Mitochondrial control region sequences from an African American population sample

Forensic Science International: Genetics

Volumn 4, Issue 1, 2009, Pages

  Diegoli, Toni M ^a   Irwin, Jodi A ^a   Just, Rebecca S ^a   Saunier, Jessica L ^a   O'Callaghan, Jennifer E ^a   Parsons, Thomas J ^a  

^a Armed Forces DNA Identification Laboratory   (United States)

Author keywords

African American; Control region; Mitochondrial DNA

Indexed keywords

MITOCHONDRIAL DNA;

AFRICAN AMERICAN; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENETIC VARIABILITY; HAPLOTYPE; HETEROPLASMY; HUMAN; MITOCHONDRIAL GENE; NUCLEOTIDE SEQUENCE; POPULATION DISTRIBUTION; POPULATION GENETICS; PRIORITY JOURNAL; REGULATOR GENE; SHORT TANDEM REPEAT; UNINDEXED SEQUENCE;

AFRICAN CONTINENTAL ANCESTRY GROUP; DNA FINGERPRINTING; DNA, MITOCHONDRIAL; GENETICS, POPULATION; HAPLOTYPES; HUMANS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; UNITED STATES;

EID: 70649091309     PISSN: 18724973     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fsigen.2009.04.010     Document Type: Article

References (41)

