Abstract
For the last fifteen years, researchers have been using SINE (short interspersed elements; non-autonomous retroposons) insertion polymorphism as characters for phylogeny. Although the collection of these characters is much less straightforward and much more work intensive than for classical sequence data, they are subject to very little homoplasy, and therefore allow more reliable determination of the phylogeny of species. As reversions are very rare, and the ancestral state (absence of the insertion) is known, these characters are orientated a priori. They are also good markers for population genetics. Because of their almost complete lack of homoplasy, character conflict in these characters is a better indicator of incomplete lineage sorting and hybridization than other types of data, even for ancient divergences. Only a few examples of convergencies and reversions have been identified, and after looking through hundreds of characters; moreover, most instances of homoplasy are identifiable as such, so SINE insertion polymorphism can still be regarded as very high quality characters. Constant progress has been made through the years for the isolation of new SINEs as well as for the isolation of new insertion loci, both by bioinformatic methods and by benchwork. Numerous dedicated computer programs are available, and the newly sequenced complete genomes allow their full scale utilization. SINE insertion polymorphism data has proved its interest on complex phylogenetic problems where morphological and sequence data were not resolutive. The improvements in its portability encourage an enlargement of its application to new taxa, where it will provide novel and high quality phylogenetic information.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Badge RM, Alisch RS, Moran JV (2003) ATLAS: A system to selectively identify human specific L1 insertions. Am J Human Genet 72:823–838
Bamshad M, Kivisild T, Watkins WS, Dixon ME, Ricker CE, Rao BB, Naidu JM, Prasad BVR, Reddy PG, Rasanayagam A, Papiha SS, Villems R, Carroll ML, Nguyen SV, Batzer MA, Jorde LB (2001) Genetic evidence on the origins of Indian caste populations. Genome Res 11:994–1004
Bamshad MJ, Wooding S, Watkins WS, Ostler C, Batzer MA, Jorde LB (2003) Human population genetic structure and inference of group membership. Am Human Genet 72:578–589
Barnes MJ, Lobo NF, Coulibaly MB, Sagnon NF, Costantini C, Besansky NJ (2005) SINE insertion polymorphism on the X chromosome differentiates Anopheles gambiae molecular forms. Insect Mol Biol 14(4):353–363
Bashir A, Ye C, Price AL, Bafna V (2006) Orthologous repeats and mammalian phylogenetic inference. Genome Res 15:998–1006
Batzer MA, Deininger PL (1991) A human-specific subfamily of Alu sequences. Genomics 9:481–487
Batzer MA, Deininger PL (2002) Alu repeats and human genomic diversity. Nature Reviews Genet 3:370–379
Batzer MA, Gudi VA, Mena C, Foltz DW, Herrera RJ, Deininger PL (1991) Amplification dynamics of Human-specific (HS) Alu family members. Nucleic Acids Res 19:3619–3623
Batzer MA, Stoneking M, Alegria-Hartman M, Bazan H, Kass DH, Shaikh TH, Novick GE, Ioannou PA, Scheer WD, Herrera RJ (1994) African origin of human-specific polymorphic Alu insertions. Proc Natl Acad Sci USA 91(25):12288–12292
Batzer MA, Rubin CM, Hellmann-Blumberg U, Alegria-Hartman M, Leeflang EP, Stern JD, Bazan HA, Shaikh TH, Deininger PL, Schmid CW (1995) Dispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats. J Mol Biol 247(3):418–427
Batzer MA, Deininger PL, Hellmann-Blumberg U, Jurka J, Labuda D, Rubin CM, Schmid CW, Zietkiewicz E, Zuckerkandl E (1996) Standardized nomenclature for Alu repeats. J Mol Evol 42:3–6
