Publications by authors named "Dorian Q Fuller"

53 Publications

The Evolutionary History of Wild, Domesticated, and Feral Brassica Oleracea (Brassicaceae).

Mol Biol Evol 2021 Jun 22. Epub 2021 Jun 22.

Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A.

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.
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http://dx.doi.org/10.1093/molbev/msab183DOI Listing
June 2021

Monsoon forced evolution of savanna and the spread of agro-pastoralism in peninsular India.

Sci Rep 2021 Apr 27;11(1):9032. Epub 2021 Apr 27.

Research Station of Quaternary Palaeontology, Senckenberg Research Institute, Am Jakobskirchhof 4, 99423, Weimar, Germany.

An unresolved issue in the vegetation ecology of the Indian subcontinent is whether its savannas, characterized by relatively open formations of deciduous trees in C-grass dominated understories, are natural or anthropogenic. Historically, these ecosystems have widely been regarded as anthropogenic-derived, degraded descendants of deciduous forests. Despite recent work showing that modern savannas in the subcontinent fall within established bioclimatic envelopes of extant savannas elsewhere, the debate persists, at least in part because the regions where savannas occur also have a long history of human presence and habitat modification. Here we show for the first time, using multiple proxies for vegetation, climate and disturbances from high-resolution, well-dated lake sediments from Lonar Crater in peninsular India, that neither anthropogenic impact nor fire regime shifts, but monsoon weakening during the past ~ 6.0 kyr cal. BP, drove the expansion of savanna at the expense of forests in peninsular India. Our results provide unambiguous evidence for a climate-induced origin and spread of the modern savannas of peninsular India at around the mid-Holocene. We further propose that this savannization preceded and drove the introduction of agriculture and development of sedentism in this region, rather than vice-versa as has often been assumed.
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http://dx.doi.org/10.1038/s41598-021-88550-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8079367PMC
April 2021

People have shaped most of terrestrial nature for at least 12,000 years.

Proc Natl Acad Sci U S A 2021 Apr;118(17)

School of Earth and Environmental Sciences, The University of Queensland, Brisbane, Australia 4072.

Archaeological and paleoecological evidence shows that by 10,000 BCE, all human societies employed varying degrees of ecologically transformative land use practices, including burning, hunting, species propagation, domestication, cultivation, and others that have left long-term legacies across the terrestrial biosphere. Yet, a lingering paradigm among natural scientists, conservationists, and policymakers is that human transformation of terrestrial nature is mostly recent and inherently destructive. Here, we use the most up-to-date, spatially explicit global reconstruction of historical human populations and land use to show that this paradigm is likely wrong. Even 12,000 y ago, nearly three quarters of Earth's land was inhabited and therefore shaped by human societies, including more than 95% of temperate and 90% of tropical woodlands. Lands now characterized as "natural," "intact," and "wild" generally exhibit long histories of use, as do protected areas and Indigenous lands, and current global patterns of vertebrate species richness and key biodiversity areas are more strongly associated with past patterns of land use than with present ones in regional landscapes now characterized as natural. The current biodiversity crisis can seldom be explained by the loss of uninhabited wildlands, resulting instead from the appropriation, colonization, and intensifying use of the biodiverse cultural landscapes long shaped and sustained by prior societies. Recognizing this deep cultural connection with biodiversity will therefore be essential to resolve the crisis.
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http://dx.doi.org/10.1073/pnas.2023483118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8092386PMC
April 2021

Two-season agriculture and irrigated rice during the Dian: radiocarbon dates and archaeobotanical remains from Dayingzhuang, Yunnan, Southwest China.

Archaeol Anthropol Sci 2021 13;13(4):62. Epub 2021 Mar 13.

Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.

