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Items: 40

1.

Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production.

Gutaker RM, Zaidem M, Fu YB, Diederichsen A, Smith O, Ware R, Allaby RG.

Sci Rep. 2019 Jan 30;9(1):976. doi: 10.1038/s41598-018-37086-5.

2.

A re-evaluation of the domestication bottleneck from archaeogenomic evidence.

Allaby RG, Ware RL, Kistler L.

Evol Appl. 2018 Sep 8;12(1):29-37. doi: 10.1111/eva.12680. eCollection 2019 Jan.

3.

Multiproxy evidence highlights a complex evolutionary legacy of maize in South America.

Kistler L, Maezumi SY, Gregorio de Souza J, Przelomska NAS, Malaquias Costa F, Smith O, Loiselle H, Ramos-Madrigal J, Wales N, Ribeiro ER, Morrison RR, Grimaldo C, Prous AP, Arriaza B, Gilbert MTP, de Oliveira Freitas F, Allaby RG.

Science. 2018 Dec 14;362(6420):1309-1313. doi: 10.1126/science.aav0207.

PMID:
30545889
4.

Geographic mosaics and changing rates of cereal domestication.

Allaby RG, Stevens C, Lucas L, Maeda O, Fuller DQ.

Philos Trans R Soc Lond B Biol Sci. 2017 Dec 5;372(1735). pii: 20160429. doi: 10.1098/rstb.2016.0429.

5.

Small RNA Activity in Archeological Barley Shows Novel Germination Inhibition in Response to Environment.

Smith O, Palmer SA, Clapham AJ, Rose P, Liu Y, Wang J, Allaby RG.

Mol Biol Evol. 2017 Oct 1;34(10):2555-2562. doi: 10.1093/molbev/msx175.

6.

Uncovering the dispersion history, adaptive evolution and selection of wheat in China.

Zhou Y, Chen Z, Cheng M, Chen J, Zhu T, Wang R, Liu Y, Qi P, Chen G, Jiang Q, Wei Y, Luo MC, Nevo E, Allaby RG, Liu D, Wang J, Dvorák J, Zheng Y.

Plant Biotechnol J. 2018 Jan;16(1):280-291. doi: 10.1111/pbi.12770. Epub 2017 Jul 17.

7.

A new model for ancient DNA decay based on paleogenomic meta-analysis.

Kistler L, Ware R, Smith O, Collins M, Allaby RG.

Nucleic Acids Res. 2017 Jun 20;45(11):6310-6320. doi: 10.1093/nar/gkx361.

8.

Barley domestication: the end of a central dogma?

Allaby RG.

Genome Biol. 2015 Aug 26;16:176. doi: 10.1186/s13059-015-0743-9.

9.

Archaeology. Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago.

Smith O, Momber G, Bates R, Garwood P, Fitch S, Pallen M, Gaffney V, Allaby RG.

Science. 2015 Feb 27;347(6225):998-1001. doi: 10.1126/science.1261278.

10.

Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant-hominin co-evolution back to the Pliocene.

Allaby RG, Kistler L, Gutaker RM, Ware R, Kitchen JL, Smith O, Clarke AC.

J Hum Evol. 2015 Feb;79:150-7. doi: 10.1016/j.jhevol.2014.10.014. Epub 2015 Jan 8.

11.

Surprisingly Low Limits of Selection in Plant Domestication.

Allaby RG, Kitchen JL, Fuller DQ.

Evol Bioinform Online. 2016 Apr 5;11(Suppl 2):41-51. doi: 10.4137/EBO.S33495. eCollection 2015.

12.

Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops.

Allaby RG, Gutaker R, Clarke AC, Pearson N, Ware R, Palmer SA, Kitchen JL, Smith O.

Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130377. doi: 10.1098/rstb.2013.0377. Review.

13.

Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process.

Smith O, Clapham AJ, Rose P, Liu Y, Wang J, Allaby RG.

Sci Rep. 2014 Jul 4;4:5559. doi: 10.1038/srep05559.

14.

Current perspectives and the future of domestication studies.

Larson G, Piperno DR, Allaby RG, Purugganan MD, Andersson L, Arroyo-Kalin M, Barton L, Climer Vigueira C, Denham T, Dobney K, Doust AN, Gepts P, Gilbert MT, Gremillion KJ, Lucas L, Lukens L, Marshall FB, Olsen KM, Pires JC, Richerson PJ, Rubio de Casas R, Sanjur OI, Thomas MG, Fuller DQ.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6139-46. doi: 10.1073/pnas.1323964111. Epub 2014 Apr 22.

15.

Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record.

Fuller DQ, Denham T, Arroyo-Kalin M, Lucas L, Stevens CJ, Qin L, Allaby RG, Purugganan MD.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6147-52. doi: 10.1073/pnas.1308937110. Epub 2014 Apr 21.

16.

Storytelling and story testing in domestication.

Gerbault P, Allaby RG, Boivin N, Rudzinski A, Grimaldi IM, Pires JC, Climer Vigueira C, Dobney K, Gremillion KJ, Barton L, Arroyo-Kalin M, Purugganan MD, Rubio de Casas R, Bollongino R, Burger J, Fuller DQ, Bradley DG, Balding DJ, Richerson PJ, Gilbert MT, Larson G, Thomas MG.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6159-64. doi: 10.1073/pnas.1400425111. Epub 2014 Apr 21.

17.

A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus.

