New archaeobotanical information on plant domestication from macro-remains: tracking the evolution of domestication syndrome traits more

Biodiversity in Agriculture Domestication, Evolution, and Sustainability Edited by PAUL GEPTS, THOMAS R. FAMULA, ROBERT L. BETTINGER, STEPHEN B. BRUSH. ARDESHIR B. DAMANIA, PATRICK E. MCGUIRE, and CALVIN 0. QUALSET University of California, Davis, USA CAMBRIDGE UNIVERSITY PRESS CAMBRIDGE UNIVERSITY PRESS Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore, Sao Paulo, Delhi, Tokyo, Mexico City Cambridge University Press The Edinburgh Building, Cambridge CB2 8RU, UK Published in the United States of America by Cambridge University Press, New York www.cambridge.org Information on this title: www.cambridge.org/9780521764599 (0 Cambridge University Press 2012 This publication is in copyright. Subject to statutory exception and to the provisions of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. First published 2012 Printed in the United Kingdom at the University Press, Cambridge A catalogue record for this publication is available front the British Library Library of Congress Cataloguing in Publication data Harlan Symposium (2nd : 2008: University of California, Davis) Biodiversity in agriculture : domestication, evolution, and sustainability / edited by Paul Gepts ... [et all p. cm. "The presentations of the second edition of the Harlan Symposium, held September 14-18, 2008, on the campus of the University of California, Davis ..."—Foreword. Includes index. ISBN 978-0-521-76459-9 (Hardback) — ISBN 978-0-521-17087-1 (l'aperback) 1. Agrobiodiversity—Congresses. I. Gepts, Paul L. II. Title. S494.5.A43H37 2008 63l.5'8—dc23 2011026300 ISBN 978-0-521-76459-9 Hardback ISBN 978-0-521-17087-1 Paperback Cambridge University Press has no responsibility for the persistence or accuracy of URLs for external or third-party internet websites referred to in this publication, and does not guarantee that any content on such websites is, or will remain, accurate or appropriate. Contents List of tables List of figures Foreword B.D. Smith List of contributors Acknowledgments P. Gepts and T. Famula Introduction: The Domestication of Plants and Animals: Ten Unanswered Questions 1 P. Gepts, R. Bettinger, S. Brush, A. Damania, T. Famula, P. McGuire, and C. Oualset 1 The Local Origins of Domestication J. Diamond 9 Section I Early Steps in Agricultural Domestication R. Bettinger 2 Evolution of Agroecosystems: Biodiversity, Origins, and Differential Development D.R. Harris 21 3 From Foraging to Farming in Western and Eastern Asia 0. Bar Yosef - 57 4 Pre-Domestic Cultivation during the Late Pleistocene and Early Holocene in the Northern Levant G VV,Jcox 92 5 New Archaeobotanical Information on Plant Domestication from Macro-Remains: Tracking the Evolution of Domestication Syndrome Traits 110 0 Fuller 6 New Archaeobotanical Information on Early Cultivation and Plant Domestication Involving Microplant (Phytolith and Starch Grain) Remains D.R. Piperno 136 vi Contents Contents vii 7 How and Why Did Agriculture Spread? P. Bellwood 160 18 Agrobiodiversity Shifts on Three Continents Since Vavilov and Harlan: Assessing Causes, Processes, and Implications for Food Security G.P. Nabhan, K. Wilson, 0. Aknazarov, K.-A. Kassam, L. Monti, D. Cavagnaro, S. Kelly, T. Johnson, and F. Sekacucu 407 8 California Indian Proto-Agriculture: Its Characterization and Legacy M.K. Anderson and E. Wohlgemuth 190 1 19 Indigenous Peoples Conserving, Managing, and Creating Biodiversity J. Salick 426 Section II Domestication of Animals and Impacts on Humans T. Famula 20 227 Land Architecture in the Maya Lowlands: Implications for Sustainability B.L. Turner II and D. Lawrence 445 9 Pathways to Animal Domestication M.A. Zeder 21 260 10 Genetics of Animal Domestication L. Andersson Agrobiodiversity and Water Resources in Agricultural Landscape Evolution (Andean Valley Irrigation, Bolivia, 1986 to 2008) K S. Lirrimerer 464 11 Genome-Wide Approaches for the Study of Dog Domestication B.M. vonHoldt, M.M. Gray, and R.K. Wayne 275 Section V Uses of Biodiversity and New and Future Domestications P. McGuire and C. Cua!set 12 Malaria and Rickets Represent Selective Forces for the Convergent Evolution of Adult Lactase Persistence L Cordain, M.S. Hickey, and K. Kim 299 22 Participatory Domestication of Indigenous Fruit and Nut Trees: New Crops for Sustainable Agriculture in Developing Countries R.R.B. Leakey 479 Section III Issues in Plant Domestication P. Gepts 23 The Introduction and Dispersal of Vitis vinifera into California: A Case Study of the Interaction of People, Plants, Economics, and Environment J. Lapsley 502 13 The Dynamics of Rice Domestication: A Balance between Gene Flow and Genetic Isolation S.R. McCouch, M.J. Kovach, M. Sweeney, H. Jiang, and M. Sewn 311 24 Genetic Resources of Yeast and Other Micro-Organisms C.W. Bamforth 515 14 Domestication of Lima Beans: A New Look at an Old Problem M.I. ChacOn S., J.R. Motta-Aldana, M.L. Serrano S., and D.G. Debouck 330 25 Biodiversity of Native Bees and Crop Pollination with Emphasis on California R W Thorp 526 15 Genetic Characterization of Cassava (Manihot esculenta Crantz) and Yam (Dioscorea trifida L.) Landraces in Swidden Agriculture Systems in Brazil E.A. Veasey, E.A. Bressan, M.V.B.M. Siqueira, A. Borges, J.R. Oueiroz-Silva, K.J.C. Pereira, G.H. Recchia, and L.C. Ming 26 344 Aquaculture, the Next Wave of Domestication D. Hedgecock 538 27 361 Genetic Sustainability and Biodiversity: Challenges to the California Dairy Industry J.F. Medrano 549 16 Pigeonpea: From an Orphan to a Leader in Food Legumes C.L. Laxmipathi Gowda, K.B. Saxena, R.K. Srivastava,I-I.D. Upadhyaya, and S.N. Sifim Index 562 Section IV Traditional Management of Biodiversity S. Brush The color plates will be found between pages 78 and 79. 377 17 Ecological Approaches to Crop Domestication D.B. McKey, M. Elias, B. Pujol, and A Duputie New Archaeobotanical Information on Plant Domestication from Macro Remains - 111 5 New Archaeobotanical Information on Plant Domestication from Macro-Remains: Tracking the Evolution of Domestication Syndrome Traits •s =b17 FUSEIMIONINXIMMEUMM. 