Alu elements and hominid phylogenetics

Abstract

Alu elements have inserted in primate genomes throughout the evolution of the order. One particular Alu lineage (Ye) began amplifying relatively early in hominid evolution and continued propagating at a low level as many of its members are found in a variety of hominid genomes. This study represents the first conclusive application of short interspersed elements, which are considered nearly homoplasy-free, to elucidate the phylogeny of hominids. Phylogenetic analysis of Alu Ye5 elements and elements from several other subfamilies reveals high levels of support for monophyly of Hominidae, tribe Hominini and subtribe Hominina. Here we present the strongest evidence reported to date for a sister relationship between humans and chimpanzees while clearly distinguishing the chimpanzee and human lineages.

Fig. 1.

Alu consensus sequence alignment. Shown is the alignment of the consensus sequences of each Alu subfamily used in the study. The dots represent the same base present in the Y subfamily consensus sequence. Mutations are denoted by the appropriate base, and deletions are denoted by dashes.

Fig. 2.

Phylogenetic analysis of the expansion of the Alu Ye subfamily. Several examples of gel chromatographs used to determine the phylogenetic origin of individual Ye5 Alu subfamily members in primates are shown. Upper DNA fragments indicate “filled” sites where an Alu has inserted. Lower fragments indicate “empty” sites, the orthologous locus where no Alu has inserted. For example, Alu Ye5AH148 is found within the genomes of all apes. By contrast, Alu Ye5AH110 is found only in the human genome and is absent from all nonhuman primates, indicative of its relatively recent origin.

Fig. 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.

Fig. 4.

Lineage sorting model proposed for the Alu Ya5AH137 locus. In this model, Alu Ye5AH137 is polymorphic (indicated as +/–) in the ancestral population that gave rise to humans, chimpanzees, and gorillas. Random fixation of the alternative alleles in each of the three subsequent lineages results in a pattern supporting the Homo–Gorilla association instead of Homo–Pan.