Smith O, Clapham A, Rose P, Liu Y, Wang J, Allaby RG.

Sci Rep. 2014 Feb 6;4:4003. doi: 10.1038/srep04003.

18.

Systems Modeling at Multiple Levels of Regulation: Linking Systems and Genetic Networks to Spatially Explicit Plant Populations.

Kitchen JL, Allaby RG.

Plants (Basel). 2013 Jan 25;2(1):16-49. doi: 10.3390/plants2010016. Review.

19.

MCMC-ODPR: primer design optimization using Markov Chain Monte Carlo sampling.

Kitchen JL, Moore JD, Palmer SA, Allaby RG.

BMC Bioinformatics. 2012 Nov 5;13:287. doi: 10.1186/1471-2105-13-287.

20.

The limits of mean-field heterozygosity estimates under spatial extension in simulated plant populations.

Kitchen JL, Allaby RG.

PLoS One. 2012;7(8):e43254. doi: 10.1371/journal.pone.0043254. Epub 2012 Aug 27.

21.

Locus-specific view of flax domestication history.

Fu YB, Diederichsen A, Allaby RG.

Ecol Evol. 2012 Jan;2(1):139-52. doi: 10.1002/ece3.57.

22.

Archaeogenomic evidence of punctuated genome evolution in Gossypium.

Palmer SA, Clapham AJ, Rose P, Freitas FO, Owen BD, Beresford-Jones D, Moore JD, Kitchen JL, Allaby RG.

Mol Biol Evol. 2012 Aug;29(8):2031-8. doi: 10.1093/molbev/mss070. Epub 2012 Feb 14.

PMID:
22334578
23.

Early agricultural pathways: moving outside the 'core area' hypothesis in Southwest Asia.

Fuller DQ, Willcox G, Allaby RG.

J Exp Bot. 2012 Jan;63(2):617-33. doi: 10.1093/jxb/err307. Epub 2011 Nov 4. Review.

PMID:
22058404
24.

The blossoming of plant archaeogenetics.

Palmer SA, Smith O, Allaby RG.

Ann Anat. 2012 Jan 20;194(1):146-56. doi: 10.1016/j.aanat.2011.03.012. Epub 2011 Apr 9. Review.

PMID:
21531123
25.

Comment on "30,000-year-old wild flax fibers".

Bergfjord C, Karg S, Rast-Eicher A, Nosch ML, Mannering U, Allaby RG, Murphy BM, Holst B.

Science. 2010 Jun 25;328(5986):1634; author reply 1634. doi: 10.1126/science.1186345.

PMID:
20576873
26.

Archaeogenetic evidence of ancient nubian barley evolution from six to two-row indicates local adaptation.

Palmer SA, Moore JD, Clapham AJ, Rose P, Allaby RG.

PLoS One. 2009 Jul 22;4(7):e6301. doi: 10.1371/journal.pone.0006301.

27.

The complex origins of domesticated crops in the Fertile Crescent.

Brown TA, Jones MK, Powell W, Allaby RG.

Trends Ecol Evol. 2009 Feb;24(2):103-9. doi: 10.1016/j.tree.2008.09.008. Epub 2008 Dec 25.

PMID:
19100651
28.

The genetic expectations of a protracted model for the origins of domesticated crops.

Allaby RG, Fuller DQ, Brown TA.

Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):13982-6. doi: 10.1073/pnas.0803780105. Epub 2008 Sep 3.

29.

Phylogenetics in the bioinformatics culture of understanding.

Allaby RG, Woodwark M.

Comp Funct Genomics. 2004;5(2):128-46. doi: 10.1002/cfg.381.

30.

TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism.

Moore JD, Allaby RG.

Bioinformatics. 2008 Mar 1;24(5):717-8. doi: 10.1093/bioinformatics/btn027. Epub 2008 Jan 19.

PMID:
18204056
31.

Elevated substitution rates estimated from ancient DNA sequences.

Ho SY, Kolokotronis SO, Allaby RG.

Biol Lett. 2007 Dec 22;3(6):702-5.

32.
33.

Evidence of the domestication history of flax (Linum usitatissimum L.) from genetic diversity of the sad2 locus.

Allaby RG, Peterson GW, Merriwether DA, Fu YB.

Theor Appl Genet. 2005 Dec;112(1):58-65. Epub 2005 Oct 8.

PMID:
16215731
34.

AFLP data and the origins of domesticated crops.

Allaby RG, Brown TA.

Genome. 2003 Jun;46(3):448-53.

PMID:
12834061
35.
36.
37.

Evolution of the high molecular weight glutenin loci of the A, B, D, and G genomes of wheat.

Allaby RG, Banerjee M, Brown TA.

Genome. 1999 Apr;42(2):296-307.

PMID:
10231962
38.

PCR-based identification of wheat genomes.

Sallares R, Allaby RG, Brown TA.

Mol Ecol. 1995 Aug;4(4):509-14.

PMID:
8574448
39.

DNA in wheat seeds from European archaeological sites.

Brown TA, Allaby RG, Brown KA, O'Donoghue K, Sallares R.

Experientia. 1994 Jun 15;50(6):571-5. Review.

PMID:
8020618
40.

Biomolecular archaeology of wheat: past, present and future.

Brown TA, Allaby RG, Brown KA, Jones MK.

World Archaeol. 1993 Jun;25(1):64-73. No abstract available.

PMID:
16471027

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