11111•1•12011 80 70 60 50 40 30 20 10 Near East (pre-ceramic only) • —tuning total - - • flotation India & Pakistan '—e--total sites floated Neo/Chalc —6—Southern Neolithic e Dorian Q. Fuller The growth of archaeobotany Archaeobotany is the specialist study at the frontier of archaeology and plant evolution. By the study of preserved plant remains from ancient human sites, archaeobotany provides evidence for use of plant resources by past cultures but also provides a record of datable ancient remains from which to document trends in the morphological evolution of crop species. As the available archaeobotanical data grow (Figure 5.1) it becomes increasingly possible to look comparatively at the trends in crop evolution, although we are still at an early stage in such research. The paper will explore some preliminary syntheses of such data, organized around a few traits of the "domestication syndrome" that are best documented in archaeobotanical macro-remains. In this exploration we focus on domestication as morphological adaptation on the part of plants, which results from the impact of human behaviors, represented by the term cultivation. An adaptive syndrome of recurrent traits associated with cereal domestication was laid out by Jack Harlan, with his colleagues De Wet and Price, in 1973. Drawing mainly on comparative field observations of crops, their weedy races, and wild progenitors, this paper proposed both the morphological adaptations of crops and the selective pressures of human cultivators that were expected to select for them. These features were later incorporated into the taxonomically broader "domestication syndrome" of Hammer (1984). It is usually inferred that conscious intent on the part of cultivators was not necessary to explain the evolution of these traits, but rather these represented adaptation via natural selection to the anthropogenic environment of the cultivated field. As such, most domestication traits have been assumed to evolve by unconscious selection (e.g., Heiser 1988, Zohary 2004, Purugganan and Fuller 2009). Later in this chapter, Northern Africa (excluding Egyptian Nile) ,cfP Q os, 0 4° ,4 ,e Figure 5.1. Charts of the quantitative growth of archaeobotany, indicating the cumulative number of published archaeobotanical reports in five increments. The top chart shows pre-ceramic Near East (after Fuller 2008a, based on data from S. Colledge). The middle chart shows India and Pakistan, with additional curves for the Neolithic/Chalcolithic and the Neolithic of Southern India (author's database). The bottom chart shows growth in northern and western Africa (excluding the Egyptian Nile) (after Fuller 2008a, data from Pelling 2007). Biodiversity in Agriculture: Domestication. Evolution, and Sustainability, edited by P. Gepts, T.R. Famula, R.L. Bettinger et al. Published by Cambridge University Press. (C) Cambridge University Press 2012. : through a consideration of melon domestication, I will suggest that some cases of conscious, intentional selection may differ from typical domestication processes by being faster. At the time that Harlan et al. wrote that paper, and Harlan (1975, second edition 1992) prepared the first edition of his Crops and Man reference book, archaeobotany was still in its infancy. While some archaeobotanical evidence was available to illustrate some early crops, and to confirm, in broad terms, the geography of domestication inferred from wild progenitors (also Zohary 1969, Zohary and Hopf 1973), the available evidence was rather inadequate for documenting the processes of morphological evolution at a population level. 112 Dorian Q. Fuller .111•••• T New Archaeobotanical Information on Plant Domestication from Macro-Remains 113 As systematic archaeobotany, using collection methods of flotation, and where appropriate wet-sieving, has taken hold around the world, the available archaeobotanical data set of macro-remains (grains and chaff) has grown rapidly (Figure 5.1). In the Near Eastern data, we also see clearly that since the 1960s flotation has become standard and therefore systematically collected data have become more common. A similar trend is true for Africa but is complicated by the use of intensive dry-sieving in several dry regions, including the Western Desert of Egypt and rock shelters in Southwest Libya. This same trend appears again in India, but it should be noticed that in some subregions, such as South India, archaeobotanical data have only become available quite recently, providing for postulation of an additional potential center of crop domestication (Fuller et al. 2004, Harris 2005, Barker 2006). This growth of archaeobotanical data was accompanied by the maturation of this field of study, with the adoption of systematic collection and study methods and the growth of communities of specialists replacing earlier generations of avocational botanists who dabbled in this research (Fuller 2002, 2008a). In the past decade or so it has become possible to begin to document archaeologically the evolution of the domestication syndrome, as least for a few betterdocumented crops and regions (Fuller 2007). We are able to suggest something about the rates and orders in which different morphological traits in different crops evolved. The present chapter will review and summarize what we know about these processes, especially in Asia and Africa, with some comparisons to North American data. 2 The evolution of nonshattering cereals: the case of wheat and barley For many researchers (e.g., Helbaek 1960, Zohary 1969, Hillman and Davies 1990, 1992, Harris 1996, Zohary and Hopf 2000) dependence upon the human farmer for seed dispersal, owing to loss of natural seed dehiscence, is seen as the most important trait of domesticated seed crops. To quote Harlan: Of all the adaptations that separate wild from cultivated cereals, the nonshattering trait of cultivated races is the most conspicuous. It is taxonomically the most diagnostic in separating domestic subspecies from spontaneous subspecies and is crucial in establishing the disruptive selection that effectively maintains separation of the two kinds of populations. Most of the seeds that shatter escape the harvest. (Harlan 1992:118) In cereals this occurs by suppression of abscission at the abscission scars, such as the rachis attachment points in wheat or barley ears or the rachilla to spikelet base attachment in panicled cereals (rice and millets). The result is that, instead of shedding seeds when they are mature, a plant retains them, and they are then usually separated by the addition of human labor (threshing and winnowing). Higher yields can be produced because the farmer could wait until all, or most, of the grains on a plant have matured, whereas earlier harvesting would have had to balance loss of grain through shedding, as they matured, with reduced yields through grains harvested immature (i.e., before spikelets have filled entirely). This would have been a particular