doi: 10.1080/10635150600865419.
SINEs of a nearly perfect character
Affiliations
- PMID:17345674
- DOI: 10.1080/10635150600865419
Item in Clipboard
SINEs of a nearly perfect character
David A Ray et al. Syst Biol.2006 Dec.
Display options
Format
Display options
Format
Abstract
Mobile elements have been recognized as powerful tools for phylogenetic and population-level analyses. However, issues regarding potential sources of homoplasy and other misleading events have been raised. We have collected available data for all phylogenetic and population level studies of primates utilizing Alu insertion data and examined them for potentially homoplasious and other misleading events. Very low levels of each potential confounding factor in a phylogenetic or population analysis (i.e., lineage sorting, parallel insertions, and precise excision) were found. Although taxa known to be subject to high levels of these types of events may indeed be subject to problems when using SINE analysis, we propose that most taxa will respond as the order Primates has--by the resolution of several long-standing problems observed using sequence-based methods.
Similar articles
- True Homoplasy of Retrotransposon Insertions in Primates.Doronina L, Reising O, Clawson H, Ray DA, Schmitz J.Doronina L, et al.Syst Biol. 2019 May 1;68(3):482-493. doi: 10.1093/sysbio/syy076.Syst Biol. 2019.PMID:30445649
- Alu insertion loci and platyrrhine primate phylogeny.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.Ray DA, et al.Mol Phylogenet Evol. 2005 Apr;35(1):117-26. doi: 10.1016/j.ympev.2004.10.023. Epub 2005 Jan 18.Mol Phylogenet Evol. 2005.PMID:15737586
- A mobile element based phylogeny of Old World monkeys.Xing J, Wang H, Han K, Ray DA, Huang CH, Chemnick LG, Stewart CB, Disotell TR, Ryder OA, Batzer MA.Xing J, et al.Mol Phylogenet Evol. 2005 Dec;37(3):872-80. doi: 10.1016/j.ympev.2005.04.015. Epub 2005 Jun 3.Mol Phylogenet Evol. 2005.PMID:15936216
- Evolutionary history of 7SL RNA-derived SINEs in Supraprimates.Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J.Kriegs JO, et al.Trends Genet. 2007 Apr;23(4):158-61. doi: 10.1016/j.tig.2007.02.002. Epub 2007 Feb 20.Trends Genet. 2007.PMID:17307271Review.
- Primate phylogeny: molecular evidence from retroposons.Schmitz J, Roos C, Zischler H.Schmitz J, et al.Cytogenet Genome Res. 2005;108(1-3):26-37. doi: 10.1159/000080799.Cytogenet Genome Res. 2005.PMID:15545713Review.
Cited by
- Alu insertion polymorphisms shared byPapio baboons andTheropithecus gelada reveal an intertwined common ancestry.Walker JA, Jordan VE, Storer JM, Steely CJ, Gonzalez-Quiroga P, Beckstrom TO, Rewerts LC, St Romain CP, Rockwell CE, Rogers J, Jolly CJ, Konkel MK; Baboon Genome Analysis Consortium; Batzer MA.Walker JA, et al.Mob DNA. 2019 Nov 26;10:46. doi: 10.1186/s13100-019-0187-y. eCollection 2019.Mob DNA. 2019.PMID:31788036Free PMC article.
- Whole-genome analyses resolve early branches in the tree of life of modern birds.Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G.Jarvis ED, et al.Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.Science. 2014.PMID:25504713Free PMC article.
- Population and clinical genetics of human transposable elements in the (post) genomic era.Rishishwar L, Wang L, Clayton EA, Mariño-Ramírez L, McDonald JF, Jordan IK.Rishishwar L, et al.Mob Genet Elements. 2017 Jan 11;7(1):1-20. doi: 10.1080/2159256X.2017.1280116. eCollection 2017.Mob Genet Elements. 2017.PMID:28228978Free PMC article.Review.
- An Alu-based phylogeny of gibbons (hylobatidae).Meyer TJ, McLain AT, Oldenburg JM, Faulk C, Bourgeois MG, Conlin EM, Mootnick AR, de Jong PJ, Roos C, Carbone L, Batzer MA.Meyer TJ, et al.Mol Biol Evol. 2012 Nov;29(11):3441-50. doi: 10.1093/molbev/mss149. Epub 2012 Jun 7.Mol Biol Evol. 2012.PMID:22683814Free PMC article.
- The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds.Suh A, Smeds L, Ellegren H.Suh A, et al.PLoS Biol. 2015 Aug 18;13(8):e1002224. doi: 10.1371/journal.pbio.1002224. eCollection 2015 Aug.PLoS Biol. 2015.PMID:26284513Free PMC article.
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources