• Experimental characterization of transposon fitness landscapes
  • Tc1/mariner binding specificity:
    • Lampe DJ, Walden KK, Robertson HM.  Loss of transposase-DNA interaction may underlie the divergence of mariner family transposable elements and the ability of more than one mariner to occupy the same genome.  Mol Biol Evol. 2001 Jun;18(6):954-61.
  • Drew Endy's work with T7:
    • Chan LY, Kosuri S, Endy D.  Refactoring bacteriophage T7.  Mol Syst Biol. 2005;1:2005.0018. Epub 2005 Sep 13.
    • Endy D, You L, Yin J, Molineux IJ.  Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes.  Proc Natl Acad Sci U S A. 2000 May 9;97(10):5375-80.
    • Endy D, Kong D, Yin J.  Intracellular kinetics of a growing virus: A genetically structured simulation for bacteriophage T7.  Biotechnol Bioeng. 1997 Jul 20;55(2):375-89.
  • Jef Boeke's synthetic retrotransposon:
    • Han JS, Boeke JD.  A highly active synthetic mammalian retrotransposon.  Nature. 2004 May 20;429(6989):314-8.
• Experimental phylogenetics
  • Hillis DM, Bull JJ, White ME, Badgett MR, Molineux IJ.  Experimental phylogenetics: generation of a known phylogeny.  Science. 1992 Jan 31;255(5044):589-92.
  • Fares MA, Barrio E, Becerra N, Escarmis C, Domingo E, Moya A.  The foot-and-mouth disease RNA virus as a model in experimental phylogenetics.  Int Microbiol. 1998 Dec;1(4):311-8.
    • Viruses are cases where the mutation rate is high enough and the phylogeny is known. Reconstruction accuracy in longitudinal studies...?
  • Sanson GF, Kawashita SY, Brunstein A, Briones MR.  Experimental phylogeny of neutrally evolving DNA sequences generated by a bifurcate series of nested polymerase chain reactions.  Mol Biol Evol. 2002 Feb;19(2):170-8.
    • Scale up with Tecans & similar liquid-handling robots?
  • Sousa A, Ze-Ze L, Silva P, Tenreiro R.  Exploring tree-building methods and distinct molecular data to recover a known asymmetric phage phylogeny.  Mol Phylogenet Evol. 2008 Aug;48(2):563-73. Epub 2008 Apr 29.
  • Bollback JP, Huelsenbeck JP.  Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence.  Genetics. 2009 Jan;181(1):225-34. Epub 2008 Nov 10.
  • Vaguely related: experimental design in phylogenetic reconstruction
    • Geuten K, Massingham T, Darius P, Smets E, Goldman N.  Experimental design criteria in phylogenetics: where to add taxa.  Syst Biol. 2007 Aug;56(4):609-22.

Tracking the passage of transposons in multi-genome alignments

• Pace JK 2nd, Gilbert C, Clark MS, Feschotte C.  Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods.  Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17023-8. Epub 2008 Oct 20.
• Ray DA, Feschotte C, Pagan HJ, Smith JD, Pritham EJ, Arensburger P, Atkinson PW, Craig NL.  Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus.  Genome Res. 2008 May;18(5):717-28. Epub 2008 Mar 13.
• Lots more from Cedric Feschotte

Random interesting-looking papers from a pubmed search for "transposon population dynamics" (43 hits as of 12/31/2008):