Historical sources describe irrigation and intensive agriculture being practiced in lowland Yunnan from at least the first century AD, but so far archaeobotanical remains allowing investigation of this issue have been scarce. Here, we present new archaeobotanical evidence, including macro-botanical and phytoliths results, from the Dian settlement site of Dayingzhuang, with direct AMS radiocarbon dates on two wheat grains falling between 750 and 390 BC. We compare these results with contemporary Dian sites and analyse the agricultural systems in Central Yunnan between the eight and fourth centuries BC. We propose that agriculture was intensified toward the end of the Dian through both multiple cropping seasons and increased evidence for irrigated rice fields.

Supplementary Information: The online version contains supplementary material available at 10.1007/s12520-020-01268-y.
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http://dx.doi.org/10.1007/s12520-020-01268-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7956011PMC
March 2021

Agricultural diversification in West Africa: an archaeobotanical study of the site of Sadia (Dogon Country, Mali).

Archaeol Anthropol Sci 2021 8;13(4):60. Epub 2021 Mar 8.

Laboratoire Archéologie et Peuplement de l'Afrique (APA), Anthropology Unit of the Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland.

While narratives of the spread of agriculture are central to interpretation of African history, hard evidence of past crops and cultivation practices are still few. This research aims at filling this gap and better understanding the evolution of agriculture and foodways in West Africa. It reports evidence from systematic flotation samples taken at the settlement mounds of Sadia (Mali), dating from 4 phases (phase 0=before first-third century AD; phase 1=mid eighth-tenth c. AD; phase 2=tenth-eleventh c. AD; phase 3=twelfth-late thirteenth c. AD). Flotation of 2200 l of soil provided plant macro-remains from 146 archaeological samples. As on most West African sites, the most dominant plant is pearl millet (). But from the tenth century AD, sorghum () and African rice () appear in small quantities, and fonio () and barnyard millet/hungry rice ( sp.), sometimes considered weeds rather than staple crops, are found in large quantities. Some samples also show remains of tree fruits from savannah parklands, such as baobab (), marula (), jujube ( sp.), shea butter () and African grapes (). Fonio and sp. cultivation appears here to be a later addition that helped to diversify agriculture and buffer against failures that might affect the monoculture of pearl millet. This diversification at the end of the 1st millennium AD matches with other evidence found in West Africa.
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http://dx.doi.org/10.1007/s12520-021-01293-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7937602PMC
March 2021

Genomic history and ecology of the geographic spread of rice.

Nat Plants 2020 05 15;6(5):492-502. Epub 2020 May 15.

Center for Genomics and Systems Biology, New York University, New York, NY, USA.

Rice (Oryza sativa) is one of the world's most important food crops, and is comprised largely of japonica and indica subspecies. Here, we reconstruct the history of rice dispersal in Asia using whole-genome sequences of more than 1,400 landraces, coupled with geographic, environmental, archaeobotanical and paleoclimate data. Originating around 9,000 yr ago in the Yangtze Valley, rice diversified into temperate and tropical japonica rice during a global cooling event about 4,200 yr ago. Soon after, tropical japonica rice reached Southeast Asia, where it rapidly diversified, starting about 2,500 yr BP. The history of indica rice dispersal appears more complicated, moving into China around 2,000 yr BP. We also identify extrinsic factors that influence genome diversity, with temperature being a leading abiotic factor. Reconstructing the dispersal history of rice and its climatic correlates may help identify genetic adaptations associated with the spread of a key domesticated species.
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http://dx.doi.org/10.1038/s41477-020-0659-6DOI Listing
May 2020

Agricultural systems in Bangladesh: the first archaeobotanical results from Early Historic Wari-Bateshwar and Early Medieval Vikrampura.

Archaeol Anthropol Sci 2020 15;12(1):37. Epub 2020 Jan 15.

3UCL Institute of Archaeology, 31-34 Gordon Square, London, WC1H 0PY UK.

The present paper reports the first systematic archaeobotanical evidence from Bangladesh together with direct AMS radiocarbon dates on crop remains. Macro-botanical remains were collected by flotation from two sites, Wari-Bateshwar (WB), an Early Historic archaeological site, dating mainly between 400 and 100 BC, with a later seventh century AD temple complex, and Raghurampura Vikrampura (RV), a Buddhist Monastery () located within the Vikrampura city site complex and dating to the eleventh and sixteenth centuries AD. Despite being a tropical country, with high rainfall and intensive soil processes, our work demonstrates that conventional archaeobotany, the collection of macro-remains through flotation, has much potential towards putting together a history of crops and agricultural systems in Bangladesh. The archaeobotanical assemblage collected from both sites indicates the predominance of rice agriculture, which would have been practiced in summer. Spikelet bases are of domesticated type rice, while grain metrics suggest the majority of rice was probably subspecies The presence of some wetland weeds suggests at least some of the rice was grown in wet (flooded) systems, but much of it may have been rainfed as inferred from the Southeast Asian weed . Other crops include winter cereals, barley and possible oat, and small numbers of summer millets (, , ), a wide diversity of summer and winter pulses (14 spp.), cotton, sesame and mustard seed. Pulse crops included many known from India. Thus, while most crops indicate diffusion of crops from India eastwards, the absence of rice could also indicate some diffusion from Southeast Asia. The later site RV also produced evidence of the rice bean (), a domesticate of mainland Southeast Asia. These data provide the first empirical evidence for reconstructing past agriculture in Bangladesh and for the role of connections to both India and mainland Southeast Asia in the development of crop diversity in the Ganges delta region.
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http://dx.doi.org/10.1007/s12520-019-00991-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6962288PMC
January 2020

Assessing the occurrence and status of wheat in late Neolithic central China: the importance of direct AMS radiocarbon dates from Xiazhai.

Veg Hist Archaeobot 2020 3;29(1):61-73. Epub 2019 Jun 3.

9Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029 China.

The introduction of wheat into central China is thought to have been one of the significant contributions of interactions between China and Central Asia which began in the 3rd millennium bc. However, only a limited number of Neolithic wheat grains have been found in central China and even fewer have been directly radiocarbon dated, making the date when wheat was adopted in the region and its role in subsistence farming uncertain. Based on systematic archaeobotanical data and direct dating of wheat remains from the Xiazhai site in central China, as well as a critical review of all reported discoveries of Neolithic and Bronze Age wheat from this region, we conclude that many wheat finds are intrusive in Neolithic contexts. We argue that the role of wheat in the subsistence of the late Neolithic and early Bronze Age of central China was minimal, and that wheat only began to increase in its subsistence role in the later Bronze Age during the Zhou dynasty after ca. 1000 bc.
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http://dx.doi.org/10.1007/s00334-019-00732-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6942569PMC
June 2019

The domestication syndrome in vegetatively propagated field crops.

Ann Bot 2020 03;125(4):581-597

University College London, Institute of Archaeology, 31-34 Gordon Square, London, UK.

Background: Vegetatively propagated crops are globally significant in terms of current agricultural production, as well as for understanding the long-term history of early agriculture and plant domestication. Today, significant field crops include sugarcane (Saccharum officinarum), potato (Solanum tuberosum), manioc (Manihot esculenta), bananas and plantains (Musa cvs), sweet potato (Ipomoea batatas), yams (Dioscorea spp.) and taro (Colocasia esculenta). In comparison with sexually reproduced crops, especially cereals and legumes, the domestication syndrome in vegetatively propagated field crops is poorly defined.

Aims And Scope: Here, a range of phenotypic traits potentially comprising a syndrome associated with early domestication of vegetatively propagated field crops is proposed, including: mode of reproduction, yield of edible portion, ease of harvesting, defensive adaptations, timing of production and plant architecture. The archaeobotanical visibility of these syndrome traits is considered with a view to the reconstruction of the geographical and historical pathways of domestication for vegetatively propagated field crops in the past.

Conclusions: Although convergent phenotypic traits are identified, none of them are ubiquitous and some are divergent. In contrast to cereals and legumes, several traits seem to represent varying degrees of plastic response to growth environment and practices of cultivation, as opposed to solely morphogenetic 'fixation'.
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http://dx.doi.org/10.1093/aob/mcz212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102979PMC
March 2020

New findings on the significance of Jebel Moya in the eastern Sahel.

