Bontrop RE. Non-human primates: essential partners in biomedical research. Immunol Rev. 2001;183(1):5–9.
Article
CAS
PubMed
Google Scholar
Jolly CJ. A proper study for mankind: analogies from the Papionin monkeys and their implications for human evolution. Am J Phys Anthropol. 2001;116(S33):177–204.
Article
Google Scholar
Patterson JL, Carrion R. Demand for nonhuman primate resources in the age of biodefense. ILAR J. 2005;46(1):15–22.
Article
CAS
PubMed
Google Scholar
Goodman S, Check E. Animal experiments: the great primate debate. Nature. 2002;417(6890):684–7.
Article
CAS
PubMed
Google Scholar
Phillips KA, Bales KL, Capitanio JP, Conley A, Czoty PW, Hart BA, Hopkins WD, Hu S-L, Miller LA, Nader MA, et al. Why primate models matter. Am J Primatol. 2014;76(9):801–27.
Article
PubMed
PubMed Central
Google Scholar
Cox LA, Comuzzie AG, Havill LM, Karere GM, Spradling KD, Mahaney MC, Nathanielsz PW, Nicolella DP, Shade RE, Voruganti S, et al. Baboons as a model to study genetics and epigenetics of human disease. ILAR J. 2013;54(2):106–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dormehl IC, Hugo N, Beverley G. The baboon: an ideal model in biomedical research. Anesth Pain Control Dent. 1992;1(2):109–15.
CAS
PubMed
Google Scholar
VandeBerg JL, Williams-Blangero S, Tardif SD. The baboon in biomedical research: Springer New York; 2009.
Book
Google Scholar
McGill HC, McMahan CA, Kruski AW, Mott GE. Relationship of lipoprotein cholesterol concentrations to experimental atherosclerosis in baboons. Arterioscler Thromb Vasc Biol. 1981;1(1):3–12.
Article
CAS
Google Scholar
Jerome C, Kimmel D, McAlister J, Weaver D. Effects of ovariectomy on iliac trabecular bone in baboons (Papio anubis). Calcif Tissue Int. 1986;39(3):206–8.
Article
CAS
PubMed
Google Scholar
Kammerer CM, Cox LA, Mahaney MC, Rogers J, Shade RE. Sodium-lithium countertransport activity is linked to chromosome 5 in baboons. Hypertension. 2001;37(2):398–402.
Article
CAS
PubMed
Google Scholar
Strum SC, Mitchell W. Baboon models and muddles. In: Kinzey WG, editor. The evolution of human behavior: primate models. New York: New York State University Press; 1987. p. 87–104.
Rodseth L, Wrangham RW, Harrigan AM, Smuts BB, Dare R, Fox R, King BJ, Lee PC, Foley RA, Muller JC, et al. The human community as a primate society [and comments]. Curr Anthropol. 1991;32(3):221–54.
Article
Google Scholar
Jablonski NG, Frost SR. Cercopithecoidea. In: Cenozoic mammals of Africa. Werdelin L, Sanders WJ. Berkeley: University of California Press; 2010. p. 393–428.
Chapter
Google Scholar
Racimo F, Sankararaman S, Nielsen R, Huerta-Sanchez E. Evidence for archaic adaptive introgression in humans. Nat Rev Genet. 2015;16(6):359–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sankararaman S, Mallick S, Dannemann M, Prüfer K, Kelso J, Pääbo S, Patterson N, Reich D. The landscape of Neandertal ancestry in present-day humans. Nature. 2014;507(7492):354–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kopp GH, Roos C, Butynski TM, Wildman DE, Alagaili AN, Groeneveld LF, Zinner D. Out of Africa, but how and when? The case of hamadryas baboons (Papio hamadryas). J Hum Evol. 2014;76:154–64.