problem with cereals such as wild rice, which has a long period of grain maturation, and which may have grown in wetland environments in which shed grains were lost (Fuller et al. 2007a, 2008, Fuller and Qin 2008). It was probably also a challenge for smaller-seeded millets, in contrast to large-spikelet cereals, like wheat and barley, which could be collected easily even if fallen (Kislev et al. 2004). The evolution of nonshattering would have occurred as a result of particular methods of harvesting that favored nonshattering (tough rachis) mutants in harvested populations, which were then sown (Hillman and Davies 1990, 1992). Harlan et al. (1973:314-315) and Harlan (1992:118) proposed that disruptive selection by human harvesting might be expected to strongly select for this domestication trait, leading to rapid fixation; and this postulate appeared to be borne out by extrapolation from experimental harvesting by Hillman and Davies (1990, 1992). The empirical record of archaeology, however, appears to show this hypothesis to be false. Growing data sets for Near Eastern wheat and barley can be considered and these will be compared below to rice. In a compilation of data from five representative sites, three with einkorn wheat and two with barley, Tanno and Willcox (2006) suggested that cereal domestication might take millennia, perhaps as long as 3,000 years, while Weiss etal. (2006) accepted at least a 1,000-year period (also Feldman and Kislev 2007). A larger data set, based on nearly 5,000 einkorn spikelet bases (albeit many indeterminate) and nearly 5,000 barley rachises (Fuller 2007), indicates that there is a dominance of wild types through the Pre-Pottery Neolithic A (PPNA) and early Pre-Pottery Neolithic B (PPNB) but a dominance of domesticated types in the Late PPNB (see also Willcox, Chapter 4, this volume). These data also provide a crude approximation of the rate of change in the proportion of domesticated cereals, i.e., a rate at which nonshattering moved towards fixation (see Figures 5.2 and 5.3). The overall regional pattern indicates the replacement of entirely wild (shattering) barley with predominantly domesticated (nonshattering) barley by the end of the pre-pottery Neolithic periods, a domestication process taking at least 1,500 to 2,000 years, starting c. 9,500 BC. This can be inferred to be probably 1,000 to 2,000 years longer, if the process is regarded as starting from the Late Pleistocene cultivation inferred from the emergence of an arable weed flora at Abu Hureyra by 11,500 to 11,000 BC (Hillman et al. 2001, Willcox et al. 2008, see Willcox, Chapter 4, this volume). Although given that the evidence for cultivation at Abu Hureyra 1 seems to be focused only on rye, not barley and perhaps not wheat, it may be a "red herring" in terms of evidence for the beginnings of the sustained tradition of agriculture (see Willcox et al. 2009). Intriguingly, the domestication rate appears slightly faster in barley than in wheat (Fuller 2007). This is counterintuitive to conventional logic, by which cross-pollination slows down domestication (cf. Hillman and Davies 1990, 1992), since barley is often regarded as slightly more prone to cross-pollination (c.2%) than wheat (c.1%) (Hillman and Davies 1990, Morrell et al. 2005). 144 Dorian O. Fuller New Archaeobotanical Information on Plant Domestication from Macro-Remains 115 (a) g _.+.v 0. 9 0.7 0.6 0 112 ets (a) a domestic fraction x domestic + indeterminate trend of minimum domestic 1 0 0.8 $2, E O t 0. 0 Cl domestic fraction per site , trend of minimum domestic fraction (polynomial) fraction (polynomial) 0 0.5 I D 0.4 0.3 0.2 0.1 1 phase sum of domestic and indeterminate phase sum of domestic . - max. estimated domestic . • . trendline (linear) 11000 1 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 D O 0 0 0 3 •-• 8_ 10000 9000 8000 7000 6000 rD 0 459 3.2 3 2.8 2.6 2.4 2.2 2 1.8 1.6 1.4 1 1.2 1 0.8 0.6 yrs so (b) 3 2.5 2 5000 cal. BC mean thickness with standard dev. + max thickness L- min thickness x x X ♦ wheat breadth x + E 1.5 E E E 0.5 0 -12000 -10000 X f -8000 -6000 ave. & std. dev. + max - min single grains from Abu Hureyra X Abu H rye x - - Abu H einkorn -4000 cal. BC 0 0 0 0 o rn 0 CO 0 0 0 0 0 CD 0 0 0 0 0 0 0 0 0 o N - Figure 5.2. Charts comparing the change in domestication traits over time in the Near East for barley. (a) The percentage of domesticated (nonshattering rachis remains), through the pre-ceramic periods of the Near East, based on plotting minimum and maximum estimates of individual sites against a point estimate of site's median date (after Fuller 2007). (b) Trends in grain size shown as mean, standard deviation, and outlying minimum and maximum for individual site assemblages, plotted against a point estimate of site's median date (data compiled from various primary reports). Figure 5.3. Charts comparing the change in domestication traits over time in the Near East for einkorn wheat (including some rye). (a) The percentage of domesticated (nonshattering rachis remains), through the pre-ceramic periods of the Near East, based on plotting minimum and maximum estimates of individual sites against a point estimate of site's median date (after Fuller 2007). (b) Trends in grain size shown as mean, standard deviation, and outlying minimum and maximum for individual site assemblages, plotted against a point estimate of site's median date (data compiled from various primary reports). Abu H, Abu Hureyra. to a minority. Thus there is a majority-rule tipping point at which a population of crops can he regarded as domesticated. While the predominance of domesticated-type (nonshattering) barley on most Near Eastern sites may have waited until c. 7,000 BC or after, by this period crops had dispersed already towards Europe, reaching mainland Greece and Crete (see Colledge et al. 2004, 2005), where fully domesticated forms dominate. Even earlier, by 8,400 to 8,000 BC, cereals had been transferred to Cyprus (Peltenberg et al. 2000), where domesticated chaff remains also dominate (although assemblages are very small) (Colledge 2004), although some wild barley was reported to be present in southern Cyprus at Pre-Pottery Shillourokambos (Willcox 2001, Colledge and Conolly 2006). This may suggest that local bottleneck effects sped up the domestication in dispersing crops that moved outside the region of the wild progenitor, or full domestication occurred during the less well-documented middle PPNB, or rates appear slower in the centers of origin because wild-gathered or The evidence that allows us