Azania 2019 Dec 27;54(4):425-444. Epub 2019 Nov 27.

This paper presents new excavation data and new radiometric dates for Jebel Moya, south-central Sudan. These data suggest revisions to previous chronological understandings of the site. New excavations, initiated in 2017, show a longer, more continuous occupation of the site than has been previously recognised. Archaeozoological and archaeobotanical analyses provide evidence for domesticated taxa. Archaeobotanical evidence is dominated by domesticated sorghum (), radiocarbon dated to . 2550-2210 BC. Faunal remains include cattle and goat/sheep. A late third-millennium BC date on the human skeleton excavated in the 2017 season also shows that mortuary activity began early in the site's history, contemporary with domesticated faunal and botanical remains. These initial results indicate the long-term association of the site with pastoralism and agriculture and with environmental change. Jebel Moya's continued potential to serve as a chronological and cultural reference point for future studies in south-central Sudan and the eastern Sahel is reinforced.
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http://dx.doi.org/10.1080/0067270X.2019.1691845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6920046PMC
December 2019

A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history.

Nat Plants 2019 11 4;5(11):1120-1128. Epub 2019 Nov 4.

Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK.

Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world's most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 BC in the Levant and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, C dated to the New Kingdom, 1130-1000 BC. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.
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http://dx.doi.org/10.1038/s41477-019-0534-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858886PMC
November 2019

Sedentism and plant cultivation in northeast China emerged during affluent conditions.

PLoS One 2019 18;14(7):e0218751. Epub 2019 Jul 18.

Institute of Archaeology, University College London, London, England.

The reasons and processes that led hunter-gatherers to transition into a sedentary and agricultural way of life are a fundamental unresolved question of human history. Here we present results of excavations of two single-occupation early Neolithic sites (dated to 7.9 and 7.4 ka) and two high-resolution archaeological surveys in northeast China, which capture the earliest stages of sedentism and millet cultivation in the second oldest center of domestication in the Old World. The transition to sedentism coincided with a significant transition to wetter conditions in north China, at 8.1-7.9 ka. We suggest that these wetter conditions were an empirical precondition that facilitated the complex transitional process to sedentism and eventually millet domestication in north China. Interestingly, sedentism and plant domestication followed different trajectories. The sedentary way of life and cultural norms evolved rapidly, within a few hundred years, we find complex sedentary villages inhabiting the landscape. However, the process of plant domestication, progressed slowly over several millennia. Our earliest evidence for the beginning of the domestication process appear in the context of an already complex sedentary village (late Xinglongwa culture), a half millennia after the onset of cultivation, and even in this phase domesticated plants and animals were rare, suggesting that the transition to domesticated (sensu stricto) plants in affluent areas might have not played a substantial role in the transition to sedentary societies.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0218751PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6638895PMC
February 2020

Between domestication and civilization: the role of agriculture and arboriculture in the emergence of the first urban societies.

Veg Hist Archaeobot 2019 20;28(3):263-282. Epub 2019 Apr 20.

1Institute of Archaeology, University of London, 31-34 Gordon Square, London, WC1H 0PY UK.