Article
PubMed
Google Scholar
Winney BJ, Hammond RL, Macasero W, Flores B, Boug A, Biquand V, Biquand S, Bruford MW. Crossing the Red Sea: phylogeography of the hamadryas baboon, Papio hamadryas hamadryas. Mol Ecol. 2004;13(9):2819–27.
Article
CAS
PubMed
Google Scholar
Groucutt HS, Petraglia MD, Bailey G, Scerri EML, Parton A, Clark-Balzan L, Jennings RP, Lewis L, Blinkhorn J, Drake NA, et al. Rethinking the dispersal of Homo sapiens out of Africa. Evol Anthropol. 2015;24(4):149–64.
Article
PubMed
Google Scholar
Wildman DE, Bergman TJ, al-Aghbari A, Sterner KN, Newman T, Phillips-Conroy JE, Jolly CJ, Disotell TR. Mitochondrial evidence for the origin of hamadryas baboons. Mol Phylogenet Evol. 2004;32:287.
Article
CAS
PubMed
Google Scholar
Barrett L, Henzi SP. Baboons. Curr Biol. 2008;18(10):R404–6.
Article
CAS
PubMed
Google Scholar
Caldecott JO, Miles L. Programme UNE, Centre WCM: world atlas of great apes and their conservation: University of California Press; 2005.
Google Scholar
Eeley HAC, Foley R. Species richness, species range size and ecological specialisation among African primates: geographical patterns and conservation implications. Biodivers Conserv. 1999;8(8):1033–56.
Article
Google Scholar
Jolly CJ. Species, subspecies, and baboon systematics. In: Kimbel WH, Martin LB, editors. Species, species concepts and primate evolution. Boston: Springer US; 1993. p. 67–107.
Chapter
Google Scholar
Groves CP. Primate taxonomy. Washington DC: Smithsonian Institution Press; 2001.
Google Scholar
Zinner D, Wertheimer J, Liedigk R, Groeneveld LF, Roos C. Baboon phylogeny as inferred from complete mitochondrial genomes. Am J Phys Anthropol. 2013;150(1):133–40.
Article
PubMed
PubMed Central
Google Scholar
Jolly CJ, Burrell AS, Phillips-Conroy JE, Bergey C, Rogers J. Kinda baboons (Papio kindae) and grayfoot chacma baboons (P. ursinus griseipes) hybridize in the Kafue river valley, Zambia. Am J Primatol. 2011;73(3):291–303.
Article
CAS
PubMed
Google Scholar
Walker JA, Jordan VE, Steely CJ, Beckstrom TO, McDaniel CL, St. Romain CP, Bennett EC, Robichaux A, Clement BN, Konkel MK, et al. Papio baboon species indicative Alu elements. Genome Biol Evol. 2017;9(6):1788–96.
Article
PubMed
PubMed Central
Google Scholar
Steely CJ, Walker JA, Jordan VE, Beckstrom TO, McDaniel CL, St Romain CP, Bennett EC, Robichaux A, Clement BN, Raveendran M, et al. Alu insertion polymorphisms as evidence for population structure in baboons. Genome Biol Evol. 2017;9(9):2418–27.
Article
PubMed
PubMed Central
Google Scholar
Zinner D, Groeneveld LF, Keller C, Roos C. Mitochondrial phylogeography of baboons (Papio spp.) – indication for introgressive hybridization? BMC Evol Biol. 2009;9:83.
Article
PubMed
PubMed Central
Google Scholar
Alberts SC, Altmann J. Immigration and hybridization patterns of yellow and anubis baboons in and around Amboseli, Kenya. Am J Primatol. 2001;53:139.
Article
CAS
PubMed
Google Scholar
Bergman T, Phillips-Conroy JE, Jolly CJ. Behavioral variation and reproductive success of male baboons (Papio anubis × Papio hamadryas) in a hybrid social group. Am J Primatol. 2008;70:136.
Article
PubMed
Google Scholar
Maples WR, McKern TW. A preliminary report on classification of the Kenya baboon. In: Vagtborg H, editor. The baboon in medical research, vol. 2. San Antonio: University of Texas Press; 1967. p. 13–22.
