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Evolutionary Cell Biology
Journal Club

Meetings are currently held on Thursdays, 11:30-12:30pm in the Lieber Room.

Science. 2013 Oct 4;342(6154):104-108.
Following Gene Duplication, Paralog Interference Constrains Transcriptional Circuit Evolution.
Baker CRHanson-Smith VJohnson AD.
Mol Cell. 2013 Sep 26;51(6):792-806. doi: 10.1016/j.molcel.2013.08.017. Epub 2013 Sep 12.
Circular Intronic Long Noncoding RNAs.
Zhang YZhang XOChen TXiang JFYin QFXing YHZhu SYang LChen LL.
PLoS Genet. 2013 May;9(5):e1003330. doi: 10.1371/journal.pgen.1003330. Epub 2013 May 9.
Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses.
Woods SCoghlan ARivers DWarnecke TJeffries SJKwon TRogers AHurst LDAhringer J.
Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11543-8. doi: 10.1073/pnas.0912989107. Epub 2010 Jun 7.
Visualizing high error levels during gene expression in living bacterial cells.
Meyerovich MMamou GBen-Yehuda S.
Biochimie. 2013 Aug;95(8):1593-604. doi: 10.1016/j.biochi.2013.04.016. Epub 2013 May 11.
Rooted phylogeny of the three superkingdoms.
Harish ATunlid AKurland CG.
Nature. 2013 Sep 4. doi: 10.1038/nature12511. [Epub ahead of print]
Genome-wide signatures of convergent evolution in echolocating mammals.
Parker JTsagkogeorga GCotton JALiu YProvero PStupka ERossiter SJ.
Cell. 2013 Jul 18;154(2):452-64. doi: 10.1016/j.cell.2013.06.022.
Genome-wide Generation and Systematic Phenotyping of Knockout Mice Reveals New Roles for Many Genes.
White JKGerdin AKKarp NARyder EBuljan MBussell JNSalisbury JClare SIngham NJPodrini CHoughton REstabel JBottomley JRMelvin DG,Sunter DAdams NCSanger Institute Mouse Genetics ProjectTannahill DLogan DWMacarthur DGFlint JMahajan VBTsang SHSmyth IWatt FM,Skarnes WCDougan GAdams DJRamirez-Solis RBradley ASteel KP.
Nat Genet. 2013 Aug 28;45(9):1021-8. doi: 10.1038/ng.2713. Epub 2013 Jul 28.
Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.
Smith RP, Taher L, Patwardhan RP, Kim MJ, Inoue F, Shendure J, Ovcharenko I, Ahituv N.
Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):E831-40. doi: 10.1073/pnas.1117408109. Epub 2012 Mar 13.
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly.
Yang JR, Liao BY, Zhuang SM, Zhang J.
Cell. 2013 Aug 1;154(3):583-95. doi: 10.1016/j.cell.2013.06.052.
Orchestrated intron retention regulates normal granulocyte differentiation.
Wong JJ, Ritchie W, Ebner OA, Selbach M, Wong JW, Huang Y, Gao D, Pinello N, Gonzalez M, Baidya K, Thoeng A, Khoo TL, Bailey CG, Holst J, Rasko JE.
Nature. 2013 Aug 29;500(7464):571-4. doi: 10.1038/nature12344. Epub 2013 Jul 21.
Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations.
Lang GI, Rice DP, Hickman MJ, Sodergren E, Weinstock GM, Botstein D, Desai MM.
Here is a blog article reviewing the paper :
Nature. 2013 Aug 22;500(7463):453-7. doi: 10.1038/nature12326. Epub 2013 Jul 21.
Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.
Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EG, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthélémy RM, Bast J, Bazykin GA, Chabrol O, Couloux A, Da Rocha M, Da Silva C, Gladyshev E, Gouret P, Hallatschek O, Hecox-Lea B, Labadie K, Lejeune B, Piskurek O, Poulain J, Rodriguez F, Ryan JF, Vakhrusheva OA, Wajnberg E, Wirth B, Yushenova I, Kellis M, Kondrashov AS, Mark Welch DB, Pontarotti P, Weissenbach J, Wincker P, Jaillon O, Van Doninck K.
Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11463-8. doi: 10.1073/pnas.1304246110. Epub 2013 Jun 25.
Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean.
Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, González JM, Luo H, Wright JJ, Landry ZC, Hanson NW, Thompson BP, Poulton NJ, Schwientek P, Acinas SG, Giovannoni SJ, Moran MA, Hallam SJ, Cavicchioli R, Woyke T, Stepanauskas R.
Genetics. 2013 Jan;193(1):303-7. doi: 10.1534/genetics.112.145656. Epub 2012 Oct 31.
Genome reduction promotes increase in protein functional complexity in bacteria.
Kelkar YDOchman H.
Genome Biol Evol. 2013;5(6):1049-59. doi: 10.1093/gbe/evt074.
All or nothing: protein complexes flip essentiality between distantly related eukaryotes.
Ryan CJ, Krogan NJ, Cunningham P, Cagney G.
PLoS Comput Biol. 2012;8(5):e1002514. doi: 10.1371/journal.pcbi.1002514. Epub 2012 May 17.
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs.
Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C.
Nat Struct Mol Biol. 2012 Oct;19(10):998-1004. doi: 10.1038/nsmb.2373. Epub 2012 Sep 9.
Argonaute proteins couple chromatin silencing to alternative splicing.
Ameyar-Zazoua MRachez CSouidi MRobin PFritsch LYoung RMorozova NFenouil RDescostes NAndrau JCMathieu JHamiche AAit-Si-Ali S,Muchardt CBatsché EHarel-Bellan A.
PLoS Genet. 2013 May;9(5):e1003527. doi: 10.1371/journal.pgen.1003527. Epub 2013 May 30.
Strong purifying selection at synonymous sites in D. melanogaster.
Lawrie DS, Messer PW, Hershberg R, Petrov DA.;jsessionid=4D997EA96522DDA03DF6718E249BEFAA
Cell. 2013 Apr 25;153(3):666-77. doi: 10.1016/j.cell.2013.03.021.
Punctuated evolution of prostate cancer genomes.
Baca SCPrandi DLawrence MSMosquera JMRomanel ADrier YPark KKitabayashi NMacdonald TYGhandi MVan Allen EKryukov GVSboner A,Theurillat JPSoong TDNickerson EAuclair DTewari ABeltran HOnofrio RCBoysen GGuiducci CBarbieri CECibulskis KSivachenko ACarter SL,Saksena GVoet DRamos AHWinckler WCipicchio MArdlie KKantoff PWBerger MFGabriel SBGolub TRMeyerson MLander ESElemento OGetz G,Demichelis FRubin MAGarraway LA.
Genetics. 2012 Jan;190(1):203-16. doi: 10.1534/genetics.111.134494. Epub 2011 Oct 31.
Altitudinal variation at duplicated β-globin genes in deer mice: effects of selection, recombination, and gene conversion.
Storz JF, Natarajan C, Cheviron ZA, Hoffmann FG, Kelly JK.
Cell. 2013 Apr 11;153(2):461-70. doi: 10.1016/j.cell.2013.02.044.
Protein complexes are under evolutionary selection to assemble via ordered pathways.
Marsh JA, Hernández H, Hall Z, Ahnert SE, Perica T, Robinson CV, Teichmann SA.
Genome Res. 2013 Feb;23(2):300-11. doi: 10.1101/gr.146662.112. Epub 2012 Dec 28.
Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method.
Makanae K, Kintaka R, Makino T, Kitano H, Moriya H.
Nature. 2013 Mar 28;495(7442):512-5. doi: 10.1038/nature11989.
Accelerated gene evolution through replication-transcription conflicts.
Paul S, Million-Weaver S, Chattopadhyay S, Sokurenko E, Merrikh H.
Mol Biol Evol. 2013 Apr;30(4):853-64. doi: 10.1093/molbev/mss272. Epub 2012 Nov 30.
Recombination rates and genomic shuffling in human and chimpanzee--a new twist in the chromosomal speciation theory.
Farré M, Micheletti D, Ruiz-Herrera A.
BMC Biol. 2011 Sep 27;9:64. doi: 10.1186/1741-7007-9-64.
Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis.
Davila JIArrieta-Montiel MPWamboldt YCao JHagmann JShedge VXu YZWeigel DMackenzie SA.
Mol Biol Evol. 2013 Feb 5. [Epub ahead of print]
Organelle Genome Complexity Scales Positively with Organism Size in Volvocine Green Algae.
Smith DRHamaji TOlson BJDurand PMFerris PMichod REFeatherston JNozaki HKeeling PJ.
Cell. 2012 Dec 7;151(6):1243-55. doi: 10.1016/j.cell.2012.10.045.
Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement.
Fang WWang XBracht JRNowacki MLandweber LF.