Bedell JA, Korf I, Gish W (2000) MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics 16(11):1040–1041
Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE (2004) Natural genetic variation caused by transposable elements in humans. Genetics 168(2):933–951
Borodulina OR, Kramerov DA (1999) Wide distribution of short interspersed elements among eukaryotic genomes. FEBS Lett 457(3):409–413
Borodulina OR, Kramerov DA (2005) PCR-based approach to SINE isolation: Simple and complex SINEs. Gene 349:197–205
Burton FH, Loeb DD, Edgell MH, Hutchison CA, III (1991) L1 gene conversion or same-site transposition. Mol Biol Evol 8:609–619
Cantrell MA, Filanoski BJ, Ingermann AR, Olsson K, DiLuglio N, Lister Z, Wichman HA (2001) An ancient retrovirus-like element contains hot spots for SINE insertion. Genetics 158(2):769–777
Carroll ML, Roy-Engel AM, Nguyen SV, Salem AH, Vogel E, Vincent B, Myers J, Ahmad Z, Nguyen L, Sammarco M, Watkins WS, Henke J, Makalowski W, Jorde LB, Deininger PL, Batzer MA (2001) Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J Mol Biol 311(1):17–40
Chen WJ, Orti G, Meyer A (2004) Novel evolutionary relationship among four fish model systems. Trends Genet 20(9):424–431
Cheng C, Tsuchimoto S, Ohtsubo H, Ohtsubo E (2002) Evolutionary relationships among rice species with AA genome based on SINE insertion analysis. Genes Genet Syst 77(5):323–334
Cheng C, Motohashi R, Tsuchimoto S, Fukuta Y, Ohtsubo H, Ohtsubo E (2003) Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol Biol Evol 20(1):67–75
Churakov G, Smit AF, Brosius J, Schmitz J (2005) A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus). Mol Biol Evol 22(4):886–893
Comas D, Calafell F, Benchemsi N, Helal A, Lefranc G, Stoneking M, Batzer MA, Bertranpetit J, Sajantila A (2000) Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits. Human Genet 107(4):312–319
Comas D, Schmid H, Braeuer S, Flaiz C, Busquets A, Calafell F, Bertranpetit J, Scheil HG, Huckenbeck W, Efremovska L, Schmidt H (2004) Alu insertion polymorphisms in the Balkans and the origins of the Aromuns. Annals Human Genet 68(2):120–127
Conley ME, Partain JD, Norland SM, Shurtleff SA, Kazazian HH Jr (2005) Two independent retrotransposon insertions at the same site within the coding region of BTK. Hum Mutat 25(3):324–325
Cook J, Tristem M (1997) `SINEs of the times' – transposable elements as clade markers for their hosts. TREE 12(8):295–297
Cotton JA (2005) Analytical methods for detecting paralogy in molecular datasets. Methods Enzym 395:700–724
Darlu P, Tassy P (1994) La reconstruction phylogénétique. http://lis.snv.jussieu.fr/sfs/publications_sfs.shtml
Deininger PL, Jolly DJ, Rubin CM, Friedmann T, Schmid CW (1981) Base sequence study of 300 nucleotide renatured repeated human DNA clones. J Mol Biol 151:17–33
Deininger PL, Batzer AM (1999) Alu repeats and human disease. Mol Genet Metabol 67:183–193
Van Dellen K, Field J, Wang Z, Loftus B, Samuelson J (2002) LINEs and SINE-like elements of the protist Entamoeba histolytica. Gene 297(1–2):229–239
Dewannieux M, Esnault C, Heidmann T (2003) LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35:41–48
Bao Z, Eddy SR (2002) Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res 12(8):1269–1276
Edgar RC, Myers EW (2005) PILER: identification and classification of genomic repeats. Bioinformatics 21(S1):i152–i158
Eickbush TH, Furano AV (2002) Fruit flies and humans respond differently to retrotransposons. Curr Opin Genet Dev 12(6):669–674
Endoh H, Okada N (1986) Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures. Proc Natl Acad Sci USA 83(2):251–255
