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An ancient retrovirus-like element contains hot spots for SINE insertion
M A Cantrell1, B J Filanoski, A R Ingermann
1Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
Genetics
|June 19, 2001
Summary
Short interspersed elements (SINEs) can insert into the same DNA site independently. This challenges their use as reliable phylogenetic markers in rodent evolution studies.
Area of Science:
- Molecular Evolution
- Genomics
- Phylogenetics
Background:
- Vertebrate retrotransposons are crucial for phylogenetic and molecular evolution studies.
- Presence/absence of specific elements at a locus was considered a homoplasy-free phylogenetic character.
- Mys elements are LTR-containing retrotransposons found in Sigmodontine rodents.
Purpose of the Study:
- Investigate the phylogenetic utility of SINE insertions within the mys-9 retrotransposon locus.
- Determine if independent SINE insertions occur at identical sites.
- Assess the homoplasy-free nature of SINE insertions as phylogenetic markers.
Main Methods:
- Comparative sequence analysis of the mys-9 retrotransposon across Peromyscus species.
- Identification of short interspersed element (SINE) insertions within the mys-9 locus.
- Analysis of SINE insertion site identity and frequency.
Main Results:
- The mys-9 insert is ancient, present across multiple Peromyscus species.
- Variations in mys-9 insert size are attributed to ongoing SINE insertions.
- Two "hot spots" within mys-9 show evidence of independent SINE insertions at identical sites.
Conclusions:
- Independent SINE insertions at the same locus can occur, challenging previous assumptions.
- Phylogenetic conclusions based on SINE presence at specific loci require caution.
- SINE insertions are not entirely homoplasy-free phylogenetic markers.