Also, a perspective paper in Bioessays written by the authors:
PLoS Biol. 2013;11(2):e1001497. doi: 10.1371/journal.pbio.1001497. Epub 2013 Feb 26.
Indirect evolution of hybrid lethality due to linkage with selected locus in Mimulus guttatus.
Wright KM, Lloyd D, Lowry DB, Macnair MR, Willis JH.
Curr Biol. 2012 Dec 18;22(24):2303-12. doi: 10.1016/j.cub.2012.10.036. Epub 2012 Nov 15.
Loss of nucleosomal DNA condensation coincides with appearance of a novel nuclear protein in dinoflagellates.
Gornik SG, Ford KL, Mulhern TD, Bacic A, McFadden GI, Waller RF.
Genome Biol Evol. 2011;3:1006-13. doi: 10.1093/gbe/evr086. Epub 2011 Aug 22.
Detecting past positive selection through ongoing negative selection.
Bazykin GA, Kondrashov AS.
PLoS Genet. 2013;9(1):e1003176. doi: 10.1371/journal.pgen.1003176. Epub 2013 Jan 3.
The roles of whole-genome and small-scale duplications in the functional specialization of Saccharomyces cerevisiae genes.
Fares MA, Keane OM, Toft C, Carretero-Paulet L, Jones GW.
Nature. 2013 Jan 10;493(7431):216-20. doi: 10.1038/nature11690. Epub 2012 Nov 28.
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.
Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ; NHLBI Exome Sequencing Project, Akey JM.
PLoS Biol. 2012 Dec;10(12):e1001446. doi: 10.1371/journal.pbio.1001446. Epub 2012 Dec 11.
Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication.
Voordeckers KBrown CAVanneste Kvan der Zande EVoet AMaere SVerstrepen KJ.
Genetics. 2010 Feb;184(2):529-45. doi: 10.1534/genetics.109.103556. Epub 2009 Dec 4.
Gene genealogies strongly distorted by weakly interfering mutations in constant environments.
Seger JSmith WAPerry JJHunn JKaliszewska ZASala LLPozzi LRowntree VJAdler FR.

Nature. 2012 Dec 6;492(7427):59-65. doi: 10.1038/nature11681. Epub 2012 Nov 28.
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.
Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJ, Herman EK, Klute MJ, Nakayama T, Oborník M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale CJ, Hempel F, Henrissat B, Höppner MP, Ishida K, Kim E, Kořený L, Kroth PG, Liu Y, Malik SB, Maier UG, McRose D, Mock T, Neilson JA, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE, Keeling PJ, Gray MW, Grigoriev IV, Archibald JM.
Genome Res. 2012 Dec;22(12):2356-67. doi: 10.1101/gr.139725.112. Epub 2012 Jun 21.
Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints.
Irimia M, Tena JJ, Alexis MS, Fernandez-Miñan A, Maeso I, Bogdanovic O, de la Calle-Mustienes E, Roy SW, Gómez-Skarmeta JL, Fraser HB.
Genome Biol. 2012 Oct 3;13(10):R94. [Epub ahead of print]
Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis.
Berke L, Sanchez-Perez GF, Snel B.

Nature. 2012 Oct 25;490(7421):535-8. doi: 10.1038/nature11510. Epub 2012 Oct 14.
Epistasis as the primary factor in molecular evolution.
Breen MSKemena CVlasov PKNotredame CKondrashov FA.


