In 2003, Dr. Salem and his colleagues analyzed short interspersed elements common to primates, called Alus, to determine the phylogeny of Hominids. Of special interest was the grouping of chimpanzees, humans, and orangutans, as data from comparative anatomy, hybridization, mitochondrial DNA, and nuclear DNA had been inconsistent.
Despite that “the consensus approach identifies the chimpanzee as the nearest living relative of humans (Salem et al., 2003, p. 12787),” different sources have yielded different answers to the question: “Which of the four possible relationships, ((H,C)G), ((H,G)C), ((C,G)H), and (H,C,G), reflects the true phylogeny of the three species (Salem et al., 2003, p. 12787)?”
To elucidate the true phylogeny, the human genome was searched for Ye5 subfamily Alus using a sequence common to that subfamily. This yielded 153 elements. A consensus sequence was constructed from them, and was then used as a BLAST query against the genomes of P. Troglodytes and P. paniscus. All matches greater than or equal to 90% were aligned to the human genome with BLAT, and the sequences present only in chimpanzees were isolated. Oligonucleotide primers were designed for loci involving these isolated sequences, as well as those identified in the search of the human genome. It was found that 117 elements in the human genome and 14 elements only in the chimpanzee genome were suitable for PCR analysis. PCR was performed using primers for these loci and two others, which were “informative with regard to the human–chimpanzee–gorilla trichotomy issue (Salem et al., 2003, p. 12788),” and with genomic DNA from various members of Hominidae, Cercopitheciodae, and Platyrrhini. This data was then used to construct a phylogenetic tree via Dollo parsimony analysis.
The resulting phylogenetic tree indicated that of the 133 Alu elements analyzed, 95 were unambiguously hierarchically grouped. Six elements were unambiguously specific to chimpanzees, with a bootstrap value of 100. Seven were present only in chimpanzees and humans (bootstrap: 99), and 33 present only in chimpanzees, humans, and gorillas (bootstrap: 100). Of the remaining 38 elements, 37 did not deviate from the nested hierarchy, but were ambiguous due to non-amplification events that left the possibility for deviation.
Only one of the 133 elements (Ye5AH137) was observed to deviate, as it was present in humans and gorillas, yet not in chimpanzees (with non-amplification in the orangutan DNA sample). This was hypothesized to be the result of an insertion in the chimpanzee-human-gorilla common ancestor that remained heterozygous in the populations across two divergences; ultimately fixing the allele with the preintegration site in the chimpanzee lineage, and fixing the Alu insertion in the human and gorilla lineages. This hypothesis was supported by the age estimate of the Ye5AH137 element. Using CpG mutation densities, it was dated to ~6.85 mya; around the same time other sequence data indicates that gorillas diverged. The same dating method yielded considerably younger ages for the 7 sequences shared only by chimpanzees and humans (Salem et al., 2003, p. 12790).
The conclusion drawn from these results was that Alu data robustly supports the same hypothesis supported by the consensus approach; that gorillas first diverged, then humans, then common chimpanzees and bonobos.
Salem, A. H., D. A. Ray, J. Xing, P. A. Callinan, J. S. Myers, D. J. Hedges, R. K. Garber, D. J. Witherspoon, L. B. Jorde, and M. A. Batzer. "Alu Elements and Hominid Phylogenetics." Proc Natl Acad Sci U S A 100.22 (2003 Oct 28): 12787-2791. <http://www.pnas.org/content/100/22/12787.full>.