The transition to urbanism has long focused on annual staple crops (cereals and legumes), perhaps at the expense of understanding other changes within agricultural practices that occurred between the end of the initial domestication period and urbanisation. This paper examines the domestication and role of fruit tree crops within urbanisation in both Western Asia and China, using a combination of evidence for morphological change and a database that documents both the earliest occurrence of tree fruit crops and their spread beyond their wild range. In Western Asia the domestication of perennial fruit crops likely occurs between 6500 bc and 3500 bc, although it accompanies a shift in location from that of the earliest domestications within the Fertile Crescent to Mesopotamia, where the earliest urban societies arose. For China, fruit-tree domestication dates between ca 4000 and 2500 bc, commencing after millet domestication and rice domestication in Northern and Southern China, respectively, but within the period that led up to the urban societies that characterised the Longshan period in the Yellow River basin and the Liangzhu Culture in the Lower Yangtze. These results place the domestication of major fruit trees between the end of the domestication of staple annual crops and the rise of urbanism. On this basis it is argued that arboriculture played a fundamental role within the re-organisation of existing land use, shifting the emphasis from short-term returns of cereal crops into longer term investment in the developing agricultural landscape in both Western and East Asia. In this respect perennial tree crops can be placed alongside craft specialisation, such as metallurgy and textiles, in the formation of urban centres and the shaping the organisational administration that accompanied the rise of urbanism.
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http://dx.doi.org/10.1007/s00334-019-00727-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499764PMC
April 2019

A domestication history of dynamic adaptation and genomic deterioration in Sorghum.

Nat Plants 2019 04 8;5(4):369-379. Epub 2019 Apr 8.

School of Life Sciences, University of Warwick, Coventry, UK.

The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated episodes of introgression. Genomes of archaeological crops have the potential to reveal these dynamics without being obscured by recent breeding or introgression. We report a temporal series of archaeogenomes of the crop sorghum (Sorghum bicolor) from a single locality in Egyptian Nubia. These data indicate no evidence for the effects of a domestication bottleneck, but instead reveal a steady decline in genetic diversity over time coupled with an accumulating mutation load. Dynamic selection pressures acted sequentially to shape architectural and nutritional domestication traits and to facilitate adaptation to the local environment. Later introgression between sorghum races allowed the exchange of adaptive traits and achieved mutual genomic rescue through an ameliorated mutation load. These results reveal a model of domestication in which genomic adaptation and deterioration were not focused on the initial stages of domestication but occurred throughout the history of cultivation.
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http://dx.doi.org/10.1038/s41477-019-0397-9DOI Listing
April 2019

Cross-species hybridization and the origin of North African date palms.

Proc Natl Acad Sci U S A 2019 01 14;116(5):1651-1658. Epub 2019 Jan 14.

Center for Genomics and Systems Biology, New York University Abu Dhabi Research Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates;

Date palm ( L.) is a major fruit crop of arid regions that were domesticated ∼7,000 y ago in the Near or Middle East. This species is cultivated widely in the Middle East and North Africa, and previous population genetic studies have shown genetic differentiation between these regions. We investigated the evolutionary history of and its wild relatives by resequencing the genomes of date palm varieties and five of its closest relatives. Our results indicate that the North African population has mixed ancestry with components from Middle Eastern and , a wild relative endemic to the Eastern Mediterranean. Introgressive hybridization is supported by tests of admixture, reduced subdivision between North African date palm and , sharing of haplotypes in introgressed regions, and a population model that incorporates gene flow between these populations. Analysis of ancestry proportions indicates that as much as 18% of the genome of North African varieties can be traced to and a large percentage of loci in this population are segregating for single-nucleotide polymorphisms (SNPs) that are fixed in and absent from date palm in the Middle East. We present a survey of remains in the archaeobotanical record which supports a late arrival of date palm to North Africa. Our results suggest that hybridization with was of central importance in the diversification history of the cultivated date palm.
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http://dx.doi.org/10.1073/pnas.1817453116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6358688PMC
January 2019

Evolving the Anthropocene: linking multi-level selection with long-term social-ecological change.

Sustain Sci 2018 23;13(1):119-128. Epub 2017 Nov 23.

3Institute of Archaeology, University College London, London, WC1H 0PY UK.

