An Alu-Based Phylogeny of Lemurs (Infraorder: Lemuriformes)

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  McLain, Adam T ^a   Meyer, Thomas J ^a,b   Faulk, Christopher ^a,c   Herke, Scott W ^a   Oldenburg, J Michael ^a   Bourgeois, Matthew G ^a   Abshire, Camille F ^a,d   Roos, Christian ^e   Batzer, Mark A ^a  

^a LOUISIANA STATE UNIVERSITY   (United States)

^b OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^c UNIVERSITY OF MICHIGAN   (United States)

^d LOUISIANA STATE UNIVERSITY HEALTH SCIENCES CENTER   (United States)

^e GERMAN PRIMATE CENTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALU SEQUENCE; ARTICLE; DNA SEQUENCE; GENE LOCUS; GENE SEQUENCE; GENOME; LEMURIDAE; MONOPHYLY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; POLYMERASE CHAIN REACTION; SHORT INTERSPERSED REPEAT; UNINDEXED SEQUENCE;

ALU ELEMENTS; ANIMALS; EVOLUTION, MOLECULAR; GENOME; MADAGASCAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; STREPSIRHINI;

CHEIROGALEIDAE; CHEIROGALEUS; DAUBENTONIIDAE; EULEMUR; HAPALEMUR; INDRIDAE; LEMUR; LEMURIDAE; LEMURIFORMES; MEGALADAPIDAE; MICROCEBUS; MICROCEBUS MURINUS; MIRZA; MYA; PRIMATES; VARECIA;

EID: 84865491842     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0044035     Document Type: Article

References (72)

1. Mittermeier RA, Louis EE, Richardson M, Schwitzer C, Langrand O, et al. (2010) Lemurs of Madagascar. Arlington, Virginia: Conservation International Tropical Field Guide Series.
2. Yoder AD, Cartmill M, Ruvolo M, Smith K, Vigalys R, (1996) Ancient single origin for Malagasy primates. Proc Natl Acad Sci U S A 93: 5122-5126.
3. Roos C, Schmitz J, Zischler H, (2004) Primate jumping genes elucidate strepsirrhine phylogeny. Proc Natl Acad Sci U S A 101: 10650-10654.
4. Yoder AD, Yang Z, (2004) Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Mol Ecol 13: 757-773.
5. Masters JC, deWit MJ, Asher RJ, (2006) Reconciling the origins of Africa, India, and Madagascar with vertebrate dispersal scenarios. Folia Primatologica 77 (6): 399-418.
6. Tattersall I (2007) Origin of the Malagasy Strepsirrhine Primates. In: Lemurs: Ecology and Adaptation. New York, NY. Springer Publishing. 3-17.
7. Mittermeier RA, Ganzhorn JU, Konstant WR, Glander K, Tattersall I, et al. (2008) Lemur diversity in Madagascar. Int J Primatol 29: 1607-1656.
8. Tattersall I, (2007) Madagascar's Lemurs: Cryptic Diversity or Taxonomic Inflation? Evolutionary Anthropology 16: 12-23.
9. Shapiro LJ, Seiffert CVM, Godfrey LR, Jungers WL, Simons EL, et al. (2005) Morphometric analysis of lumbar vertebrae in extinct Malagasy strepsirrhines. Am J Phys Anthropol 128 (4): 823-839.
10. Eaglen RH, (1983) Lemur phylogeny and parsimony. Int J Primatol 4 (3): 249-273.
11. Groves CP, Eaglen RH, (1988) Systematics of the Lemuridae (Primates, Strepsirhini). J Hum Evol 17: 513-538.
12. Lebrun R, de Leon MP, Tafforeau P, Zollikofer C, (2010) Deep evolutionary roots of strepsirrhine primate labrynthine morphology. J Anat 216: 368-380.
13. Eckhardt RB, (1970) A Chromosome Arm Number Index and Its Application to the Phylogeny and Classificaiton of Lemurs. Am J Phys Anthrop 31: 85-88.
14. Ishak B, Warter S, Dutrillaux B, Rumpler Y, (1988) Phylogenetic Relation Between Lepilemuridae and Other Lemuriform Families. Am J Primatol 15: 275-280.
15. Delpero M, Masters JC, Cervella P, Crovella S, Ardito G, et al. (2001) Phylogenetic relationships among the Malagasy lemuriformes (Primates: Strepsirrhini) as indicated by mitochondrial sequence data from the 12S rRNA gene. Zool J Linn Soc 133: 83-103.
16. Pastorini J, Thalmann U, Martin RD, (2003) A molecular approach to comparative phylogeography of extant Malagasy lemurs. Proc Natl Acad Sci U S A 100: 5879-5884.
17. Horvath JE, Weisrock DW, Embry SL, Fiorentino I, Balhoff JP, (2008) Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar's lemurs. Genome Res 18: 489-499.
18. Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE, et al. (2011) A molecular phylogeny of living primates. PLoS Genet 7: e1001342.
19. Wyner Y, DeSalle R, Absher R, (1999) Phylogeny and Character Behavior in Family Lemuridae. Mol Phylogenet Evol 15 (1): 124-134.
20. Herke SW, Xing J, Ray DA, Zimmerman JW, Cordaux R, et al. (2007) A SINE-based dichotomous key for primate identification. Gene 390: 39-51.
21. Bochkob AV, Klimov PB, Wauthy G, (2011) Phylogeny and coevolutionary associations of makialgine mites (Acari, Psoroptidae, Makialginae) provide insight into the evolutionary history of their hosts, strepsirrhine primates. Zool J Linn Soc 162: 1-14.
22. Karanth KP, Delefosse T, Rakotosamimanana B, Parsons TJ, Yoder AD, (2005) Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates. Proc Natl Acad Sci U S A 102: 5090-5095.
23. Groves CP (2001) Primate Taxonomy. Washington, D.C: Smithsonian Press.
24. Yoder AD, (1997) Back to the Future: A synthesis of Strepsirhine systematics. Evol Anthro 6: 11-22.
25. Orlando L, Calvignac S, Schenebelen C, Douady CJ, Godfrey LR, et al. (2008) DNA from extinct giant lemurs links archaeolemurids to extant indriids. BMC Evol Biol 8: 121.
26. Luan DD, Korman MH, Jakubczak JL, Eickbush TH, (1993) Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72: 595-605.
27. Luan DD, Eickbush TH, (1995) RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol Cell Biol 15: 3882-3891.
28. Cost GJ, Feng Q, Jacquier A, Boeke JD, (2002) Human L1 element target-primed reverse transcription in vitro. Embo J 21: 5899-5910.
29. Konkel MK, Walker JA, Batzer MA, (2010) LINEs and SINEs of primate evolution. Evolutionary Anthropology 19: 236-249.
30. Batzer MA, Deininger PL, (1991) A human-specific subfamily of Alu sequences. Genomics 9: 481-487.
31. Ray DA, Xing J, Salem AH, Batzer MA, (2006) SINEs of a nearly perfect character. Syst Biol 55: 928-935.
32. Murata S, Takasaki N, Saitoh M, Okada N, (1993) Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proc Natl Acad Sci USA 90: 6995-6999.
33. Batzer MA, Stoneking M, Alegria-Hartman M, Bazan H, Kass DH, et al. (1994) African origin of human-specific polymorphic Alu insertions. Proc Natl Acad Sci U S A 91: 12288-12292.
34. Shedlock AM, Okada N, (2000) SINE insertions: powerful tools for molecular systematics. Bioessays 22: 148-160.
35. Okada N, Shedlock AM, Nikaido M, (2004) Retroposon mapping in molecular systematics. Methods Mol Biol 260: 189-226.
36. Ray DA, (2007) SINEs of progress: Mobile element applications to molecular ecology. Mol Ecol 16: 19-33.
37. Schmitz J, Ohme M, Zischler H, (2001) SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates. Genetics 157: 777-784.