1. Butler J.M., Schoske R., Vallone P.M., Redman J.W., and Kline M.C. Allele frequencies for 15 autosomal STR loci on U.S. Caucasian, African American, and Hispanic populations. J. Forensic Sci. 48 (2003) 908-911
2. Just R.S., Diegoli T.M., Saunier J.L., Irwin J.A., and Parsons T.J. Complete mitochondrial genome sequences for 265 African American and U.S. "Hispanic" individuals. Forensic Sci Int.: Gen. 2 (2008) e45-e48
3. Brandstätter A., Peterson C.T., Irwin J.A., Mpoke S., Koech D.K., Parson W., and Parsons T.J. Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database. Int. J. Legal Med. 118 (2004) 294-306
4. Irwin J.A., Saunier J.L., Strouss K.M., Sturk K.A., Diegoli T.M., Just R.S., Coble M.D., Parson W., and Parsons T.J. Development and expansion of high-quality control region databases to improve forensic mtDNA evidence interpretation. Forensic Sci. Int.: Gen. 1 (2007) 154-157
5. Anderson S., Bankier A.T., Barrell B.G., De Bruijn M.H.L., Coulson A.R., Drouin J., Eperon I.C., Nierlich D.P., Roe B.A., Sanger F., Schreier P.H., Smith A.J.H., Staden R., and Young I.G. Sequence and organization of the human mitochondrial genome. Nature 290 (1981) 457-465
6. Andrews R.M., Kubacka I., Chinnery P.F., Lightowlers R.N., Turnbull D.M., and Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nature Gen. 23 (1999) 147
7. Achilli A., Rengo C., Magri C., Battaglia V., Olivieri A., Scozzari R., Cruciani F., Zeviani M., Briem E., Carelli V., Moral P., Dugoujon J., Roostalu U., Loogvali E., Kivisild T., Bandelt H., Richards M., Villems R., Santachiara-Benerecetti A., Semino O., and Torroni A. The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am. J. Hum. Genet. 75 (2004) 910-918
8. Achilli A., Rengo C., Battaglia V., Pala M., Olivieri A., Fornarino S., Magri C., Scozzari R., Babudri N., Santachiara-Banerecetti A.S., Bandelt H.J., Semino O., and Torroni A. Saami and Berbers-an unexpected mitochondrial DNA link. Am. J. Hum. Genet. 76 (2005) 883-886
9. Allard M.W., Miller K., Wilson M., Monson K., and Budowle B. Characterization of the Caucasian haplogroups present in the SWGDAM forensic mtDNA dataset for 1771 human control region sequences. J. Forensic Sci. 47 (2002) 1215-1223
10. Allard M.W., Polanskey D., Miller K., Wilson M.R., Monson K.L., and Budowle B. Characterization of human control region sequences of the African American SWGDAM forensic mtDNA data set. Forensic Sci. Int. 148 (2005) 169-179
11. Bandelt H.J., Alves-Silva J., Guimaraes P.E., Santos M.S., Brehm A., Pereira L., Coppa A., Larruga J.M., Rengo C., Scozzari R., Torroni A., Prata M.J., Amorim A., Prado V.F., and Pena S.D. Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade. Ann. Hum. Genet. 65 (2001) 549-563
12. Brehm A., Pereira L., Bandelt H.J., Prata M.J., and Amorim A. Mitochondrial portrait of the Cabo Verde archipelago: the Senegambian outpost of Atlantic slave trade. Ann. Hum. Genet. 66 (2002) 49-60
13. Finnila S., Lehtonen M.S., and Majamaa K. Phylogenetic network for European DNA. Am. J. Hum. Genet. 68 (2001) 1315-1320
14. Kivisild T., Tolk H., Parik J., Wang Y., Papiha S., Bandelt H.J., and Villems R. The emerging limbs and twigs of the East Asian mtDNA tree. Mol. Biol. Evol. 19 (2002) 1737-1751
15. Lee H.Y., Yoo J., Park M.J., Chung U., and Shin K.J. Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control. Int. J. Legal Med. 120 (2006) 5-14
16. Macaulay V., Richards M., Hickey E., Vega E., Cruciani F., Guida V., Scozzari R., Bonne-Tamir B., Sykes B., and Torroni A. The emerging tree of west Eurasian mtDNAs: a synthesis of control region and RFLPs. Am. J. Hum. Genet. 64 (1999) 232-249
17. Mishmar D., Ruiz-Pesini E., Golik P., Macaulay V., Clark A.G., Hosseini S., Brandon M., Easley K., Chen E., Brown M.D., Sukernik R.I., Olckers A., and Wallace D.C. Natural selection shaped regional mtDNA variation in humans. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 171-176
18. Pereira L., Macaulay V., Torroni A., Scozzari R., Prata M.J., and Amorim A. Prehistoric and historic traces in the mtDNA of Mozambique: insights into the Bantu expansions and the slave trade. Ann. Hum. Genet. 65 (2001) 439-458
19. Palanichamy M.G., Sun C., Agrawal S., Bandelt H.J., Kong Q.P., Khan F., Wang C.Y., Chaudhuri T.K., Palla V., and Zhang Y.P. Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia. Am. J. Hum. Genet. 75 (2004) 966-978
20. Quintana-Murci L., Semino O., Bandelt H.J., Passarino G., McElreavey K., and Santachiara-Benerecetti A.S. Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa. Nat. Genet. 23 (1999) 437-441
21. Quintana-Murci L., Chaix R., Wells S., Behar D., Sayar H., Scozzari R., Rengo C., Al-Zahery N., Semino O., Santachiara-Benerecetti A.S., Coppa A., Ayub Z., Mohyuddin A., Tyler-Smith C., Mehdi S.Q., Torroni A., and McElreavey K. Where West meets East: the complex mtDNA landscape of the southwest and central Asian corridor. Am. J. Hum. Genet. 74 (2004) 827-845