Esnault C, Maestre J, Heidmann T (200) Human LINE retrotransposons generate processed pseudogenes. Nat Genet 24(4):363–367
Estoup A, Cornuet JM (1999) Microsatellite evolution: inferences from population data. In: Goldstein DB, Schlotterer C (eds) Microsatellites: evolution and applications. Oxford University Press, Oxford
Feschotte C, Fourrier N, Desmons I, Mouches C (2001) Birth of a retroposon: the Twin SINE family from the vector mosquito Culex pipiens may have originated from a dimeric tRNA precursor. Mol Biol Evol 18(1):74–84
Fitch WM (1970) Distinguishing homologous from analogous proteins. Syst Zool 19(2):99–113
Halling KC, Lazzaro CR, Honchel R, Bufill JA, Powell SM, Arndt CA, Lindor NM (1999) hereditary desmoid disease in a family with a germline Alu I repeat mutation of the APC gene. Hum Hered 49:97–102
Hamada M, Himberg M, Bodaly RA, Reist JD, Okada N (1998) Monophyletic origin of the genera Stenodus and Coregonus as inferred from an analysis of the insertion of SINEs (short interspersed repetitive elements). Adv Limnol 50:383–389
Hamdi H, Nishio H, Zielinski R, Dugaiczyk A (1999) Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates. J Mol Biol 289(4):861–871
Hartl DL, Clark AG (1989) Principles of population genetics. Sinauer, Sunderland Massachussets
Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR, Sherry ST (1998) Genetic traces of ancient demography. Proc Natl Acad Sci USA 95:1961–1967
He H, Rovira C, Recco-Pimentel S, Liao C, Edstrom JE (1995) Polymorphic SINEs in chironomids with DNA derived from the R2 insertion site. J Mol Biol 245(1):34–42
Hedges DJ, Callinan PA, Cordaux R, Xing J, Barnes E, Batzer MA (2004) Differential Alu mobilization and polymorphism among the human and chimpanzee lineages. Genome Res 14:1068–1075
Hennig W (1950) Grundzüge einer Theorie der phylogenetischen Systematik. Deutscher Zentralverlag, Berlin
Hennig W (1965) Phylogenetic systematics. Ann Rev Entomol 10:97–116
Hennig W (1966) Phylogenetic systematics. University of Illinois Press, Illinois
Hillis DM (1999) SINEs of the perfect character. Proc Natl Acad Sci USA 96(18):9979–9981
Ho HJ, Ray DA, Salem AH, Myers JS, Batzer MA (2005) Straightening out the LINEs: LINE-1 element orthologous loci. Genomics 85:201–207
Izsvàk Z, Ivics Z, Shimoda N, Mohn D, Okamoto H, Hackett PB (1999) Short inverted-repeat transposable elements in teleost fish and implications for a mechanism of their amplification. J Mol Evol 48(1):13–21
Jackman TR, Larson A, De Queiroz K, Losos JB (1999) Phylogenetic relationships and tempo of early diversification in Anolis lizards. Syst Biol 48(2):254–285
Jorde LB, Watkins WS, Bamshad MJ, Dixon ME, Ricker CE, Seielstad MT, Batzer MA (2000) The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y chromosome data. Am J Human Genet 66:979–988
Jurka J (1997) Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci USA 94:1872–1877
Jurka J (1998) Repeats in genomic DNA: mining and meaning. Curr Opin Struct Biol 8:333–337
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462–467
Kajikawa M, Okada N (2002) LINEs mobilize SINEs in the eel through a shared 3′sequence. Cell 111(3):433–444
Kapitonov VV, Jurka J (2003a) A novel class of SINE elements derived from 5S rRNA. Mol Biol Evol 20:694–702
Kapitonov VV, Jurka J (2003b) Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci USA 100(11):6569–6574
Kawai K, Nikaido M, Harada M, Matsumura S, Lin LK, Wu Y, Hasegawa M, Okada N (2002) Intra- and interfamily relationships of Vespertilionidae inferred by various molecular markers including SINE insertion data. J Mol Evol 55(3):284–301