38. Salem AH, Ray DA, Xing J, Callinan PA, Myers JS, et al. (2003) Alu elements and hominid phylogenetics. Proc Natl Acad Sci U S A 100: 12787-12791.
39. Shedlock AM, Takahashi K, Okada N, (2004) SINEs of speciation: tracking lineages with retroposons. Trends Ecol Evol 19: 545-553.
40. Schmitz J, Roos C, Zischler H. 2005. Primate phylogeny: molecular evidence from retroposons. Cytogenet Genome Res 108: 26-37.
41. Xing J, Wang H, Han K, Ray DA, Huang CH, et al. (2005) A mobile element based phylogeny of Old World monkeys. Mol Phylogenet Evol 37: 872-880.
42. Ray DA, Xing J, Hedges DJ, Hall M, Laborde ME, et al. (2005) Alu insertion loci and platyrrhine primate phylogeny. Mol Phylogenet Evol 35: 117-126.
43. Li J, Han K, Xing J, Kim HS, Rogers J, et al. (2009) Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements. Gene 448: 242-249.
44. Osterholz M, Walter L, Roos C, (2009) Retropositional events consolidate the branching order among New World monkey genera. Mol Phylogenet Evol 50: 507-513.
45. Roos C, Zinner D, Kubatko LS, Schwarz C, Yang M, et al. (2011) Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys. BMC Evol Biol 11: 77.
46. Meyer TJ, McLain AT, Oldenberg JM, Faulk C, Bourgeois M, et al. (2012) (In press) An Alu-based phylogeny of gibbons (Hylobatidae). Mol Biol Evol.
47. Batzer MA, Deininger PL, (2002) Alu repeats and human genomic diversity. Nat Rev Genet 3: 370-379.
48. Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J (2007) Evolutionary history of 7SL RNA-derived SINEs in Supraprimates. Trends Genet 23: 4 158-161.
49. Cordaux R, Batzer MA, (2009) The impact of retrotransposons on human genome evolution. Nat Rev Genet 10: 691-703.
50. Churakov G, Grundmann N, Kuritzin A, Brosius J, Makalowski W, et al. (2010) A novel web-based TinT application and the chronology of primate Alu retrotransposon activity. BMC Evol Biol 10: 376.
51. Liu GC, Alkan C, Jiang L, Zhao S, Eichler E, (2009) Comparative analysis of Alu repeats in primate genomes. Genome Res 19: 876-885.
52. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, et al. (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478: 476-482.
53. Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. 1996-2010&http://www.repeatmasker.org>.
54. Kent WJ, (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
55. Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2012) Ensembl 2012. Nucleic Acids Res 40 Database issue: D84-D90.
56. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, et al. (2007) Primer3Plus, an enhanced web interface to Primer3 Nucleic Acids Research. 35: W71-W74.
57. Sanger F, Nicklen S, Coulson AR, (1992) DNA Sequencing with chain-terminating inhibitors 1977. Biotechnology 24: 104-108.
58. Maddison WP, Maddison DR (2011) Mesquite: a modular system for evolutionary analysis. Version 2.75 http://mesquiteproject.org.
59. Swofford DL (2003) PAUP: Phylogenetic analysis using parsimony. Sunderland, Massachusetts: Sinauer Associates, Inc.
60. Waddell PJ, Kishino H, Ota R, (2001) A phylogenetic foundation for comparative mammalian genomics. Genome Inform Ser Workshop Genome Inform 12: 141-154.
61. Poux C, Douzery EJ, (2004) Primate phylogeny, evolutionary rate variations, and divergence times: A contribution from the nuclear gene IRBP. Am J Phys Anthropol 124: 1-16.
62. Simons EL, Rumpler Y, (1988) Eulemur new generic name for species of Lemur other than Lemur catta. CR Acad Sci Paris, ser 3 307: 547-551.
63. Tattersall I, Schwartz JH, (1991) Phylogeny and nomenclature in the "lemur-group" of Malagasy strepsirhine primates. Anthrop Pap Am Mus Nat Hist 69: 1-18.
64. Djlelati R, Brun B, Rumpler Y, (1997) Meiotic study of hybrids in the genus Eulemur and taxonomic considerations. Am J Primatol 42: 235-245.
65. Pastorini J, Forstner MRJ, Martin RD, (2000) Relationships among brown lemurs (Eulemur fulvus) based on mitochondrial DNA sequences. Mol Phylogenet Evol 16: 418-429.
66. Cerling TE, Harris JM, McFadden BJ, Leakey MG, Quade J, et al. (1997) Global vegitation change throughout the Miocene/Pliocene boundry. Nature 389: 153-158.
67. Wells NA (2003) Some hypotheses on the Mesozoic and Cenozoic paleoenvironmental history of Madagascar. In: Goodman SM, Benstead JP, editors. The natural history of Madagascar. Chicago: University of Chicago Press. 16-74.
68. Yoder AD, Irwin I, (1999) Eulemur is a phylogenetically defensible taxon (but species relationships within the genus are problematic). Lemur News 4: 31-32.
69. Rumpler Y, Warter S, Ratomponirina C, Hauwy M, Ischak B, (1985) Cytogenetic study of complex hybrids in the genus Lemur (Primates, Prosimians). Folia Primatol 44: 108-116.
70. Rabarivola C, Meyers D, Rumpler Y, (1991) Distribution and Morphological Characters of Intermediate Forms Between the Black Lemur (Eulemur macaco macaco) and the Sclater's Lemur (E. m. flavifrons). Primates 32 (2): 269-273.
71. Yoder AD, (1994) Relative Position of the Cheirogaleidae in Strepsirhine Phylogeny: A Comparison of Morphological and Molecular Methods and Results. Am J Phys Anthropol 94: 25-46.
72. Rumpler Y, (2004) Complementary approaches of cytogenetics and molecular biology to the taxonomy and study of speciation processes in lemurs. Evol Anthropol 13: 67-78.