To what degree is cultural multi-level selection responsible for the rise of environmentally transformative human behaviors? And vice versa? From the clearing of vegetation using fire to the emergence of agriculture and beyond, human societies have increasingly sustained themselves through practices that enhance environmental productivity through ecosystem engineering. At the same time, human societies have increased in scale and complexity from mobile bands of hunter-gatherers to telecoupled world systems. We propose that these long-term changes are coupled through positive feedbacks among social and environmental changes, coevolved primarily through selection acting at the group level and above, and that this can be tested by combining archeological evidence with mechanistic experiments using an agent-based virtual laboratory (ABVL) approach. A more robust understanding of whether and how cultural multi-level selection couples human social change with environmental transformation may help in addressing the long-term sustainability challenges of the Anthropocene.
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http://dx.doi.org/10.1007/s11625-017-0513-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086254PMC
November 2017

Archaeobotanical evidence reveals the origins of bread 14,400 years ago in northeastern Jordan.

Proc Natl Acad Sci U S A 2018 07 16;115(31):7925-7930. Epub 2018 Jul 16.

Department of Cross-Cultural and Regional Studies, University of Copenhagen, 2300 Copenhagen, Denmark.

The origins of bread have long been associated with the emergence of agriculture and cereal domestication during the Neolithic in southwest Asia. In this study we analyze a total of 24 charred food remains from Shubayqa 1, a Natufian hunter-gatherer site located in northeastern Jordan and dated to 14.6-11.6 ka cal BP. Our finds provide empirical data to demonstrate that the preparation and consumption of bread-like products predated the emergence of agriculture by at least 4,000 years. The interdisciplinary analyses indicate the use of some of the "founder crops" of southwest Asian agriculture (e.g., , wild einkorn) and root foods (e.g., , club-rush tubers) to produce flat bread-like products. The available archaeobotanical evidence for the Natufian period indicates that cereal exploitation was not common during this time, and it is most likely that cereal-based meals like bread become staples only when agriculture was firmly established.
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http://dx.doi.org/10.1073/pnas.1801071115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6077754PMC
July 2018

Long and attenuated: comparative trends in the domestication of tree fruits.

Authors:
Dorian Q Fuller

Veg Hist Archaeobot 2018 9;27(1):165-176. Epub 2017 Dec 9.

Institute of Archaeology, University College London, 31-34 Gordon Square, London, WC1H 0PY UK.

This paper asks whether we can identify a recurrent domestication syndrome for tree crops (fruits, nuts) and track archaeologically the evolution of domestication of fruits from woody perennials. While archaeobotany has made major contributions to documenting the domestication process in cereals and other annual grains, long-lived perennials have received less comparative attention. Drawing on examples from across Eurasia, comparisons suggest a tendency for the larger domesticated fruits to contain seeds that are proportionally longer, thinner and with more pointed (acute to attenuated) apices. Therefore, although changes in flavour, such as increased sweetness, are not recoverable, seed metrics and shape provide an archaeological basis for tracking domestication episodes in fruits from woody perennials. Where available, metrical data suggest length increases, as well as size diversification over time, with examples drawn from the Jomon of Japan (), Neolithic China () and the later Neolithic of the Near East () to estimate rates of change. More limited data allow us to also compare Mesoamerica avocado () and western Pacific sp. nuts and sp. fruits. Data from modern Indian jujube () are also considered in relation to seed length:width trends in relation to fruit contents (flesh proportion, sugar content). Despite the long generation time in tree fruits, rates of change in their seeds are generally comparable to rates of phenotypic evolution in annual grain crops, suggesting that gradual evolution via unconscious selection played a key role in initial processes of tree domestication, and that this had begun in the later Neolithic once annual crops had been domesticated, in both west and east Asia.
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http://dx.doi.org/10.1007/s00334-017-0659-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6954012PMC
December 2017

On the Origins and Dissemination of Domesticated Sorghum and Pearl Millet across Africa and into India: a View from the Butana Group of the Far Eastern Sahel.

Afr Archaeol Rev 2018 10;35(4):483-505. Epub 2018 Nov 10.

2Institute of Archaeology, University College London, London, UK.

