Evolutionary applications of MIRs and SINEs

Area of Science:

• Genomics
• Molecular Evolution
• Bioinformatics

Background:

• Short interspersed elements (SINEs) are generally considered to be irreversibly integrated into genomes.
• This characteristic has led to their proposed use in tracing evolutionary lineages, such as whale evolution.
• The association of microsatellites with SINEs prompted an investigation into SINEs within artiodactyl genomes.

Purpose of the Study:

• To investigate the evolutionary history of whales using sequence and hybridization studies of SINEs.
• To determine if putative cetacean SINEs (CetSINE1 and CetSINE2) and a bovine SINE are true SINEs or a different class of repetitive elements.
• To assess the utility of these elements in resolving evolutionary relationships within ungulates and cetaceans.

Main Methods:

• Bioinformatic screening of sequences flanking ungulate microsatellites for artiodactyl-derived SINEs.
• Sequence alignment and comparison of two putative cetacean SINEs and a bovine SINE with sequences from various ungulates.
• Hybridization studies using the identified SINEs to probe their distribution across different mammalian taxa.

Main Results:

• The bovine SINE was exclusively found in ruminants.
• CetSINE1 was detected in all tested ungulates and cetaceans, with the strongest signal in hippopotamus and beluga.
• CetSINE2 hybridized to all ungulate suborders, suggesting a broader distribution than the bovine SINE but potentially different from CetSINE1.

Conclusions:

• The investigated elements, initially presumed to be SINEs, are likely mammalian-wide interspersed repeats (MIRs).
• MIRs may have a wider distribution and different insertion dynamics compared to SINEs.
• The evolutionary resolving power of these elements for tracing whale and ungulate evolution might be less than initially anticipated due to their broader distribution and potential for remobilization.