Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution.

Abstract

Several subfamilies of the salmonid Hpa I short interspersed element (SINE) family were isolated from salmonid genomes and were sequenced. For each genomic locus that represented the subfamily, amplification by PCR of the orthologous loci in the 12 fish aflowed us to determine the order of branching of the Pacific salmonid species. The deduced phylogeny suggests three evolutionary lines, namely, a line of chum salmon, pink salmon, and kokanee; a line of coho salmon and chinook salmon; and a line ofsteelhead trout. Our data also support a change in the phylogenetic ament of steelhead trout from Salmo to Oncorhynchus. We present here an extensive phylogenetic tree constructed from an analysis of differential insertion of SINEs, and we propose that SINE insertion analysis is one of the best available methods for clarifying the order of divergence of closely related species.A retroposon is defined as a nucleotide sequence, present initially as a cellular RNA transcript, that has been reincorporated into the genome, presumably via a cDNA intermediate. Retroposons constitute roughly 10% of the human genome and are similarly abundant in other mammalian genomes (1, 2). As a result, the remarkable fluidity of eukaryotic genomes reflects the contributions of retroposition (2) as well as mechanisms operating at the DNA level such as mutation and recombination (1-4). Retroposons can be unique to one species, a few species, a genus, or in some cases a family. Retroposition is therefore a specialized form of gene duplication, which is believed to be of major importance in the creation of genetic diversity during evolution (5).Nonviral retroposons are classified into three main groups: processed retropseudogenes, LINEs (long interspersed elements), and SINEs (short interspersed elements) (6). Except for the rodent type 1 and human Alu families (7,8), all of the SINE families examined to date have been shown to be derived from tRNAs (9)(10)(11)(12)(13)(14). In contrast to DNA transposable elements, which are often capable of being excised precisely, SINEs appear to be inserted irreversibly and should therefore provide an ideal evolutionary and phylogenetic marker (4).The Pacific salmon and trout (Oncorhynchus) not in other species (16). These results suggest that these SINEs were amplified specifically within certain salmonid lineages during evolution.Our data prompted us to attempt to construct a phylogenetic tree for the salmonid species by using SINE insertions as irreversible events that would serve as informative markers of evolution. In this report, we present a characterization of the four subfamilies of the Hpa I family.t These subfamilies were amplified in the four different ancestral species within the genus Oncorhynchus. Such characterization provides a highly reliable order of branching of the various species of Oncorhynchus. MATERIALS AND METHODSExperiments were performed by using standard techniques (18)(19)(20)(21).The fish species examined in this study and their geographic sources are listed in Table ...

Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids.

“…The (Table 4). Phylogenetic relationships among the species of Oncorhynchus were recently reported by our group (30). The phylogenetic position of 0. masou is currently unknown, but the most likely relationship is indicated by a dotted line (30).…”

“…2e The type I subfamily includes three members (Hpa-12, -20, and -17) that are specifically amplified in the lineage of chum salmon. It should be noted that Hpa-51, which was demonstrated to have been amplified specifically in a common ancestor of chinook and coho salmon (30), is included in this subfamily. Therefore, the origin of the six diagnostic nucleotides common to the three Hpa I sequences amplified in the lineage of chum salmon and Hpa-51 must date back to before divergence of the five salmon species in the genus Oncorhynchus (Fig.…”

“…(Table 2), and then the polymerase chain reaction (PCR) was performed, using the genomic DNA from the seven listed species as templates. The naming of clones was as described previously (30 --- . At four loci, namely, the Hpa-12, -14, -17, and -20 loci, the member of the Hpa I subfamily was found to be present specifically only in the genome of chum salmon.…”

Phylogeny of Nolana (Solanaceae) of the Atacama and Peruvian deserts inferred from sequences of four plastid markers and the nuclear LEAFY second intron

“…The utility of 16 SINE has been basically restricted to animal phylogenetic reconstruction (Lum et al,17 2000; Murata et al, 1993;Nikaido et al, 2006;Nikaido et al, 2007;Shimamura et al, 18 1997) and has not attracted much attention among plant phylogenetists. Only a few sequence was considered to be characteristic of the TS family (Yoshioka et al, 1993).…”

CAN—a pan-carnivore SINE family

“…No mechanism of specific SINE elimination from the genome is known, and SINEs remain in the genomes of successors: MIR is found in all mammals, while Alu is specific for primates, which allows their use as independent phylogenetic markers Murata et al 1993;Shimamura et al 1997).…”