• Lilley AK, Bailey MJ, Barr M, Kilshaw K, Timms-Wilson TM, Day MJ, Norris SJ, Jones TH, Godfray HC.  Population dynamics and gene transfer in genetically modified bacteria in a model microcosm.  Mol Ecol. 2003 Nov;12(11):3097-107.
  • model microcosm -- wow!
• Dolgin ES, Charlesworth B, Cutter AD.  Population frequencies of transposable elements in selfing and outcrossing Caenorhabditis nematodes.  Genet Res. 2008 Aug;90(4):317-29.
• Romano CM, de Melo FL, Corsini MA, Holmes EC, Zanotto PM.  Demographic histories of ERV-K in humans, chimpanzees and rhesus monkeys.  PLoS ONE. 2007 Oct 10;2(10):e1026.
  • Lots more good stuff from Eddie Holmes
• Bannert N, Kurth R.  The evolutionary dynamics of human endogenous retroviral families.  Annu Rev Genomics Hum Genet. 2006;7:149-73.
  • At least one endogenous retrovirus still active in humans
• Abrusan G, Krambeck HJ.  Competition may determine the diversity of transposable elements.  Theor Popul Biol. 2006 Nov;70(3):364-75. Epub 2006 May 20.
  • Proposes RNAi as primary host defence & selection mechanism
• Averbeck KT, Eickbush TH.  Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus.  Genetics. 2005 Dec;171(4):1837-46. Epub 2005 Sep 2.
• Vieira C, Biemont C.  Transposable element dynamics in two sibling species: Drosophila melanogaster and Drosophila simulans.  Genetica. 2004 Mar;120(1-3):115-23.
• McCann J, Stabb EV, Millikan DS, Ruby EG.  Population dynamics of Vibrio fischeri during infection of Euprymna scolopes.  Appl Environ Microbiol. 2003 Oct;69(10):5928-34.
• Daboussi MJ, Capy P.  Transposable elements in filamentous fungi.  Annu Rev Microbiol. 2003;57:275-99.
• Baumel A, Ainouche M, Kalendar R, Schulman AH.  Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae).  Mol Biol Evol. 2002 Aug;19(8):1218-27.
• Wright SI, Schoen DJ.  Transposon dynamics and the breeding system.  Genetica. 1999;107(1-3):139-48.
• Wright SI, Le QH, Schoen DJ, Bureau TE.  Population dynamics of an Ac-like transposable element in self- and cross-pollinating arabidopsis.  Genetics. 2001 Jul;158(3):1279-88.
• Prieto JL, Pouilly N, Jenczewski E, Deragon JM, Chevre AM.  Development of crop-specific transposable element (SINE) markers for studying gene flow from oilseed rape to wild radish.  Theor Appl Genet. 2005 Aug;111(3):446-55. Epub 2005 Jun 8.
  • Transposons as engineered markers for tracking gene flow in plants
• Le Rouzic A, Capy P.  Population genetics models of competition between transposable element subfamilies.  Genetics. 2006 Oct;174(2):785-93. Epub 2006 Aug 3.

A few more interesting papers/ideas

• P-elements
  • Witherspoon DJ.  Selective constraints on P-element evolution.  Mol Biol Evol. 1999 Apr;16(4):472-8.
  • Silva JC, Kidwell MG.  Evolution of P elements in natural populations of Drosophila willistoni and D. sturtevanti.  Genetics. 2004 Nov;168(3):1323-35.
  • Silva JC, Kidwell MG.  Horizontal transfer and selection in the evolution of P elements.  Mol Biol Evol. 2000 Oct;17(10):1542-57.

• Transposon family database?

• Plankton & algae microcosms
  • Menge DN, Weitz JS.  Dangerous nutrients: Evolution of phytoplankton resource uptake subject to virus attack.  J Theor Biol. 2008 Nov 14.
  • Weis JJ, Madrigal DS, Cardinale BJ.  Effects of algal diversity on the production of biomass in homogeneous and heterogeneous nutrient environments: a microcosm experiment.  PLoS ONE. 2008 Jul 30;3(7):e2825.

• Zhang Y, Maksakova IA, Gagnier L, van de Lagemaat LN, Mager DL.  Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements.  PLoS Genet. 2008 Feb 29;4(2):e1000007.
  • Polymorphism of transposons within host population

S.pombe as a model (cos it has RNAi) -- v incomplete/quick set of links

• http://sete.nichd.nih.gov/tran_con_spombe.htm
• http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0000067&ct=1
• http://mbe.oxfordjournals.org/cgi/content/full/17/5/730
• http://www.pnas.org/content/105/44/17023.full
• http://www.springerlink.com/content/r83w8738580w5425/

-- IanHolmes - 01 Jan 2009