Dollo parsimony analysis of Alu elements. Primate relationships were derived from analysis of 133 Alu loci by using maximum parsimony criteria. The number of insertions observed along each branch of the tree is indicated, and bootstrap support values are placed above each node.
The figure is read similar to a family tree. Each node represents a common ancestor of all species to the right of that node. The numbers underneath the triangles indicate how many Alu elements are contained in identical locations in the genome of each species descended from that node. So, for example, humans, chimpanzees, bonobos, and gorillas all share 33 separate Alu elements at the same place in their DNA. Humans have 7 unique insertions, chimpanzees and bonobos together have 14. So for this family of Alu elements, humans and chimpanzees (including bonobos) are separated by 21 unique insertions. (If we consider all Alu families, humans have about 7,000 lineage-specific Alu insertions and chimpanzees have about 2,300.)
Yet, the unifying nature of the Alu insertions is obvious. As the authors wrote,The patterns observed clearly indicate a stepwise pattern of insertion reflecting the relative divergence of each group in the hominid lineage.
The clarity is impressive, but there is one minor snag. The authors found one Alu insertion shared between humans and gorillas that is not shared with chimpanzees. If you looked only at that insertion you would conclude that humans are more closely related to gorillas than chimpanzees. Is this a problem? No.
The splitting of the lineages that led to gorillas, chimpanzees, and humans are thought to have occurred within a few million years of each other. This has resulted in the trichotomy problem, which I have explained before (see Understanding Trichotomy). As I wrote then,Humans, chimpanzees and gorillas each have their roots in a common gene pool. However, the sorting of ancestral polymorphic alleles in the diverging lineages is subject to evolutionary processes such as genetic drift. Thus purely by chance, alleles can become fixed in a way that gives a different picture than the true species-branching pattern.
In other words, as the lineages leading to the different species were branching off from one another, the presence of that particular Alu within each population was in flux. Probably by chance, it was lost from the chimpanzee lineage and retained in the gorilla and human lineages. In support of this, the authors estimated the ages of the conflicting Alu insertions based on mutation rate and found that the anomalous insertion supporting the human-gorilla relationship is 1-4 million years older than those that support the human-chimpanzee relationship.
It is beautifully amazing to me that such short and simple pieces of DNA can provide such a clear picture of evolutionary history.
Notes:
[1] To see how the distribution of Alu families among primates also supports common descent, see Figure 3 in Roy-Engel et al.
References:
Salem AH, Ray DA, Xing J, Callinan PA, Myers JS, Hedges DJ, Garber RK, Witherspoon DJ, Jorde LB, Batzer MA. Alu elements and hominid phylogenetics. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12787-91.
Roy-Engel, A. M., M. A. Batzer and P. L. Deininger (2008) Evolution of human retrosequences: Alu. In "Encyclopedia of Life Sciences".