Kitching IJ, Forey PL, Humphries JH, Williams DM (1998) Cladistics – the theory and practice of parsimony analysis. The Systematics Association Publication n°11, Oxford University Press, New York
Krayev AS, Kramerov DA, Skryabin KG, Ryskov AP, Bayev AA, Georgiev GP (1980) The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of mouse fold-back RNA. Nucleic Acids Res 8(6):1201–1215
Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, Schmitz J (2006) Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol 4(4):e91
Kriener K, O'h Uigin C, Klein J (2000) Alu elements support independent origin of prosimian, platyrrhine, and catarrhine Mhc-DRB genes. Genome Res 10(5):634–643
Kulski JK, Dunn DS (2005) Polymorphic Alu insertions within the major histocompatibility complex class I genomic region: a brief review. Cytogenet Genome Res 110(1–4):193–202
Kulski JK, Gaudieri S, Dawkins RL (2000) Using alu J elements as molecular clocks to trace the evolutionary relationships between duplicated HLA class I genomic segments. J Mol Evol 50(6):510–519
Kulski JK, Lim CP, Dunn DS, Bellgard M (2003) Genomic and phylogenetic analysis of the S100A7 (Psoriasin) gene duplications within the region of the S100 gene cluster on human chromosome 1q21. J Mol Evol 56(4):397–406
Lander ES, International Human Genome Sequencing Consortium et al. (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860–921
Lankenau D-H (1995) Genetics of genetics in Drosophila: P elements serving the study of homologous recombination, gene conversion and targeting. Chromosoma 103:659–668
Lankenau D-H, Gloor GB (1998) In vivo gap repair in Drosophila: a one-way street with many destinations. BioEssays 20:317–327
Li TH, Schmid CW (2001) Differential stress induction of individual Alu loci: implications for transcription and retrotransposition. Gene 276(1–2):135–141
Li R, Ye J, Li S, Wang J, Han Y, Ye C, Wang J, Yang H, Yu J, Wong GK, Wang J (2005) ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol 1(4):e43
Luckett P, Hong N (1998) Phylogenetic relationships between the orders Artiodactyla and Cetacea: a combined assessment of morphological and molecular evidence. J Mammal Evol 5:127–182
Ludwig A, Rozhdestvensky TS, Kuryshev VY, Schmitz J, Brosius J (2005) An unusual primate locus that attracted two independent Alu insertions and facilitates their transcription. J Mol Biol 350(2):200–214
Luis JR, Terreros MC, Martinez L, Rojas D, Herrera RJ (2003) Two problematic human polymorphic Alu insertions. Electrophoresis 24(14):2290–2294
Lum JK, Nikaido M, Shimamura M, Shimodaira H, Shedlock AM, Okada N, Hasegawa M (2000) Consistency of SINE insertion topology and flanking sequence tree: Quantifying relationships among cetartiodactyls. Mol Biol Evol 17(10):1417–1424
Maca-Meyer N, Villar J, Perez-Mendez L, Cabrera de Leon A, Flores C (2004) A tale of aborigines, conquerors and slaves: Alu insertion polymorphisms and the peopling of Canary Islands. Annals Human Genet 68(6):600–605
Maddison WP (1989) Reconstructing character evoution on polytomous cladograms. Cladistics 5:365–377
Maddison WP, Knowles LL (2006) Inferring phylogeny despite incomplete lineage sorting. Syst Biol 55(1):21–30
Mamedov IZ, Arzumanyan ES, Amosova AL, Lebedev YB, Sverdlov ED (2005) Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach. Nucleic Acids Res 33(2):e16
Mateus Pereira LH, Socorro A, Fernandez I, Masleh M, Vidal D, Bianchi NO, Bonatto SL, Salzano FM, Herrera RJ (2005) Phylogenetic information in polymorphic L1 and Alu insertions from East Asians and Native American populations. Am J Phys Anthropology 128(1):171–184