Four decades have passed since Harlan and Stemler (1976) proposed the eastern Sahelian zone as the most likely center of domestication. Recently, new data on seed impressions on Butana Group pottery, from the fourth millennium BC in the southern Atbai region of the far eastern Sahelian Belt in Africa, show evidence for cultivation activities of sorghum displaying some domestication traits. may have been undergoing domestication shortly thereafter in the western Sahel, as finds of fully domesticated pearl millet are present in southeastern Mali by the second half of the third millennium BC, and present in eastern Sudan by the early second millennium BC. The dispersal of the latter to India took less than 1000 years according to present data. Here, we review the middle Holocene Sudanese archaeological data for the first time, to situate the origins and spread of these two native summer rainfall cereals in what is proposed to be their eastern Sahelian Sudan gateway to the Red Sea and the Indian Ocean trade.
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http://dx.doi.org/10.1007/s10437-018-9314-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394749PMC
November 2018

Geographic mosaics and changing rates of cereal domestication.

Philos Trans R Soc Lond B Biol Sci 2017 Dec;372(1735)

Institute of Archaeology, UCL, London, UK

Domestication is the process by which plants or animals evolved to fit a human-managed environment, and it is marked by innovations in plant morphology and anatomy that are in turn correlated with new human behaviours and technologies for harvesting, storage and field preparation. Archaeobotanical evidence has revealed that domestication was a protracted process taking thousands of plant generations. Within this protracted process there were changes in the selection pressures for domestication traits as well as variation across a geographic mosaic of wild and cultivated populations. Quantitative data allow us to estimate the changing selection coefficients for the evolution of non-shattering (domestic-type seed dispersal) in Asian rice ( L.), barley ( L.), emmer wheat ( (Shrank) Schübl.) and einkorn wheat ( L.). These data indicate that selection coefficients tended to be low, but also that there were inflection points at which selection increased considerably. For rice, selection coefficients of the order of 0.001 prior to 5500 BC shifted to greater than 0.003 between 5000 and 4500 BC, before falling again as the domestication process ended 4000-3500 BC. In barley and the two wheats selection was strongest between 8500 and 7500 BC. The slow start of domestication may indicate that initial selection began in the Pleistocene glacial era.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.
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http://dx.doi.org/10.1098/rstb.2016.0429DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5665816PMC
December 2017

Seed coat thinning during horsegram (Macrotyloma uniflorum) domestication documented through synchrotron tomography of archaeological seeds.

Sci Rep 2017 07 14;7(1):5369. Epub 2017 Jul 14.

University College London, Institute of Archaeology, London, WCH1 0PY, UK.

Reduction of seed dormancy mechanisms, allowing for rapid germination after planting, is a recurrent trait in domesticated plants, and can often be linked to changes in seed coat structure, in particular thinning. We report evidence for seed coat thinning between 2,000 BC and 1,200 BC, in southern Indian archaeological horsegram (Macrotyloma uniflorum), which it has been possible to document with high precision and non-destructively, through high resolution x-ray computed tomography using a synchrotron. We find that this trait underwent stepped change, from thick to semi-thin to thin seed coats, and that the rate of change was gradual. This is the first time that the rate of evolution of seed coat thinning in a legume crop has been directly documented from archaeological remains, and it contradicts previous predictions that legume domestication occurred through selection of pre-adapted low dormancy phenotypes from the wild.
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http://dx.doi.org/10.1038/s41598-017-05244-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5511171PMC
July 2017

A methodological approach to the study of archaeological cereal meals: a case study at Çatalhöyük East (Turkey).

Veg Hist Archaeobot 2017 16;26(4):415-432. Epub 2017 Mar 16.

University College London, Institute of Archaeology, 31-34 Gordon Square, London, WC1H 0PY UK.