to track the change in frequency of the wild and domesticated morphological types brings out the issue of how we define domestication more precisely. It would be too simplistic to expect to find populations of 100% nonshattering cereals in early agriculture - especially given the likely persistence of wild progenitors as weeds. As an operational definition I have referred to dominance, meaning a clear, statistically significant majority of the nonshattering domesticated types over the shattering, wild type. Recent work on archaeological rice, for example, suggests that around 65%-70% nonshattering persists as the typical figure in agriculturally focused societies of the Late Neolithic (e.g., at Liangzhu, in Fuller et al. 2009, and at other unpublished sites). Once nonshattering types outnumber the wild, shattering type it becomes increasing unlikely that chance drift or gene flow from the wild could push domesticates back 116 Dorian O. Fuller New Archaeobotanical Information on Plant Domestication from Macro-Remains 117 weedy barley continued to enter the archaeological record in this region of the wild progenitor. Certainly even in the late PPNB of the Near East there is intersite variability in the proportion of wild barley rachis, which may relate to different degrees of continued reliance on gathering from wild stands. At Wadi Jilat 13, for example, specimens are almost entirely of wild type. This could be due to predominance of a gathering strategy at this site, which can also be suggested from a diverse range of other plant remains including evidence for wild edible tubers (e.g., Cistanche sp.) (Colledge 2001). Models of the rapid fixation of domestication traits have assumed that strong directional selection on a single trait had been a predominant force (e.g.; Hillman and Davies 1990, Zohary 2004), but current evidence means we need to take more seriously the dynamics of selection, which is acting on multiple traits, in small populations that are minute in relation to the vast surrounding population of wild progenitors. Drift is just as likely to associate deleterious as adaptive traits with nonshattering. Also, the new and small "invading" population of a crop should be expected to have a disproportionate rate of gene flow from the wildadapted populations as a necessary part of the population genetics of invasions (see Currat et al. 2008). In terms of human behaviors, traditions of harvesting that had been honed for the gathering of shattering, wild cereals, may have been slow to change, and the shift to morphological domesticates would have incurred the added labor cost of threshing. It is thus something of an anachronism to presume that early cultivators would have acted in the first instance like farmers of later eras. 3 Comparing grain-size increase and nonshattering The other trait often used for inferring domestication archaeologically is grainsize increase. It is well known that wild and domesticated cereal grains differ in size and this has been used to infer the domesticated status of cereals, already in the PPNA and the earliest PPNB, including sites from the Jordan Valley, the upper Euphrates in Syria, and the first settlements on Cyprus (Colledge 2001, 2004). However, given the slow rise of nonshattering forms, it can be suggested that the rate of evolution of larger grains may have been even faster (Fuller 2007). There is a growing morphometric database for wheat and barley from the Near East (Co!ledge 2001, 2004, Peltenberg et al. 2000, Willcox 2004). This indicates that wheat and barley grains increased in size starting in the PPNA and earliest PPNB. When data are considered representing populations of a given period, as plotted in Figures 5.2B and 5.3B, it can be seen that there is marked increase in grain breadth over the course of the earlier Pre-Pottery Neolithic (PPNA, Early to Middle PPNB). This occurs both through increasingly large maximal size ranges but also by elimination of the smallest grains from populations, but it remains the populational trend over time that compellingly suggests evolution. Subsequent to that in samples through to Bronze Age and Iron Age time there is no significant trend for change in the size of grains on a population level, and thus we can conclude that the selection for increased grain size was part of crop evolution mainly in the early stages. The increase in nonshattering increases in tandem with increasing grain size, but it does seem that increased grain size may have had a slight head start. Indeed, Hillman (2000:379-82) argued that a few plump rye grains from Late Pleistocene Abu Hureyra represented "domesticated" cereals (Figure 5.3B). Although this may not be true based on a definition that emphasizes nonshattering, it is plausible that some selection for increased grain size is already indicated from the very start of cultivation. Nevertheless, an explanation of these data remains controversial. I take this to indicate evolution towards larger grain size during occupation of this site (Fuller 2007, also, Nesbitt 2004:39), whereas Willcox (2004) by contrast queries whether this is not just a product of better-tended cultivars (i.e., phenotypic plasticity) or the introduction of larger-grained varieties from elsewhere (also Willcox et al. 2008:322). This early change is indicated in seed width and thickness, but not in seed length. Whereas Willcox (2004) argues that this does not fit with evolution of larger grains under cultivation, I think that a comparative perspective indicates quite the opposite. As was hypothesized by Harlan et al. (1973), grain size should increase as a product of soil disturbance and deeper burial with cultivation (also, Harlan 1992:122). This evolutionary tendency has an established observational and experimental basis in seed ecological studies (e.g., Krishnasamy and Seshu 1989, Maranon and Grubb 1993, Baskin and Baskin 2001:214, Sadras 2007). As reviewed by Sadras (2007) there appears to be genetic constraint on an equilibrium seed size (see also Borris et al. 2004), selected by evolutionary processes, while seed number tends to be more variable in response to immediate environmental conditions. Studies on rice and barley have estimated that the heritability of grain size is high (Kato 1990, Fox et al. 2006). Nevertheless, it is clear that multiple genes affect grain size, and these often may be linked to other changes in inflorescence architecture and fruiting. A gene has recently been identified that affects panicle and grain number, plant height and grain size (Shan et al. 