22. Reidla M., Kivisild T., Metspalu E., Kaldma K., Tambets K., Tolk H.V., Parik J., Loogvali E.L., Derenko M., Malyarchuk B., Bermisheva M., Zhadanov S., Pennarun E., Gubina M., Golubenko M., Damba L., Fedorova S., Gusar V., Grechanina E., Mikerezi I., Moisan J.P., Chaventre A., Khusnutdinova E., Osipova L., Stepanov V., Voevoda M., Achilli A., Rengo C., Rickards O., De Stefano G.F., Papiha S., Beckman L., Janicijevic B., Rudan P., Anagnou N., Michalodimitrakis E., Koziel S., Usanga E., Geberhiwot T., Herrnstadt C., Howell N., Torroni A., and Villems R. Origin and diffusion of mtDNA haplogroup X. Am. J. Hum. Genet. 73 (2003) 1178-1190
23. Richards M., Macaulay V., Hickey E., Vega E., Sykes B., Guida V., Rengo C., Sellitto D., Cruciani F., Kivisild T., Villems R., Thomas M., Rychkov S., Rychkov O., Rychkov Y., Golge M., Dimitrov D., Hill E., Bradley D., Romano V., Cali F., Vona G., Demaine A., Papiha S., Triantaphyllidis C., Stefanescu G., Hatina J., Belledi M., Di Rienzo A., Novelletto A., Oppenheim A., Norby S., Al-Zaheri N., Santachiara-Benerecetti S., Scozari R., Torroni A., and Bandelt H.J. Tracing European founder lineages in the Near Eastern mtDNA pool. Am. J. Hum. Genet. 67 (2000) 1251-1276
24. Rogers A.R., and Harpending H.C. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9 (1992) 552-569
25. Salas A., Richards M., De la F.T., Lareu M.V., Sobrino B., Sanchez-Diz P., Macaulay V., and Carracedo A. The making of the African mtDNA landscape. Am. J. Hum. Genet. 71 (2002) 1082-1111
26. Schurr T., and Wallace D. Mitochondrial DNA diversity in Southeast Asian populations. Hum. Biol. 74 (2002) 431-452
27. Stepanov V., Puzyrev V., Rudan P., Balanovska E.V., Grechanina E., Richard C., Moisan J.P., Chaventré A., Anagnou N.P., Pappa K.I., Michalodimitrakis E.N., Claustres M., Gölge M., Mikerezi I., Usanga E., and Villems R. Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia. Mol. Biol. Evol. 21 (2004) 2012-2021
28. Torroni A., Rengo C., Guida V., Cruciani F., Sellitto D., Coppa A., Calderon F.L., Simionati B., Valle G., Richards M., Macaulay V., and Scozzari R. Do the four clades of the mtDNA haplogroup L2 evolve at different rates?. Am. J. Hum. Genet. 69 (2001) 1348-1356
29. Watson E., Forster P., Richards M., and Bandelt H.J. Mitochondrial footprints of human expansions in Africa. Am. J. Hum. Genet. 61 (1997) 691-704
30. Wilson F.H., Hariri A., Farhi A., Zhao H., Petersen K.F., Toka H.R., Nelson-Williams C., Raja K.M., Kashgarian M., Shulman G.I., Scheinman S.J., and Lifton R.P. A cluster of metabolic defects caused by mutation in a mitochondrial tRNA. Science 306 (2004) 1190-1194
31. Batini C., Coia V., Battaggia C., Rocha J., Pilkington M.M., Spedini G., Comas D., Destro-Bisol G., and Calafell F. Phylogeography of human mitochondrial L1c haplogroup: genetic signatures of the prehistory of Central Africa. Mol. Phylogenet. Evol. 43 (2007) 635-644
32. Salas A., Richards M., Lareu M.-V., Scozzari R., Coppa A., Torroni A., Macaulay V., and Carracedo A. The African diaspora: mitochondrial DNA and the Atlantic slave trade. Am. J. Hum. Genet. 74 (2004) 454-465
33. Behar D.M., Villems R., Soodyall H., Blue-Smith J., Pereira L., Metspalu E., Scozzari R., Makkan H., Tzur S., Comas D., Bertranpetit J., Quintana-Murci L., Tyler-Smith C., Wells R.S., and Rosset S. The Genographic Conortium. The dawn of human matrilineal diversity. Am. J. Hum. Genet. 82 (2008) 1130-1140
34. Kivisild T., Reidla M., Metspalu E., Rosa A., Brehm A., Pennarun E., Parik J., Geberhiwot T., Usanga E., and Villems R. Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am. J. Hum. Genet. 75 (2004) 752-770
35. Salas A., Richards M., Lareu M.-V., Sobrino B., Silva S., Matamoros M., Macaulay V., and Carracedo A. Shipwrecks and founder effects: divergent demographic histories reflected in Caribbean mtDNA. Am. J. Phys. Anthropol. 128 (2005) 855-860
36. M. van Oven, M. Kayser, Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation, Hum. Mutat. 29 (2008) E386-E394. http://www.phylotree.org, mtDNA tree Build 2 (14 October 2008). doi:10.1002/humu.20921.
37. Quintana-Murci L., Quach H., Harmant C., Luca F., Massonnet B., Patin E., Sica L., Mouguiama-Daouda P., Comas D., Tzur S., Balanovsky O., Kidd K., Kidd J., van der Veen L., Hombert J.-M., Gessain A., Verdu P., Froment A., Bahuchet S., Heyer E., Dausset J., Salas A., and Behar D. Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers. PNAS 105 (2008) 1596-1601
38. Kivisild T., Shen P., Wall D., Do B., Sung R., Davis K., Passarino G., Underhill P., Sharfe C., Torroni A., Scozzari R., Modiano D., Coppa A., de Knijff P., Feldman M., Cavalli-Sforza L., and Oefner P. The role of selection in the evolution of human mitochondrial genomes. Genetics 172 (2006) 373-387
39. Salas A., Carracedo A., Richards M., and Macaulay V. Charting the ancestry of African Americans. Am. J. Hum. Genet. 77 (2005) 676-680
40. Parra E.J., Marcini A., Akey J., Martinson J., Batzer M.A., Cooper R., Forrester T., Allison D.B., Deka R., Ferrell R.E., and Shriver M.D. Estimating African American admixture proportions by use of population-specific alleles. Am. J. Hum. Genet. 63 (1998) 1839-1851
41. Lincoln P., and Carracedo A. Publication of population data of human polymorphisms. Forensic Sci. Int. 110 (2000) 3-5