The potential use of repetitive sequences in phylogenetic reconstructions.

Abstract

In this paper, I will examine the virtues and problems of using repetitive DNA sequences for molecular systematics in rodents. I will concentrate on a particular family of repetitive sequences called LINES ONE or Ll for short. The prototypes for this family were the KpnI family of primates and the BamHI (also called MIF-l) family of mice (see for review Singer 1982a,b; Singer and Skowronski 1985; Rogers 1985). After the realization that the Kpnl and BamHI sequences were homologous (Singer et al. 1983), the entire family was named LINES, which is an acronym for long interspersed repeated sequences (Singer 1982a,b). The family has up to 100,000 copies per genome in rodents (Gebhard and Zachau 1983), with a somewhat lower copy number reported for primates (Grimaldi et al. 1984). Ll is the only mammalian LINES characterized with such a high copy number. It is responsible for many of the ethidium intense restriction bands observed after gel electrophoresis of restricted genomic DNA; hence the tendency to be named after restriction enzymes. Its distinguishing properties are its length and interspersion. Ll sequences are up to 7 kilobases long, although many of the copies consist of only a fraqment of the total sequence. Its distribution in the genome is roughly uniform.