(accompanying review, looks like very good epistasis background):

Trends Genet. 2011 Aug;27(8):323-31. Epub 2011 Jun 22.
Molecular mechanisms of epistasis within and between genes.
Lehner B.
Environ Mol Mutagen. 2012 Dec;53(9):777-86. doi: 10.1002/em.21728. Epub 2012 Sep 11.
DNA polymerase zeta generates clustered mutations during bypass of endogenous DNA lesions in Saccharomyces cerevisiae.
Stone JELujan SAKunkel TAKunkel TA.;jsessionid=B1E8EC013FA0E76465B99419397D91D1.d03t03

A related review is recommended as well (and has good color diagrams):

Nat Rev Mol Cell Biol. 2010 Mar;11(3):208-19.
Maintaining genome stability at the replication fork.
Branzei DFoiani M.
PLoS Genet. 2012;8(10):e1002905. doi: 10.1371/journal.pgen.1002905. Epub 2012 Oct 11.
The many landscapes of recombination in Drosophila melanogaster.
Comeron JM, Ratnappan R, Bailin S.
There is also an editorial for this article, which should provide a very interesting introduction to this topic.

Singh ND (2012) Classical genetics meets next-generation sequencing: uncovering a genome-wide recombination map in Drosophila melanogaster. PLoS Genet, 8, e1003024.

Science. 2012 Oct 19;338(6105):384-7.
Real-time evolution of new genes by innovation, amplification, and divergence.
Näsvall JSun LRoth JRAndersson DI.
Proc Natl Acad Sci U S A. 2011 May 3;108(18):7481-6. doi: 10.1073/pnas.1018249108. Epub 2011 Apr 25.
Evolutionary dynamics of bacteria in a human host environment.
Yang L, Jelsbak L, Marvig RL, Damkiær S, Workman CT, Rau MH, Hansen SK, Folkesson A, Johansen HK, Ciofu O, Høiby N, Sommer MO, Molin S.
Nature. 2012 Oct 25;490(7421):497-501. doi: 10.1038/nature11532. Epub 2012 Oct 3.
A map of rice genome variation reveals the origin of cultivated rice.
Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B.
Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6151-6. Epub 2011 Mar 28.
An actin cytoskeleton with evolutionarily conserved functions in the absence of canonical actin-binding proteins.
Paredez AR, Assaf ZJ, Sept D, Timofejeva L, Dawson SC, Wang CJ, Cande WZ.
Proc Nat Acad Sci 2012 109(36):14508-14513

Detection of ultra-rare mutations by next-generation sequencing

Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA.
Mol Biol Evol. 2007 Mar;24(3):670-8. Epub 2006 Dec 14.
Evidence of interaction network evolution by whole-genome duplications: a case study in MADS-box proteins.
Veron ASKaufmann KBornberg-Bauer E.
Cell. 2012 May 11;149(4):912-22. doi: 10.1016/j.cell.2012.03.033. Epub 2012 May 3.
Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication.
Dennis MY, Nuttle X, Sudmant PH, Antonacci F, Graves TA, Nefedov M, Rosenfeld JA, Sajjadian S, Malig M, Kotkiewicz H, Curry CJ, Shafer S, Shaffer LG, de Jong PJ, Wilson RK, Eichler EE.
Cell. 2012 Jul 6;150(1):222-32. doi: 10.1016/j.cell.2012.05.033.
Adaptive mutations that prevent crosstalk enable the expansion of paralogous signaling protein families.
Capra EJ, Perchuk BS, Skerker JM, Laub MT.
Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):9837-42. Epub 2003 Jul 21.
When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism.
Roy H, Becker HD, Reinbolt J, Kern D.
Genome Biol. 2008;9(6):R95. doi: 10.1186/gb-2008-9-6-r95. Epub 2008 Jun 9.
The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution.
Hernández-Montes G, Díaz-Mejía JJ, Pérez-Rueda E, Segovia L.
PLoS Genet. 2011 Mar;7(3):e1001321. doi: 10.1371/journal.pgen.1001321. Epub 2011 Mar 3.
Initial mutations direct alternative pathways of protein evolution.
Salverda ML, Dellus E, Gorter FA, Debets AJ, van der Oost J, Hoekstra RF, Tawfik DS, de Visser JA.