Google Scholar
Phillips-Conroy JE, Jolly CJ, Brett FL. Characteristics of hamadryas-like male baboons living in anubis baboon troops in the Awash hybrid zone, Ethiopia. Am J Phys Anthropol. 1991;86(3):353–68.
Article
CAS
PubMed
Google Scholar
Nagel U. A comparison of anubis baboons, hamadryas baboons and their hybrids at a species border in Ethiopia. Folia Primatol. 1973;19:104.
Article
CAS
PubMed
Google Scholar
Szmulewicz MN, Andino LM, Reategui EP, Woolley-Barker T, Jolly CJ, Disotell TR, Herrera RJ. An Alu insertion polymorphism in a baboon hybrid zone. Am J Phys Anthropol. 1999;109(1):1–8.
Article
CAS
PubMed
Google Scholar
McLain AT, Meyer TJ, Faulk C, Herke SW, Oldenburg JM, Bourgeois MG, Abshire CF, Roos C, Batzer MA. An Alu-based phylogeny of lemurs (Infraorder: Lemuriformes). PLoS One. 2012;7(8):e44035.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salem A-H, Ray DA, Xing J, Callinan PA, Myers JS, Hedges DJ, Garber RK, Witherspoon DJ, Jorde LB, Batzer MA. Alu elements and hominid phylogenetics. Proc Natl Acad Sci. 2003;100(22):12787–91.
Article
PubMed
PubMed Central
Google Scholar
Meyer TJ, McLain AT, Oldenburg JM, Faulk C, Bourgeois MG, Conlin EM, Mootnick AR, de Jong PJ, Roos C, Carbone L, et al. An Alu-based phylogeny of gibbons (Hylobatidae). Mol Biol Evol. 2012;29(11):3441–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Watkins WS, Rogers AR, Ostler CT, Wooding S, Bamshad MJ, Brassington AM, Carroll ML, Nguyen SV, Walker JA, Prasad BV, et al. Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms. Genome Res. 2003;13(7):1607–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xing J, Wang H, Han K, Ray DA, Huang CH, Chemnick LG, Stewart C-B, Disotell TR, Ryder OA, Batzer MA. A mobile element based phylogeny of Old World monkeys. Mol Phylogenet Evol. 2005;37(3):872–80.
Article
CAS
PubMed
Google Scholar
Li J, Han K, Xing J, Kim H-S, Rogers J, Ryder OA, Disotell T, Yue B, Batzer MA. Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements. Gene. 2009;448(2):242–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schmitz J, Ohme M, Zischler H. SINE insertions in cladistic analyses and the phylogenetic affiliations of <em>Tarsius bancanus</em> to other primates. Genetics. 2001;157(2):777–84.
CAS
PubMed
PubMed Central
Google Scholar
Xing J, Wang H, Zhang Y, Ray DA, Tosi AJ, Disotell TR, Batzer MA. A mobile element-based evolutionary history of guenons (tribe Cercopithecini). BMC Biol. 2007;5(1):5.
Article
PubMed
PubMed Central
Google Scholar
Shedlock AM, Okada N. SINE insertions: powerful tools for molecular systematics. BioEssays. 2000;22:148.
Article
CAS
PubMed
Google Scholar
Batzer MA, Arcot SS, Phinney JW, Alegria-Hartman M, Kass DH, Milligan SM, Kimpton C, Gill P, Hochmeister M, Ioannou PA, et al. Genetic variation of recent Alu insertions in human populations. J Mol Evol. 1996;42(1):22–9.
Article
CAS
PubMed
Google Scholar
Stoneking M, Fontius JJ, Clifford SL, Soodyall H, Arcot SS, Saha N, Jenkins T, Tahir MA, Deininger PL, Batzer MA. Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Res. 1997;7(11):1061–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Batzer MA, Deininger PL. Alu repeats and human genomic diversity. Nat Rev Genet. 2002;3(5):370–9.