Mefford HC, Linardopoulou E, Coil D, van den Engh G, Trask BJ (2001) Comparative sequencing of a multicopy subtelomeric region containing olfactory receptor genes reveals multiple interactions between non-homologous chromosomes. Hum Mol Genet 10(21):2363–2372
Miyamoto MM (1999) Molecular systematics: perfect SINEs of evolutionary history? Curr Biol 9(21):R816-R819
Morgulis A, Gertz EM, Schaffer AA, Agarwala R (2006) WindowMasker: window-based masker for sequenced genomes. Bioinformatics 22(2):134–141
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(15):6995–6999
Murata S, Takasaki N, Saitoh M, Tachida H, Okada N (1996) Details of retropositional genome dynamics that provide a rationale for a generic division: the distinct branching of all the Pacific salmon and trout (Oncorhynchus) from the Atlantic salmon and trout (Salmo). Genetics 142(3):915–926
Murata S, Takasaki N, Okazaki T, Kobayashi T, Numachi K, Chang K-H, Okada N (1998) Molecular evidence from short interspersed elements (SINEs) that Oncorhynchus masou (cherry salmon) is monophyletic. Canadian J Fisheries Aqua Sci 55(8):1864–1870
Nei M, Takezaki N (1996) The root of the phylogenetic tree of human populations. Mol Biol Evol 13(1):170–177
Nijman IJ, van Tessel P, Lenstra JA (2002) SINE retrotransposition during the evolution of the pecoran ruminants. J Mol Evol 54(1):9–16
Nikaido M, Matsuno F, Hamilton H, Brownell RL, Cao Y, Ding W, Zuoyan Z, Shedlock AM, Fordyce RE, Hasegawa M, Okada N (2001) Retroposon analysis of major cetacean lineages: the monophyly of toothed whales and the paraphyly of river dolphins. Proc Natl Acad Sci USA 98(13):7384–7389
Nikaido M, Nishihara H, Hukumoto Y, Okada N (2003) Ancient SINEs from African endemic mammals. Mol Biol Evol 20(4):522–527
Nikaido M, Hamilton H, Makino H, Sasaki T, Takahashi K, Goto M, Kanda N, Pastene LA, Okada N (2006) Baleen whale phylogeny and a past extensive radiation event revealed by SINE insertion analysis. Mol Biol Evol 23(5):866–873
Nishihara H, Terai Y, Okada N (2002) Characterization of novel Alu- and tRNA-related SINEs from the tree shrew and evolutionary implications of their origins. Mol Biol Evol 19(11):1964–1972
Nishihara H, Satta Y, Nikaido M, Thewissen JG, Stanhope MJ, Okada N (2005) A retroposon analysis of Afrotherian phylogeny. Mol Biol Evol 22(9):1823–1833
Nomura O, Yasue H (1999) Genetic relationships among hippopotamus, whales, and bovine based on SINE insertion analysis. Mamm Genome 10(5):526–527
Ogiwara I, Miya M, Ohshima K, Okada N (2002) V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit. Genome Res 12(2):316–324
Ohshima K, Okada N (1994) Generality of the tRNA origin of short interspersed repetitive elements (SINEs). Characterization of three different tRNA-derived retroposons in the octopus. J Mol Biol 243(1):25–37
Ohshima K, Okada N (2005) SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet Genome Res 110(1–4):475–490
Ohshima K, Koishi R, Matsuo M, Okada N (1993) Several short interspersed repetitive elements (SINEs) in distant species may have originated from a common ancestral retrovirus: characterization of a squid SINE and a possible mechanism for generation of tRNA-derived retroposons. Proc Natl Acad Sci USA 90(13):6260–6264
Okada N (1991) SINESs: short interspersed repeated elements of the eukaryotic genome. TREE 6(11):358–361
Okada N, Shedlock AM, Nikaido M (2004) Retroposon mapping in molecular systematics. Methods Mol Biol 260:189–226
Perna NT, Batzer MA, Deininger PL, Stoneking M (1992) Alu insertion polymorphism: A new type of marker for human population studies. Human Biol 64:641–648
Pevzner PA, Tang H, Tesler G (2003) De novo repeat classification and fragment assembly. Genome Res 14(9):1786–1796
