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Recent activity of the retrotransposable B2 element in hamsters and its use as a phylogenetic marker.

Article Excerpt
ABSTRACT

A recent analysis of DNA sequences of hamsters, in the rodent subfamily Cricetinae (family Cricetidae, superfamily Muroidea), generated a significant phylogenetic restructuring among the genera Tscherkia, Cricetus, Allocricetulus and Cricetulus. We present an analysis of this group of hamsters using retrotransposons as phylogenetic markers to further assess the modified phylogeny. Retrotransposons represent a group of transposable elements that integrate into new genomic locations via an RNA intermediate. The novel use of this tool is that organisms that share a specific retrotransposon integration should share a common ancestor. We present the first examples of recent retrotransposon integrations in the hamster genome and provide support for the revised phylogenetic relationship of hamsters. This study demonstrates that retrotransposons can be valuable tools in ascertaining phylogenetic relationships.

INTRODUCTION

The subfamily Cricetinae (family Cricetidae, superfamily Muroidea) consists of the group of rodents commonly referred to as hamsters. Members of Cricetinae are mouse-like animals with a thickset body, short tail, and cheek pouches (Nowak 1991). The subfamily Cricetinae is currently composed of seven genera: Allocricetulus, Cansumys, Cricetulus, Cricetus, Mesocricetus, Phodopus, and Tscherskia, with a total of eighteen species (Musser and Carleton 2005). The taxonomic relationships among extant Cricetinae were generated based on morphological (Carleton and Musser 1984) and cytological (Gamperl et al. 1978) data. Recent molecular phylogenies have been constructed for the superfamily Muroidea using DNA sequences from various genes: lecithin cholesterol acyl transferase (LCAT) gene and von Willebrand factor (vWF) gene (Michauex et al. 2001), interphotoreceptor retinoid binding protein (IRBP) gene (Jansa and Weksler 2003), growth hormone receptor (GHR), breast cancer gene 1 (BRCA1), recombination activating gene 1 (RAG1), and protooncogene c-myc (Steppan et al. 2004). However, none of these studies included adequate taxon sampling to assess the detailed phylogenetic relationships among members of the subfamily Cricetinae.

One detailed phylogenetic study of the Cricetinae subfamily (Neumann et al. 2006) utilized DNA sequences from two mitochondrial genes (cytochrome b and 12S rRNA) and one nuclear gene (von Willebrand Factor exon 28). Their phylogenetic tree argues against monophyly of the genus Cricetulus. Most notable was the formation of a clade consisting of Tscherskia triton, Cricetulus migratorius, Cricetus cricetus, and Allocricetulus eversmanni that branches off from a clade consisting of other Cricetulus species.

A relatively new phylogenetic tool involves short interspersed DNA elements (SINEs), which are groups of non-autonomous retrotransposons that are abundant in many mammalian genomes. SINEs can jump within the genome by a process called retrotransposition in which the retrotransposon "master gene" is copied into an RNA intermediate, reverse transcribed...

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