Molecular Evolution of Nuclear insertions of Mitochondrial DNA in Great Apes
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(Iván Soto-Calderón, Eun-Joo Lee, N. Jonathon Clark)
Prior to the advent of next generation sequencing technologies, much non-invasive population genetic work on wild apes was based on the mitochondrial genetic markers. However, interpretation of such sequence databases was complicated by the widespread translocation of mitochondrial DNA fragments into the nuclear genome or “numts”. To tackle this issue, we were able to develop a battery of tools for the diagnosis of both numt contaminants and their in vitro recombinants in gorilla mitochondrial DNA databases (Anthony et al., 2007b). Through an NIH-AREA award, we then employed a combination of bioinformatic and genomic surveys to assess both rates and mechanism(s) of nuclear integration in humans and chimpanzees (Jensen-Seaman et al., 2009). |
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Work on great ape genomic databases also revealed that the prevalence of control region numts is likely to be under-estimated as a result of the rapid loss of sequence identity between hyper-variable control region sequences and their numt copies (Soto-Calderon et al., 2012). Current work is focused on examining the utility of numt inserts as genetic markers in their own right as well as furthering understanding of how nuclear integration impacts patterns of molecular evolution in hyper-variable sequences. This work has been conducted in collaboration with Mike Jensen-Seaman (Duquesne University) who served as co-PI on the NIH-AREA award.
Anthony N.M., Anthony N.M., Clifford S.L., Bawe-Johnson M., Abernethy K.A., Bruford M.W. and Wickings E. J. (2007b) Distinguishing mitochondrial sequences from nuclear integrations and PCR recombinants: guidelines for their diagnosis in complex sequence databases. Molecular Phylogenetics and Evolution 43: 553-566.
Anthony N.M., Johnson-Bawe M., Jeffery K., Clifford S.L., Abernethy K.A., Tutin C.E., Lahm S.A., White L.T.J., Utley J., Wickings E.J. and Bruford M.W. (2007a) The role of Pleistocene refugia and rivers in shaping gorilla genetic diversity in central Africa. Proceedings of the National Academy of Sciences U.S.A. 104: 20432-20436.
Clifford S.L.§, Anthony N.M.§, Bawe-Johnson M., Abernethy K.A., Tutin C.E.G., White L.J.T., McFarland K., Goldsmith M.L., Bermejo M., Bruford M.W. and Wickings E.J. (2004) Mitochondrial phylogeography of western lowland gorillas Gorilla gorilla gorilla. Molecular Ecology 13: 1551-1567.
Jensen-Seaman M.I., Wildschutte J.V.H, Soto-Calderon I. and Anthony N.M. (2009). A comparative approach reveals differences in patterns of numt insertion during hominoid evolution. Journal of Molecular Evolution 68: 688-699.
Soto-Calderón I.D., Lee E.J., Jensen-Seaman M.I. and Anthony N.M. (2012) Factors affecting the relative abundance of nuclear copies of the mitochondrial control region (numts) in hominoids Journal of Molecular Evolution. doi:10.1007/s00239-012-9519-y
Anthony N.M., Anthony N.M., Clifford S.L., Bawe-Johnson M., Abernethy K.A., Bruford M.W. and Wickings E. J. (2007b) Distinguishing mitochondrial sequences from nuclear integrations and PCR recombinants: guidelines for their diagnosis in complex sequence databases. Molecular Phylogenetics and Evolution 43: 553-566.
Anthony N.M., Johnson-Bawe M., Jeffery K., Clifford S.L., Abernethy K.A., Tutin C.E., Lahm S.A., White L.T.J., Utley J., Wickings E.J. and Bruford M.W. (2007a) The role of Pleistocene refugia and rivers in shaping gorilla genetic diversity in central Africa. Proceedings of the National Academy of Sciences U.S.A. 104: 20432-20436.
Clifford S.L.§, Anthony N.M.§, Bawe-Johnson M., Abernethy K.A., Tutin C.E.G., White L.J.T., McFarland K., Goldsmith M.L., Bermejo M., Bruford M.W. and Wickings E.J. (2004) Mitochondrial phylogeography of western lowland gorillas Gorilla gorilla gorilla. Molecular Ecology 13: 1551-1567.
Jensen-Seaman M.I., Wildschutte J.V.H, Soto-Calderon I. and Anthony N.M. (2009). A comparative approach reveals differences in patterns of numt insertion during hominoid evolution. Journal of Molecular Evolution 68: 688-699.
Soto-Calderón I.D., Lee E.J., Jensen-Seaman M.I. and Anthony N.M. (2012) Factors affecting the relative abundance of nuclear copies of the mitochondrial control region (numts) in hominoids Journal of Molecular Evolution. doi:10.1007/s00239-012-9519-y