Piskurek O, Nikaido M, Boeadi, Baba M, Okada N (2003) Unique mammalian tRNA-derived repetitive elements in dermopterans: the t-SINE family and its retrotransposition through multiple sources. Mol Biol Evol 20(10):1659–1668
Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21(S1):i351–i358
Raisonnier A (1991) Duplication of the apolipoprotein C-I gene occurred about forty million years ago. J Mol Evol 32(3):211–219
Ray DA, Xing J, Hedges DJ, Hall MA, Laborde ME, Anders BA, White BR, Stoilova N, Fowlkes JD, Landry KE, Chemnick LG, Ryder OA, Batzer MA (2005a) Alu insertion loci and platyrrhine primate phylogeny. Mol Phyl Evol 35(1):117–126
Ray DA, Hedges DJ, Herke SW, Fowlkes JD, Barnes EW, LaVie DK, Goodwin LM, Densmore LD, Batzer MA (2005b) Chompy: an infestation of MITE-like repetitive elements in the crocodilian genome. Gene 362:1–10
Rinehart TA, Grahn RA, Wichman HA (2004) SINE extinction preceded LINE extinction in sigmodontine rodents: implications for retrotranspositional dynamics and mechanisms. Cytogenet Genome Res 110(1–4):416–425
Rokas A, Holland PW (2000) Rare genomic changes as a tool for phylogenetics. TREE 15:454–459
Romualdi C, Balding D, Nasidze IS, Risch G, Robichaux M, Sherry ST, Stoneking M, Batzer MA, Barbujani G (2002) Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Res 12:602–612
Roos C, Schmitz J, Zischler H (2004) Primate jumping genes elucidate strepsirrhine phylogeny. Proc Natl Acad Sci USA 101(29):10650–10654
Roy AM, Carroll ML, Kass DH, Nguyen SV, Salem A, Batzer MA, Deininger PL (1999) Recently integrated human Alu repeats: finding needles in the haystack. Genetica 107:149–161
Roy-Engel AM, Carroll ML, Vogel E, Garber RK, Nguyen SV, Salem AH, Batzer MA, Deininger PL (2001) Alu insertion polymorphisms for the study of human genomic diversity. Genetics 159(1):279–290
Roy-Engel AM, Carroll ML, El-Sawy M, Salem AH, Garber RK, Nguyen SV, Deininger PL, Batzer MA (2002) Non-traditional Alu evolution and primate genomic diversity. J Mol Biol 316(5):1033–1040
Ryan SC, Dugaiczyk A (1989) Newly arisen DNA repeats in primate phylogeny. Proc Natl Acad Sci USA 86:9360–9364
Sakamoto K, Okada N (1985) Rodent type 2 Alu family, rat identifier sequence, rabbit C family, and bovine or goat 73-bp repeat may have evolved from tRNA genes. J Mol Evol 22(2):134–140
Salem AH, Kilroy GE, Watkins WS, Jorde LB, Batzer MA (2003a) Recently integrated Alu elements and human genomic diversity. Mol Biol Evol 20(8):1349–1361
Salem AH, Ray DA, Xing J, Callinan PA, Myers JS, Hedges DJ, Garber RK, Witherspoon DJ, Jorde LB, Batzer MA (2003b) Alu elements and hominid phylogenetics. Proc Natl Acad Sci USA 100(22):12787–12791
Salem AH, Ray DA, Hedges DJ, Jurka J, Batzer MA (2005) Analysis of the human Alu Ye lineage. BMC Evol Biol 5(18):1–9
Sasaki T, Takahashi K, Nikaido M, Miura S, Yasukawa Y, Okada N (2004) First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea. Mol Biol Evol 21(4):705–715
Sato A, Takezaki N, Tichy H, Figueroa F, Mayer WE, Klein J (2003) Origin and speciation of haplochromine fishes in East African crater lakes investigated by the analysis of their mtDNA, Mhc genes, and SINEs. Mol Biol Evol 20(9):1448–1462
Sheen FM, Sherry ST, Risch GM, Robichaux M, Nasidze I, Stoneking M, Batzer MA, Swergold GD (2000) Reading between the LINEs: genomic variation induced by LINE-1 retrotransposition. Genome Res 10:1496–1508
Schmidt T (1999) LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes. Plant Mol Biol 40:903–910
Schmitz J, Ohme M, Zischler H (2001) SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates. Genetics 157(2):777–784
