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Retrotransposons are a class of repetitive mobile elements which transpose via the reverse transcription of an RNA intermediate (Boeke et al. 1985). These eukaryotic elements are abundant and widespread and are hypothesized to be of major evolutionary significance (Miller, Kruckenhauser, and Pinsker 1996; Kidwell and Lisch 1997; McDonald 1998). The yeast Ty retrotransposons (Ty1–Ty5) are arguably the best-characterized retrotransposons (Boeke 1989). A vast number of studies have elucidated in detail the mechanisms of Ty retrotransposition and the molecular interactions between Ty elements and their host genomes (Garfinkel 1992). The sequencing of the Saccharomyces cerevisiae genome (Goffeau et al. 1996) provides an unprecedented opportunity to examine the patterns of molecular variation existing among an entire complement of retrotransposons residing within a genome. Detailed analysis of these Ty element sequences promises to yield deep insight into the nature of Ty element evolution and retroelement evolution in general. Recent studies demonstrate the potential power of such analyses and have shed new light on retroelement–host coevolution (Hani and Feldman 1998; Jordan and McDonald 1998; Kim et al. 1998). We recently performed phylogenetic analyses on sequence alignments of Ty1 and Ty2 elements characterized during the yeast genome project. Also included in our analyses were previously reported Ty1 (Ty1-H3 and Ty1-912) and Ty2 (Ty2-117) sequences (Clare and Farabaugh 1985; Warmington et al. 1985; Boeke et al. 1988). The Ty1 and Ty2 element families consist of closely related elements that are similar in size and sequence. These elements consist of two long terminal repeats (LTRs), known as d sequences, which flank two open reading frames (ORFs) TYA and TYB. The d sequences are made up of the U3-R-U5 regions as defined by the initiation and termination of transcription (Boeke et al. 1985). Ty1 and Ty2 elements were previously thought to share similar d sequences but differ in their open reading frames (Curcio and Garfinkel 1994). The TYA ORF is homologous to the gag locus of retroviruses and encodes structural proteins of the viral-like particle (Clare and Farabaugh 1985). TYB is homologous to the pol locus and encodes the catalytic proteins protease

Phylogenetic perspective reveals abundant Ty1/Ty2 hybrid elements in the Saccharomyces cerevisiae genome