2009). Other studies on rice have identified key recessive mutations that seem to affect grain width by affecting the size and rows of husk cells (Fuller and Sato 2008, Shomura et al. 2008); another recessive mutation causes longer grains and higher grain mass (Fan et al. 2006). Similar mechanisms can be expected in wheat and barley. Although both size and number of seeds have a certain amount of plasticity, the relatively less plastic trait of seed size is more likely to have shown the directional change associated with early cultivation as a result of selection for genetic change. Because a larger number of potential genes contribute to grain size increase, the likelihood that a mutation in at least one of them should arise should be greater than that of mutation at single-locus traits such as nonshattering. However, rather than seeing this as a single directional process, we must consider the likelihood that there were differing selective thresholds that acted on grain size (and multiple contributing genetic loci) at different times. This is 118 Dorian Q. Fuller New Archaeobotanical Information on Plant Domestication from Macro-Remains •s ss •••• ••,,,,,,I 11 9 suggested by comparative examples, such as West African pearl millet or some pulses in which there was a lag between domestication and any appreciable increase in seed size (Fuller 2007, sec below). 90% Proportion of nonshattering spikelet bases of 80% va - 7 0 03 C ;3 1 Co • 70% 60% 50% 4 Chinese rice: a parallel case? Systematic collection of archaeobotanical evidence directly bearing on rice domestication is quite recent, but a body of data on nonshattering is now available. The recognition of the potential for study of rice spikelet bases for determining the presence and quantities of wild-type shattering for domesticated-type nonshattering rice was recognized in the mid 1990s by Thompson (1996, 1997), and the recovery and study of some rice spikelet bases followed in medieval Mali (Fuller 2000) and Bronze Age Japan (Hosoya 2002). Quantified data from South China have only been studied more recently, including a compilation of c. 300 specimens from three sites by Zheng et al. (2007) and the author's work at Tianluoshan on more than 2,600 spikelet bases (Fuller et al. 2009, 2011), and emerging data sets from additional sites in this region (Fuller and Qin 2008; Fuller et al. 2010). There have been some issues regarding the establishment of morphological criteria on which to judge domestic/wild status, with the domesticated type of Thompson (1996,1997) differing from that of Zheng et al. (2007, also Liu et al. 2007). Three clear categories can be recognized, including one that is likely immature (Fuller and Qin 2008). Although current evidence does not allow us to identify the beginnings of predomestication cultivation, we have robust evidence for the mid to late part of the sequence of evolution of domesticated rice. Early and middle levels of the site of Tianluoshan, dating from c. 4,900 to 4,600 BC, have provided c.2600 spikelet bases, indicating an increase from c. 27% to 35%-39% domesticated types through three sub-periods (Figure 5.4). This sequence also shows an increase in the proportion of rice and probable rice weeds as an overall proportion of the assemblage relative to wild-gathered staples such as acorns, Euryale ferox seeds, and Trapa water chestnuts (Fuller et al. 2009, 2011). Metrical data on rice from Tianluoshan fit with those of contemporary sites in being wider than measured populations from the early levels of Kuahuqiao, but still smaller than those of later assemblages towards the end of the Fifth Millennium BC or the early Fourth Millennium (Figure 5.4). Two factors contribute to the increasing average and upper range of grain populations: on the one hand, genetic selection for larger grains, and, on the other hand, a reduction in the proportion of immature spikelets harvested with smaller, unfilled grains (Fuller et al. 2007a, 2008). As with einkorn and barley in the Near East, grain size and nonshattering in rice evolved gradually in East Asia over more than 2,000 years, but it remains unclear which aspect of the domestication syndrome began to evolve first. Later sites in the region, Chuodun and Caoxieshan (4,200 to 3,900 BC), provide evidence for artificial field systems for wetland cultivation, i.e., paddy fields (Cao et al. 2006), and lack evidence for a a r `E: 0 o Max s Domestic Min Domestic 40% 30% 20% C 0 C 7 3.5 3 2.5 E 2 cal. BC Grain width average with standard deviation r - r r • -di-4000 re 1.5 -6000 -5500 -5000 -4500 -3500 -3000 cal. BC Rgure 5.4. Charts comparing the change in domestication traits in Asian rice. (A) Estimated percentage of domesticated (nonshattering rachis remains), based on two bracketing estimates: minimum percentage observed nonshattering, and l—% observed wild (Zheng et al. 2007, Fuller et al. 2009). (B) Trends in grain size shown as mean, standard deviation, starting at the left from the early and late periods at Kuahuqiao (based on data compiled in Fuller et al. 2007a, with additional data from Tianluoshan). TLS, Tianluoshan, with stratigraphic layer number; L, Longqiuzhang, with layer number; Chuodun measurements have been conservatively dated to the early Liangzhu phase since the paddy-field features at this site are overlain by Liangzhu levels. significant reliance on acorns, suggesting that reliance on agriculture had taken over by c. 4,000 BC (Fuller et al. 2008). 5 An alternative case: African pearl millet In the case of pearl millet, we have some metrical data from West Africa from which to examine grain size change during and after domestication (Figure 5.5). Pearl millet domestication is evident from ceramic impressions of pearl millet chaff that include the stalk, which are present by 1,700 to 1,500 BC in Mauretania (Amblard and Pernes 1989, MacDonald et al. 2003, Fuller et al. 2007h), and slightly later in Nigeria (Klee et al., 2000, 2004), and there is new early evidence from the Tilemsi valley as early as 2,500 BC (Manning etal. 2011). While early grain assemblages, from 1,700 BC, show the subtle change towards domesticated grain shape, becoming apically thicker and more club-shaped (D'Andrea et al. 2001, Zach and Klee 2003), a major increase in seed size appears 120 Dorian Q. Fuller New Archaeobotanical Information on Plant Domestication from Macro-Remains 121 3 2.5 E E 2 (a) 9 Iva annua achene length 8 African site ave. with std. dev Indian site ave. with std. dev. max. min size shift (India) trend (Africa) 45 1.5 ,0 _o (13 - 7 6 E 5 