Schmitz J, Zischler H (2003) Analysis of retrotransposons in dermopterans uncover a new family of tRNA-derived SINEs and support a monophyletic origin of the order primates. Mol Phyl Evol 28:341–349
Schmitz J, Churakov G, Zischler H, Brosius J (2004) A novel class of mammalian-specific tailless retropseudogenes. Genome Res 14(10A):1911–1915
Schmitz J, Roos C, Zischler H (2005) Primate phylogeny: molecular evidence from retroposons. Cytogenet Genome Res 108(1–3):26–37
Shedlock AM, Milinkovitch MC, Okada N (2000) SINE evolution, missing data, and the origin of whales. Syst Biol 49(4):808–817
Shedlock AM, Okada N (2000) SINE insertions: powerful tools for molecular systematics. Bioessays 22(2):148–160
Shedlock AM, Takahashi K, Okada N (2004) SINEs of speciation: tracking lineages with retroposons. TREE 19(10):545–553
Sherry ST, Harpending HC, Batzer MA, Stoneking M (1997) Alu evolution in human populations: using the coalescent to estimate effective population size. Genetics 147(4):1977–1982
Shimamura M, Yasue H, Ohshima K, Abe H, Kato H, Kishiro T, Goto M, Munechika I, Okada N (1997) Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 388(6643):666–670
Pecon-Slattery J, Wilkerson AJP, Murphy WJ, O'Brien SJ (2000) Phylogenetic assessment of introns and SINEs within the Y chromosome using the cat family Felidae as a species tree. Mol Biol Evol 21(12):2299–2309
Springer MS, Stanhope MJ, Madsen O, de Jong WW (2004) Molecules consolidate the placental mammal tree. TREE 19(8):430–438
Stoneking M, Fontius JJ, Clifford SL, Soodyall H, Arcot SS, Saha N, Jenkins T, Tahir MA, Deininger PL, Batzer MA (1997) Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Res 7(11):1061–1071
Szmulewicz MN, Andino LM, Reategui EP, Woolley-Barker T, Jolly CJ, Disotell TR, Herrera RJ (1999) An Alu insertion polymorphism in a baboon hybrid zone. Am J Phys Anthropology 109(1):1–8
Takahashi K, Terai Y, Nishida M, Okada N (1998) A novel family of short interspersed repetitive elements (SINEs) from cichlids: the patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika. Mol Biol Evol 15(4):391–407
Takahashi K, Terai Y, Nishida M, Okada N (2001a) Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons. Mol Biol Evol 18(11):2057–2966
Takahashi K, Nishida M, Yuma M, Okada N (2001b) Retroposition of the AFC family of SINEs (short interspersed repetitive elements) before and during the adaptive radiation of cichlid fishes in Lake Malawi and related inferences about phylogeny. J Mol Evol 53(4–5):496–507
Tatout C, Lavie L, Deragon JM (1998) Similar target site selection occurs in integration of plant and mammalian retroposons. J Mol Evol 47(4):463–470
Tatout C, Warwick S, Lenoir A, Deragon JM (1999) Sine insertions as clade markers for wild crucifer species. Mol Biol Evol 16(11):1614–1621
Terai Y, Takahashi K, Nishida M, Sato T, Okada N (2003) Using SINEs to probe ancient explosive speciation: hidden radiation of African cichlids? Mol Biol Evol 20(6):924–930
Terai Y, Takezaki N, Mayer WE, Tichy H, Takahata N, Klein J, Okada N (2004) Phylogenetic relationships among East African haplochromine fish as revealed by short interspersed elements (SINEs). J Mol Evol 58(1):64–78
Tishkoff SA, Pakstis AJ, Ruano G, Kidd KK (2000) The accuracy of statistical methods for estimation of haplotype frequencies: an example from the CD4 locus. Am J Human Genet 67(2):518–522
Tu Z (1999) Genomic and evolutionary analysis of Feilai, a diverse family of highly reiterated SINEs in the yellow fever mosquito, Aedes aegypti. Mol Biol Evol 16(6):760–772
Ullu E, Tschudi C (1984) Alu sequences are processed 7SL RNA genes. Nature 312:171–172
