Allaby, Robin G.. (2010) Integrating the processes in the evolutionary system of domestication. Journal of Experimental Botany, Vol.61 (No.4). pp. 935-944. ISSN 0022-0957

PDF WRAP_Allaby_0380313-hr-080410-allaby2010.pdf - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader Download (1211Kb)

Abstract

Genetics has long been used as a source of evidence to understand domestication origins. A recent shift in the emphasis of archaeological evidence from a rapid transition paradigm of hunter-gatherers to agriculturalists, to a protracted transition paradigm has highlighted how the scientific framework of interpretation of genetic data was quite dependent on archaeological evidence, resulting in a period of discord in which the two evidence types appeared to support different paradigms. Further examination showed that the discriminatory power of the approaches employed in genetics was low, and framed within the rapid paradigm rather than testing it. In order to interpret genetic data under the new protracted paradigm it must be taken into account how that paradigm changes our expectations of genetic diversity. Preliminary examination suggests that a number of features that constituted key evidence in the rapid paradigm are likely to be interpreted very differently in the protracted paradigm. Specifically, in the protracted transition the mode and mechanisms involved in the evolution of the domestication syndrome have become much more influential in the shape of genetic diversity. The result is that numerous factors interacting over several levels of organization in a domestication system need to be taken into account in order to understand the evolution of the process. This presents a complex problem of integration of different data types which is difficult to describe formally. One possible way forward is to use Bayesian approximation approaches that allow complex systems to be measured in a way that does not require such formality.