4 3 2 _ 01 • L ave. with std. dev + max min — — Linear c 1 8, 0.5 0 Ce O 0 0 O 0 CT1 0 0 CM 00 O O O O O 0 O O BC/AD (b) Figure 5.5. Archaeobotanical data for the evolution of domesticated pearl millet (Pennisetum glaucum), indicating grain-breadth measurements (mean and standard 14 12 10 o L ave. with std. dev deviation, maxima and minima) for measured archaeological populations, plotted against approximate median age (data as compiled in Fuller 2007). Early and rapid trends for size increase in Indian populations are indicated by dotted lines, the more gradual trend in African populations is represented by a linear regression (dashed line). African sites from left to right: Birimi, Kursakata, Jarma (early, mid), Qasr Ibrim, Arondo, Jarma Late, Gao. Indian sites from left to right: Surkotada, Narhan, Nevasa; note the apparently earlier evolution of large grains in India. Arrows indicate archaeologically documented domesticated (nonshattering) populations based on impressions in pottery: a. Tilcmsi valley (Manning et al. 2011); b, Dhar Nema (Fuller et al. 2007b); c, Ganjiganna (Klee et al. 2004). + Max - Min — — Linear (L ave.) § age BC/AD Figure 5.6. Metrical data of achene length (L) plotted against time for two North American domesticated Asteraceae, Iva annua and Helianthus annuus. Data from Asch and Asch (1985); see also Smith (1992:42). 6 delayed. Early West African populations, as well as those introduced to Gujarat, India by c. 1,700 BC, appear small, within in the wild size range. By contrast, rather later seeds of a North Indian (Gangetic) population from Narhan are markedly larger, suggesting selection for larger-grained pearl millet by 1,400 to 1,000 BC. Meanwhile in Africa there was a more gradual trend towards larger grain sizes, with some larger populations by the early first millennium BC and more by the later part of that millennium or the early centuries AD. From the more rapid increase in size on arrival in the Ganges plain in India, where mung beans also show a similarly timed size increase (see below), it can be hypothesized that size increase was driven by a similar selection pressure, such as deeper seed burial due to the introduction of and tillage (Fuller and Harvey 2006, Fuller 2007). In the context of Africa it may be other forms of agricultural intensification which drove the later millet grain-size increase in some regions, although it was previously suggested (Fuller 2007) that large-grained forms evolved in regions with animal tillage, such as Nubia or Southwest Libya, and might then have dispersed back to sub-Saharan West Africa. Another issue of particular relevance to pearl millet is the balance of selection for more seeds versus the selection for larger. seeds, for which there are apparent trade-offs. While at present we have enough data to outline the broad pattern of change in pearl millet, further research is needed to explain this pattern. Some comparisons from eastern North America Two of the cultivars of the putative Eastern Woodlands center of domestication in North America have documented evidence for seed size increase, namely sunflower (Helianthus annuus) and the now extinct domesticated form of Iva annua (Smith 1992, 2006). Widely available data for these taxa (Asch and Asch 1985) reflect this process. When plotted as means and standard deviations against estimates of median age, like species considered above, trends towards size increase are clear (Figure 5.6). Significant size increase related to domestication can be estimated to have taken up to c. 1,500 years in Iva (between 3,500 and 2,000 BC), while in sunflower it was a very slow and gradual process, which may have begun already between 5,000 and 3,000 BC but is clear by about 1,500 BC (cf. Smith 1992). 7 Contradictory patterns in pulses Pulse crops do not appear to show the same pattern of early and marked seed-size Increase. A lag between domestication and any appreciable seed-size increase appears to be the case in Indian Vigna spp., i.e., mungbean and urd bean (Fuller and Harvey 2006, Fuller 2007), West African Vigna unguiculata (D'Andrea et al. 2007), and possibly soybean (cf. Crawford and Lee 2003, Fuller and Zhang 2007, 122 Dorian Q. Fuller New Archaeobotanical Information on Plant Domestication from Macro-Remains 123 (a) 5 4.5 4 3.5 A + South India ave. L with std. dev - population min. + population max. t North India ave. L with std. dev - population min. + population max. Harappan sites T ave L with std. dev. - population min. + population max. modern wild range with 20% shrinkage x modern domestic with 20% shrinkage 3 A 2.5 2 1.5 1 -2500 -2000 -1500 ca l. -1000 -500 0 (b) BC 5. 00 4 00 3.00 2.00 1.00 0.00 o Near Eastern sites ave. length & std. dev. - population min. + population max. - trendline (linear) (c o Near East Pisum Length with std. dev. - population min. + population max. o Greek Pisum Length with std. dev. - population min. + population max. • Indian PismnLength vnth slit. dev.. - population mm. + population max. A Ge rman -9500 -8500 -7500 -6500 -5500 -4500 -3500 -2500 -1500 -500 dev.m Length wh std. Plu it - population min. + population max. cal. BC - -Trend in German groups Figure 5.7. Metrical data plotted against time for selected pulse crops. (a) Mang beans from South Asia; (b) lentils from the Near East (middle); (c) peas from various regions of the Old World (bottom). Compiled from many primary data sources, summarized in Fuller and Harvey (2006) and Jupe (2003). Zhao 2007). This may suggest that a higher selective pressure was needed to cross (Fuller et al. 2007c). In this period we might expect the beginnings of ard tillage. In contrast, evidence from sites in the Ganges basin suggest an early seed-size increase in Vigna. The earliest Gangetic finds of this species suggest that this species was introduced (probably from South India) in the early second millennium BC as a small-seeded crop, and size change was marked by c. 1,400 BC, suggesting a slightly earlier shift to large seeds in Gangetic populations than in South India. As with South India, this can be suggested to correlate with a period of cultural change (the Chalcolithic transition) towards more hierarchical societies presumably with more intensive agriculture. This period also saw the adoption of textile production and fiber crops (cotton and flax) (see Fuller 2008b). In Near Eastern lentils, size change appears to have been much slower and more gradual than in the cereals, without a clear leveling off after the Neolithic (Figure 5.7b). This may suggest an initially weaker