van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL (2005) Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res 15(9):1243–1249
van Oppen MJH, Rico C, Turner GF, Hewitt GM (2000) Extensive homoplasy, nonstepwise mutations, and shared ancestral polymorphism at a complex microsatellite locus in Lake Malawi cichlids. Mol Biol Evol 17:489–498
Vincent BJ, Myers JS, Ho HJ, Kilroy GE, Walker JA, Watkins WS, Jorde LB, Batzer MA (2003) Following the LINEs: an analysis of primate genomic variation at human-specific LINE-1 insertion sites. Mol Biol Evol 20(8):1338–1348
Vishwanathan H, Edwin D, Usharani MV, Majumder PP (2003) Insertion/deletion polymorphisms in tribal populations of southern India and their possible evolutionary implications. Human Biol 75(6):873–887
Volfovsky N, Haas BJ, Salzberg SL (2001) A clustering method for repeat analysis in DNA sequences. Genome Biol 2(8):RESEARCH0027
Waddell PJ, Kishino H, Ota R (2001) A phylogenetic foundation for comparative mammalian genomics. Genome Informatics 12:141–154
Wang JL, Song MK, Gonder S, Azrak D, Ray A, Batzer MA, Tishkoff SA, Liang P (2006) Whole genome computational comparative genomics: a fruitful approach for ascertaining Alu insertion polymorphisms. Gene 365:11–20
Watkins WS, Ricker CE, Bamshad MJ, Carroll ML, Nguyen SV, Batzer MA, Harpending C, Rogers AR, Jorde LB (2001) Patterns of ancestral human diversity: an analysis of Alu insertion and restriction site polymorphisms. Am J Human Genet 68:738–752
Watkins WS, Rogers AR, Ostler CT, Wooding S, Bamshad MJ, Brassington AM, Carroll ML, Nguyen SV, Walker JA, Prasad BV, Reddy PG, Das PK, Batzer MA, Jorde LB (2003) Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms. Genome Res 13(7):1607–1618
Weiner AM (1980) An abundant cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. Cell 22:209–218
Weiner AM, Deininger PL, Efstratiadis A (1986) Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem 55:631–661
Wulff K, Gazda H, Schroder W, Robicka-Milewska R, Herrmann FH (2000) Identification of a novel large F9 gene mutationan insertion of an Alu repeated DNA element in exon e of the factor 9 gene. Hum Mutat 15:299
Xing J, Salem AH, Hedges DJ, Kilroy GE, Watkins WS, Schienman JE, Stewart CB, Jurka J, Jorde LB, Batzer MA (2003) Comprehensive analysis of two Alu Yd subfamilies. J Mol Evol 57:S76–S89
Xing J, Wang H, Han K, Ray DA, Huang CH, Chemnick LG, Stewart CB, Disotell TR, Ryder OA, Batzer MA (2005) A mobile element based phylogeny of Old World monkeys. Mol Phyl Evol 37(3):872–880
Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC (2004) Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res 14:517–527
Acknowledgments
Agnes Dettaï was supported by an Alexander von Humboldt postdoctoral Fellowship. The Volff group is funded by the Biofuture program of the German Bundesministerium für Bildung und Forschung (BMBF). We received helpful comments on this manuscript from Gael Lancelot, Matthieu Andro, and Julien Lorion.
Author information
Authors and Affiliations
Corresponding author
Editor information
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Dettaï, A., Volff, JN. (2006). Morphological Characters from the Genome: SINE Insertion Polymorphism and Phylogenies. In: Lankenau, DH., Volff, JN. (eds) Transposons and the Dynamic Genome. Genome Dynamics and Stability, vol 4. Springer, Berlin, Heidelberg. https://doi.org/10.1007/7050_018
Download citation
DOI: https://doi.org/10.1007/7050_018
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-02004-9
Online ISBN: 978-3-642-02005-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)