Nuclear integrations of mitochondrial DNA in great apes

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DESCRIPTION (provided by applicant): - This is a proposal to examine Numts (mtDNA genes translocated to the nucleus) in humans and great apes. It will involve blast searches for hypervariable 1 gene (HV1) from mtDNA transcripts, inserted into nuclear genomes. These have elevated frequencies in gorillas, and hundreds have been described for humans. The fact that there is recombination even in vitro suggests that the phenomenon may not be all that rare. First, the strategy is (1) to screen Numts from chimpanzee and gorilla BAC libraries for nuclear insertions, as well as to search nuclear-enriched DNA phage libraries from sperm heads from several chimpanzees and gorillas. Then, these sequences will be compared with the pre-existing BLAST surveys of those species. Human Numts will be drawn from BLAST searches. Te comparative work is motivated by four questions: (a) Are HV1 integrants elevated in gorillas? (b) Is the rate of integration constant over time, or are there phylogenetic bursts? (c) Do rates of nucleotide evolution differ for mitochondrial and nuclear-integrated copies? (d) How well do the Numts match up with the classic gorilla subspecific taxonomy. Second, the idea is to map the insertion sites, using nuclear flanking sequences and mtDNA break sites for identification, and to determine whether there has been subsequent gene duplication in the nucleus, addressing three questions: (a) Are the sites of integration random, or are they sequence-regular? (b) What is the fraction of post-integration duplication? (c) Are there specific sequence motifs that are particularly prone to mobilization or to insertion? Third, an attempt will be made to use the Numts to reconstruct gorilla population history, since there are a great many in hand from the 1st phase of the study, addressing two questions: (a) Can we use polymorphic Numts to reconstruct gorilla population history? (b) Are the major gorilla subspecific clades evident in the HV1 data in the mitochondrion also evident in the Numts? The basic intent is twofold: (a) to explore the sorts of inferential difficulty caused by our inability to detect Numts in previous work, and (b) to determine the extent to which they can used to advantage for taxonomic or population genetic purposes.