selection, but may also indicate that seed size is more plastic in pulses, and that there were numerous local equilibrium sizes selected in different times and places. In peas (Pisum sativum) a directional trend in seed size increase is even harder to see, although there is certainly increasing diversity in size between measured archaeological populations (Figure 5.7c). Nevertheless over the course of the PPNB (8,500 to 6,000 BC) there does appear to be a trend for larger seeds, judging by assemblage maxima, but there is no clear trend in assemblage averages. This suggests that early cultivation provided a context in which seed size could be more plastic and larger forms could occur, but there was no clear selection pressure, and it is unclear whether this represents phenotypic plasticity or increased genetic variation in seed size. The very small seed sizes from some populations, such as some from Neolithic Greece and later in India, may suggest that in some local environments smaller-seeded populations had an advantage: the balance between yield increases through seed size and seed number may have differed under various cultivation regimes, and whether use was as a dry pulse or a green seed. Nevertheless, if only the measured populations from Germany are taken into account there is a clear trend towards increasing size from the Early Neolithic onwards (Figure 5.7c), which might be suggested to relate to increasingly intensive field agriculture and the introduction of ards by the Late Neolithic (Sherratt 1997:230-1). There is thus no recurrent pattern in the evolution of seed size in pulses. This may have something to do with the diversity of cultivation regimes to which pulses were subjected, e.g., whether they were tended in small garden plots more like vegetables or sown in single-species fields, or intercropped with cereals. The necessarily strong selection for the loss of wild-type germination inhibition in pulses may also have had pleiotropic effects on seed size. the threshold into big-seeded pulses; a threshold inferred by Fuller and Harvey (2006) to be ploughing (ard tillage). When plotted as a time series, it can be seen that South Indian Vigna radiara seeds increase markedly in width between 1,400 and 1,000 BC (Figure 5.7a). This period correlates with the end of the South Indian Neolithic and the transition to the Iron Age, which witnessed increased social complexity as well as the intensification and diversification of agriculture 8 The reduction of germination inhibition Domestication normally involved the loss of germination inhibition. This may be the key trait in allowing species with highly dormant seeds, such as pulses 124 Dorian Q. Fuller New Archaeobotanical Information on Plant Domestication from Macro-Remains ••—s . .1..-,MONM7MNII!Mara,IVIIMINO••••••••—sss _ 125 like the lentil, to be cultivated successfully (Ladizinsky 1987). While this change is associated generally with changes such as the thinning of seed coats, the lightening of seed-coat color, and the loss of rugae or papillae, and such traits can be documented in parallel across many families, genera, and world regions, these are difficult to detect archaeologically. Detailed studies are only available for a few species. One challenge is preservational: seed coats are often not preserved on charred pulses. This is clearly the case with Indian Vigna spp., for example (Fuller and Harvey 2006). Even when preserved there is no guarantee that seed coat thickness is informative for all species. In Near Eastern pulse crops, for example, Butler (1989, 1990) was able to document clear morphological differences in the seed coats of wild and domesticated peas, but not of lentils, chickpeas, or species of Vicia, where morphological variation falls along a spectrum from thicker (and sometimes ornamented) seed coats in wild populations and some cultivars, to thinner, smooth forms in other cultivars. Those species which have been best documented are New World Chenopodium domesticates (e.g., Smith, 1989, 1992, 1995, Bruno and Whitehead 2003, Bruno 2006). In a classic case of the fossil record (archaeobotany) identifying an extinct crop, Smith (1989, 1992, 2006) tracked a marked decrease in seed coat thickness in Chenopodium berlandieri seeds from sites in the Eastern Woodlands of the United states between c. 2,500 BC and 1,500 BC. In addition to thinning seed coats, presumably linked to loss of wild-type germination inhibition, seeds tended to change shape and size, although wild-type forms persisted as weeds alongside the Chenopodium crop (Gremillion 1993). Bruno (2006) has developed a similar approach to studying South American Chenopodium domestication, although variation in seed coat thickness amongst wild species makes this more difficult, requiring the use of additional size and shape characters. 9 The increase in fruit size in cucurbits: evidence for conscious selection Melon and squash domestication provides an example of a mode of domestication quite different from that of cereals and pulses. Melons, like other soft-stemmed fruits, possess elements of a recurrent domestication syndrome (Hammer 1984), such as larger fruit and seed size, loss of bitterness, and annuality. These may be plausibly attributed to a degree of conscious selection on the part of human cultivators rather than unconscious selection. Seed size may be readily documented through preserved macro-remains, and long Cucurbita seeds provide the earliest evidence for a morphological domesticate in Mesoamerica by c. 7,900 BC, although in this case it was suggested that seed size increased through unconscious selection because it preceded ring and peduncle thickening (Smith 1997). Nevertheless, presumably seed size and fruit size increase are linked allometrically, with conscious selection for larger fruits selecting for larger seeds as well; other traits may represent a separate selective process. Distinctive phytoliths (micro-remains) from the rinds of Cucurbita also appear to be allometrically linked to fruit size (Piperno and Stothert 2003, Piperno and Pearsall 1998:194-5). Metrical data from such phytoliths provides evidence for the relative scale and rate of size increase in some early New World Cucurbita populations, such as probable C. ecuadorensis (Piperno and Stothert 2003). In this case phytolith measurements suggest a quite gradual trend in fruit size increase between 11,000 and 6,000 cal. BC. In this chapter, I will consider the Old World melon (Cucumis melo), and in particular new data for a comparatively rapid local