Item Type:	Journal Article
Subjects:	Q Science > QH Natural history > QH426 Genetics
Divisions:	Faculty of Science > Life Sciences (2010- ) > Warwick HRI (2004-2010)
Library of Congress Subject Headings (LCSH):	Plants, Cultivated -- Genetic aspects, Domestication -- Genetic aspects, Evolutionary genetics, Bayesian statistical decision theory, Plants, Cultivated -- History
Journal or Publication Title:	Journal of Experimental Botany
Publisher:	Oxford University Press
ISSN:	0022-0957
Date:	March 2010
Volume:	Vol.61
Number:	No.4
Page Range:	pp. 935-944
Identification Number:	10.1093/jxb/erp382
Status:	Peer Reviewed
Access rights to Published version:	Restricted or Subscription Access
References:	Allaby RG (2008) The rise of plant domestication: life in the slow lane. Biologist 55: 94- 99. Allaby R.G., Fuller D.Q., Brown T.A. (2008) The genetic expectations of a protracted model for the origins of domesticated crops. Proceedings of the National Academy of Sciences USA 105:13982-13986. Allaby RG, Peterson G, Merriwether DA, Fu Y-B (2005) Evidence of the domestication history of flax (Linum usitatissimum L.) from genetic diversity of the sad2 locus. Theor Appl Genet 112:58-65. Azguvel P, Komatsuda T (2007) A phylogenetic analysis based on nucleotide sequence of a marker linked to the brittle rachis locus indicates a diphyletic origin of barley. Ann. Bot. 100:1009-1015. Badr A, Müller K, Schäfer-Pregl R, El Rabey H, Effgen S, Ibrahim HH, Pozzi C, Rohde W and Salamini F (2000) On the Origin and Domestication History of Barley. Mol Biol Evol 17:499-510 Beaumont MA, Zhang W, Balding DJ (2002) Approximate Bayesian Computation in population genetics. Genetics 162:2025-2035. Blumer MA (1992) Independent inventionism and recent genetic evidence on plant domestication. Econ. Bot. 46:98-111. Brown T.A., Lindsay S., and Allaby R.G. (2006) Using modern landraces of wheat to study the origins of European Agriculture. In Darwin's Harvest. Pp. 197-212. Eds. Motley, T.J., Zeregra, N., Cross, H. Columbia University Press, New York. Darwin C (1859) Variation under domestication. In Origin of Species, Murray, London, pp 7-43. Darwin C (1868) Variation of Animals and Plants under Domestication, 2 vols, Murray, London. Flannery K (1969) Origins and ecological effects of early domestication in Iran and the Near East. P. 73-100 in The domestication and exploitation of plants and animals, eds. Ucko P and Dimbleby G. Duckworth, London. Fuller D (2007) Contrasting Patterns in Crop Domestication and Domestiation Rates: Recent Archaeobotanical Insights from the Old World. Annals of Botany 100: 903-924. Fuller DQ, Allaby RG, Stevens C (2009a) Domestication as Innovation: The entanglement of techniques, technology and chance in the domestication of cereal crops. World Archaeology in press. Fuller DQ, Qin L, Zheng Y, Zhao Z, Chen X, Hosoya LA, Sun G-P (2009b) The Domestication process and domestication rate in rice: spikelet bases from the Lower Yangtze. Science 323: 1607-1610. Gepts P (2004) Crop domestication as a long term selection experiment. Plant Breeding Reviews 24(2): 1-44. Harris DR (1986). An evolutionary continuum of people-plant interaction. In Foraging and Farming: the evolution of plant exploitation. Eds. Harris DR, Hillman GC. Unwin Hyman, London. Pp 11-26. Heun M, Schäfer-Pregl R, Klawan D, Castagna R, Accerbi M, Borghi B, Salamini F (1997) Site of einkorn wheat domestication identified by DNA fingerprinting. Science 278:1312-1314. Hillman GC (1975) The plant remains from Tell Abu Hureyra: A preliminary report. Proc. Prehist. Soc. 41:70-73. Hillman GC and Davies MS (1990) Domestication rates in wild-type wheats and barley under primitive cultivation. Biological Journal of the Linnean Society 39:39-78. Jones H, Leigh F, Mackay I, Bower M, Smith L, Charles M, Jones G, Jones M, Brown T, Powell W 2008. Population based re-sequencing reveals that the flowering time adaptation of cultivated barley originated east of the Fertile Crescent. Molecular Biology and Evolution 25:2211-2219. Kimura M, Ohta T (1973) The age of a neutral mutant persisting in a finite population. Genetics 75:199-212. Kislev ME, Weiss E, Hartmann A (2004) Impetus for sowing and the beginning of agriculture: Ground collecting of wild cereals. Proceedings of the National Academy of Sciences USA 101:2692-2695. Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M (2006) A SNP caused loss of seed shattering during rice domestication. Science 312: 1392-1396. Kovach MJ, Calingacion MN, Fitzgerald MA, McCouch S (2009) The origin and evolution of fragrance in rice (Oryza sativa L.). Proceedings of the National Academy of Sciences USA 106:14444-14449. Le Thierry D’Ennequin M , Toupance B, Godelle B, Gouyon PH (1999) Plant domestication: a model for studying the selection of linkage. J Evol Biol 12:1138‐ 1147. Li C, Zhou A, Sang T (2006). Rice domestication by reducing shattering. Science 311:1936-1939. Lin Z, Griffith ME, Li X, Zhu Z, Tan L, Fu Y, Zhang W, Wang X, Xie D, Sun C (2007) Origin of seed shattering in rice (Oryza sativa L.). Planta 226:11-20. Londo JP, Chiang, Y-C, Hung K-H, Chiang T-Y, Schaal BA (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cutivated rice, Oryza sativa. Proc Natl Acad Sci USA 103:9578-9583. Marjoram P, Tavaré S (2006) Modern computational approaches for analysing molecular genetic variation data. Nat. Rev. Genet. 7:759-770. Matsuoka Y, Vigouroux, Y, Goodman, MM, Sanchez G, J, Buckler, E & Doebley, J (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci USA 99:6080-6084. Molina-Cano JL, Russell JR, Moralejo MA, Escacena JL, Arias G and Powell W (2005) Chloroplast DNA microsatellite analysis supports a polyphyletic origin for barley. Theor Appl Genet 110:613-619. Moore AMT, Hillman GC (1992) The Pleistocene to Holocene transition and human economy in Southwest Asia: The impact of the Younger Dryas. American Antiquity 57:482-494. Oka H-I, Morishima H (1971) The dynamics of plant domestications: cultivation experiments with Oryza perennis and its hybrid with O. sativa. Evolution 25:356-364. Shomura A, Izawa, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nature Genetics 40:1023-1028. Stiner M (2001) Thirty years on the “Broad Spectrum Revolution” and paleolithic demography. Proc. Natl. Acad. Sci. USA 98:6993-6996. Sweeney MT, Thompson MJ, Cho YG, Park YJ, Williamson SH, Bustamante CD, McCouch S (2007) Global dissemination of a single mutation conferring white pericarp in rice. Plos Genetics 3:1418-1424. Ross-Ibarra J, Tenaillon M, Gaut B (2009) Historical divergence and gene flow in the genus Zea. Genetics 181:1399-1413. Takahashi R (1972) Non-brittle rachis 1 and non-brittle rachis 2. Barley Genetics Newsletter 2:181-182. Tanno KI and Willcox G (2006) How Fast Was Wild Wheat Domesticated? Science 311: 1886. Weiss E, Kislev ME and Hartmann A (2006) Autonomous Cultivation Before Domestication. Science 312: 1608-1610. Weiss E, Wetterstrom W, Nadel D and Bar-Yosef O (2004) The broad spectrum revisited: Evidence from plant remains. Proceedings of the National Academy of Sciences USA 101: 9551-9555. Willcox (2004) Measuring grain size and identifying Near Eastern cereal domestication: evidence from the Euphrates valley. Journal of Archaeological Science 31:145-150. Willcox G (2005) The distribution, natural habitats and availability of wild cereals in relation to their domestication in the Near East: multiple events, multiple centres. Vegetation history and archaeobotany. 14: 534-541. Willcox G, Fornite S and Herveux L (2008) Early Holocene cultivation before domestication in northern Syria. Vegetation history ad archaeobotany 17: 313-325. Willcox G, Buxo R, Herveux L (2009) Late Pleistocene and Early Holocene climate and the beginnings of cultivation in northern Syria. Holocene 19:151-158. Wright HE (1976) The Environmental Setting for Plant Domestication in the Near East. Science 194:385-389. Yamanaka S, Nakamura I, Watanabe KN, Sato Y-I (2004) Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice. Theoretical and Applied Genetics 108:1200-1204. Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Yasuda S, Dubcovsky J 2006. The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proceedings of the National Academy of Sciences USA 103:19581-19586. Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J 2003. Positional cloning of the wheat vernalization gene VRN1. Proceedings of the National Academy of Sciences USA 100:6263-6268. Yan L, Helguera M, Kato K, Fukuyama S, Sherman J, Dubcovsky J 2004b. Allelic variation at the VRN-1 promoter region in polyploidy wheat. Theoretical and Applied Genetics 109:1677-1686. Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, San Miguel P, Bennetzen JL, Echenique V, Dubcovsky J 2004a. The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640-1644. Zhu Q, Zheng X, Luo J, Gaut B and Song G (2007) Multilocus Analysis of Nucleotide Variation of Oryza sativa and Its Wild Relatives: Severe Bottleneck during Domestciation of Rice. Molecular Biology and Evolution 24:875-888. Zohary D (1999) Monophyletic vs. polyphyletic origin of crops found in the Near East Genet Res Crop Evol 46:133-142. Zohary D and Hopf M (2000) Domestication of Plants in the Old World. Third Edition. Oxford University Press, Oxford.
URI:	http://wrap.warwick.ac.uk/id/eprint/3011

Request changes to a record

Actions (login required)

View Item