Article
CAS
PubMed
Google Scholar
Deininger PL, Batzer MA. Mammalian retroelements. Genome Res. 2002;12(10):1455–65.
Article
CAS
PubMed
Google Scholar
Roy-Engel A, Batzer MA, Deininger P. Evolution of human retrosequences: Alu; 2008.
Book
Google Scholar
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W. Initial sequencing and analysis of the human genome. Nature. 2001;409:860.
Article
CAS
PubMed
Google Scholar
Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005;437(7055):69–87.
Article
Google Scholar
Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007;316(5822):222–34.
Article
CAS
PubMed
Google Scholar
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 2011;469(7331):529–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, et al. Insights into hominid evolution from the gorilla genome sequence. Nature. 2012;483:169.
Article
CAS
PubMed
PubMed Central
Google Scholar
Luan DD, Korman MH, Jakubczak JL, Eickbush TH. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell. 1993;72(4):595–605.
Article
CAS
PubMed
Google Scholar
Luan DD, Eickbush TH. RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol Cell Biol. 1995;15(7):3882–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cost GJ, Feng Q, Jacquier A, Boeke JD. Human L1 element target-primed reverse transcription in vitro. EMBO J. 2002;21(21):5899–910.
Article
CAS
PubMed
PubMed Central
Google Scholar
Comeaux MS, Roy-Engel AM, Hedges DJ, Deininger PL. Diverse cis factors controlling Alu retrotransposition: what causes Alu elements to die? Genome Res. 2009;19(4):545–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dewannieux M, Esnault C, Heidmann T. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet. 2003;35(1):41–8.
Article
CAS
PubMed
Google Scholar
Ray DA, Xing J, Salem AH, Batzer MA. SINEs of a nearly perfect character. Syst Biol. 2006;55:928.
Article
PubMed
Google Scholar
Konkel MK, Walker JA, Batzer MA. LINEs and SINEs of primate evolution. Evol Anthropol. 2010;19(6):236–49.
Article
PubMed
PubMed Central
Google Scholar
Batzer MA, Deininger PL. A human-specific subfamily of Alu sequences. Genomics. 1991;9:481–7.
Article
CAS
PubMed
Google Scholar
Roos C, Geissmann T. Molecular phylogeny of the major hylobatid divisions. Mol Phylogenet Evol. 2001;19(3):486–94.
Article
CAS
PubMed
Google Scholar
Coordinators NR. Database resources of the national center for biotechnology information. Nucleic Acids Res. 2016;44(Database issue):D7–d19.
Google Scholar
Leinonen R, Sugawara H, Shumway M, on behalf of the International Nucleotide Sequence Database C. The sequence read archive. Nucleic Acids Res. 2011;39(Database issue):D19–21.
Article
CAS
PubMed
Google Scholar
Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE. Active Alu retrotransposons in the human genome. Genome Res. 2008;18(12):1875–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Batzer MA, Kilroy GE, Richard PE, Shaikh TH, Desselle TD, Hoppens CL, Deininger PL. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 1990;18(23):6793–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carroll ML, Roy-Engel AM, Nguyen SV, Salem A-H, Vogel E, Vincent B, Myers J, Ahmad Z, Nguyen L, Sammarco M, et al. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity11Edited by J. Karn. J Mol Biol. 2001;311(1):17–40.
Article
CAS
PubMed
Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, vol. 1303; 2013.
Google Scholar
Jurka J. Repeats in genomic DNA: mining and meaning. Curr Opin Struct Biol. 1998;8(3):333–7.
Article
CAS
PubMed
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Swofford DL. PAUP*: phylogenetic analysis using parsimony, version 4.0b10. 2011.
Google Scholar
Durrant SD, Simpson GG. The major features of evolution. J Mammal. 1953;35(4):600–1.
Article
Google Scholar