domestication in the Lower Yangzte region. The melon is inferred to have multiple domestications across its former wild range. Wild Cucumis melo L. subsp. agrestis occurs from Africa and the Near East, through Central India (Madhya Pradesh; western Jharkand and Chattisgarh), as well as in central and eastern China (Chakravarty 1959, Kirkbride 1993, Zohary and Hopf 2000, Akasi et al. 2002, Lu et al. 2006, Zheng and Chen 2006). Archaeobotanical evidence of apparently morphologically wild melon seeds from the Lower Yangzte in the mid-Holocene suggest an extirpation of wild populations there during recent millennia (see below). Zohary and Hopf (2000) accept at least two domestications, one focused on the Near East (Egypt?) and one on South Asia (the Indus?), but we can now document a likely (third?) domestication episode in Eastern China, as previously suggested by Walters (1989). A sub-Saharan African domestication, often suggested from modern genetic diversity (e.g., Kirkbride 1993, Akasi et al. 2002), lacks archaeological support: melon cultivars were present in Egypt, the Indus, and the Yangzte (by third millennium BC) before any agriculture was present in most of sub-Saharan Africa! In recent years, melon seeds, usually waterlogged, have been recovered from eight archaeological sites for which metrical data are available (data from six sites published in Zheng and Chen 2006, two additional sites documented by this author). The earliest finds are 15 seeds from Tianluoshan dating from c. 4,600 BC (full archaeobotanical evidence in Fuller et al., 2011). From close to 4,000 BC a few seeds are available from Chuodun and from c. 3,300 BC from Puanqiao (DQ Fuller & L Qin, unpublished data), while a series of melon assemblages from the third millennium to the early second millennium BC are collected in Zheng and Chen (2006). Based on modern domesticated melons, 5mm is a suggested minimum seed length for domesticated melons. The seed length data from lower Yangzte archaeological populations are shown in Figure 5.8, and it can be seen that populations are firmly within the wild size range from the fifth millennium BC to the mid-third millennium BC. Only at the sites of Tadi and Qianshanyang of the late third millennium BC is there marked increase in population averages, including seeds significantly above the 5mm threshold. This suggests domestication, and that this shift to larger seed (and fruit) size evolved rapidly, perhaps within a century around c. 2,200 BC. 128 Dorian 0. Fuller New Archaeobotanical Information on Plant Domestication from Macro-Remains 129 around a millennium, as in Near Eastern cereals, pearl millet, and North American Asteraceae, or slow, where 2,000 years or more were needed, as in Asian rice, perhaps lentils and peas. In some taxa, such as cereals and perhaps North American crops, size increase seems to have occurred with the start of cultivation, while in taxa such as pulses and perhaps pearl millet, it was delayed until some later period. This suggests, in turn, that certain factors in cultivation regimes interact with the inherent variability and genetic architecture of seed size traits within particular taxa in ways that are not uniform across taxa. It has been suggested that the size trait be regarded as "semi-domestication" as it is a quantitative population-level trait that is selected at some stage during human cultivation but not necessarily linked directly to key domestication traits, such as nonshattering (Fuller 2007). By contrast, nonshattering can he qualitatively determined on individual specimens. Seed size and other such traits constitute a kind of "soft" selection in relation to the cultivated environment and probably a high degree of within-population variability built on a multi-genic basis (Sadras 2007:132-3, Fuller and Allaby 2009). The differences between crops should be related to differing selective thresholds relating to the histories of cultivation of these species and the particular genetic architectures of grain-size traits. Archaeobotanical data then concur with the conclusions of Harlan (1992) and Heiser (1990:199) that it is "more likely that large seeds result from unconscious selection over a period of time". Only in the cases of the most rapid change, like that of melons, does conscious selection seem likely. Intriguingly the protracted fixation of nonshattering in cereals is paralleled across species (wheat, barley, rice) and regions (Near East and China), at a surprisingly similar rate of change (and thus coefficient of selection) (Purugganan and Fuller 2009). This is contrary to the accepted wisdom of strong selection and rapid evolution under "sickle pressure" (e.g. Wilke et al. 1972, Hillman and Davies 1990, 1992, Willcox 1999), leading to disruptive selection (Harlan 1992:118). Thus sickles as the main driving force are open to question (Fuller 2007). Indeed, in some regions like the Near East sickles clearly precede domestication by many thousands of years, while in other regions like the Yangtze valley of China sickles or harvesting knives appear absent until introduced from the millet zone to the north, after rice was already domesticated (Fuller 2007, Fuller et al. 2008). As suggested by Willcox el al. (2008) the recurrent bolstering of cereal store from wild stands also must have played a role. What seems to be clear is that disruptive selection appears to have not occurred or to have been very weak, and the role of balancing selection for wild-type adaptation and gene flow, even at low crosspollination rates, needs to be taken into account (see Allaby et al. 2008). The pristine harvesting experiments of Hillman and Davies (1990), divorced from the real environments of the Near East, with gene flow, and concurrent selection for other domestication syndrome traits, were not an analogue for the Epipalaeolithic of the Near East. Lu (2006) has recently shown experimentally how weak sickle pressure would be in the context of harvesting (mature) wild Asian rice. Further archaeobotanical evidence, real-world experiments, and extended biological systems simulations in silico (as per Allaby et al. 2008) are needed. The cases explored in this chapter argue that we need to consider different aspects of the domestication syndrome separately, even different aspects of grain shape and size change. Nevertheless, there are cases of parallel trends seen in unrelated cereals and centers of origins which suggest that some of the same fundamental evolutionary processes were at work. 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