Alu elements and primate genomics

Alu elements are a primate-specific non-autonomous retrotransposon of ~300 base pairs (bp). A Short INterspersed Element (SINE), Alu elements are found in high copy number in genomes across the primate radiation. Alu elements have a history of effective use as a phylogenetic marker due to the presence-absence nature of their retrotransposition, and have been implicated in the cause of a number of genetic diseases. Various subfamilies of Alu elements have gone through periods of increased activity during the history of the primate radiation, with the overwhelming majority of elements classified as genomic fossils which no longer propagate but can serve as useful markers in elucidating phylogenies. Lemurs (Infraorder: Lemuriformes) are a monophyletic radiation of strepsirrhine primates indigenous to the Island of Madagascar. The Lemuriformes are taxonomically subdivided into 5 families and \u3e100 species, with numerous questions remaining to be answered about evolutionary relationships at the family, genus, and species levels. We computationally examined the grey mouse lemur (Microcebus murinus) genome for the presence of informative Alu elements and constructed a phylogenetic tree of 22 lemur species and 2 out-group species using the 138 loci retrieved. Alu element activity level in primate genomes varies widely across species examined. The genome of the Western lowland gorilla (Gorilla gorilla gorilla) was sequenced in 2012 and made available for study. We examined this genome for the presence of AluY elements. AluY is the youngest Alu subfamily and the one most active in the hominid lineage. Our study elucidated 1,075 western lowland gorilla-specific AluY elements classified into 10 subfamilies based on diagnostic mutations in the sequence of the element