This paper presents an integrated methodology for the analysis of archaeological remains of cereal meals, based on scanning electronic microscopic analyses of microstructures of charred food fragments from Neolithic Çatalhöyük (Turkey). The remains of cereal foods as 'bread-like' or 'porridge-like' small charred lumps of various amalgamated plant materials are frequently recovered from Neolithic and later archaeological sites in southwest Asia and Europe. Cereal food remains have recently attracted interest because the identification of their plant contents, the forms of food that they represent and the methods used in their creation can provide unique information about ancient culinary traditions and routine food processing, preparation and cooking techniques. Here, we focus on three methodological aspects: (1) the analysis of their composition; (2) the analysis of their microstructure to determine preparation and cooking processes; (3) the comparison with experimental reference materials. Preliminary results are presented on the botanical composition and cooking processes represented by the charred cereal preparations found at Neolithic Çatalhöyük (Turkey), for example cereals processed into bread, dough and/or porridge.
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http://dx.doi.org/10.1007/s00334-017-0602-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5486841PMC
March 2017

The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice.

Mol Biol Evol 2017 04;34(4):969-979

Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY.

The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1-24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus rice.
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http://dx.doi.org/10.1093/molbev/msx049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400379PMC
April 2017

Between China and South Asia: A Middle Asian corridor of crop dispersal and agricultural innovation in the Bronze Age.

Holocene 2016 Oct 1;26(10):1541-1555. Epub 2016 Jun 1.

Institute of Archaeology, University College London, UK.

The period from the late third millennium BC to the start of the first millennium AD witnesses the first steps towards food globalization in which a significant number of important crops and animals, independently domesticated within China, India, Africa and West Asia, traversed Central Asia greatly increasing Eurasian agricultural diversity. This paper utilizes an archaeobotanical database (AsCAD), to explore evidence for these crop translocations along southern and northern routes of interaction between east and west. To begin, crop translocations from the Near East across India and Central Asia are examined for wheat () and barley () from the eighth to the second millennia BC when they reach China. The case of pulses and flax () that only complete this journey in Han times (206 BC-AD 220), often never fully adopted, is also addressed. The discussion then turns to the Chinese millets, and , peaches () and apricots (), tracing their movement from the fifth millennium to the second millennium BC when the reaches Europe and Northern India, with peaches and apricots present in Kashmir and Swat. Finally, the translocation of rice from China to India that gave rise to rice is considered, possibly dating to the second millennium BC. The routes these crops travelled include those to the north via the Inner Asia Mountain Corridor, across Middle Asia, where there is good evidence for wheat, barley and the Chinese millets. The case for rice, apricots and peaches is less clear, and the northern route is contrasted with that through northeast India, Tibet and west China. Not all these journeys were synchronous, and this paper highlights the selective long-distance transport of crops as an alternative to demic-diffusion of farmers with a defined crop package.
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http://dx.doi.org/10.1177/0959683616650268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5125436PMC
October 2016

Domestication history and geographical adaptation inferred from a SNP map of African rice.

Nat Genet 2016 09 8;48(9):1083-8. Epub 2016 Aug 8.

Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA.

African rice (Oryza glaberrima Steud.) is a cereal crop species closely related to Asian rice (Oryza sativa L.) but was independently domesticated in West Africa ∼3,000 years ago. African rice is rarely grown outside sub-Saharan Africa but is of global interest because of its tolerance to abiotic stresses. Here we describe a map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces. Population genomic analysis shows a population bottleneck in this species that began ∼13,000-15,000 years ago with effective population size reaching its minimum value ∼3,500 years ago, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation. Genome-wide association studies (GWAS) for six salt tolerance traits identify 11 significant loci, 4 of which are within ∼300 kb of genomic regions that possess signatures of positive selection, suggesting adaptive geographical divergence for salt tolerance in this species.
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http://dx.doi.org/10.1038/ng.3633DOI Listing
September 2016

Reply to Westaway and Lyman: Emus, dingoes, and archaeology's role in conservation biology.

Proc Natl Acad Sci U S A 2016 08 26;113(33):E4759-60. Epub 2016 Jul 26.

Max Planck Institute for the Science of Human History, Jena D-07743, Germany;

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http://dx.doi.org/10.1073/pnas.1610697113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995951PMC
August 2016

Reply to Ellis et al.: Human niche construction and evolutionary theory.

Proc Natl Acad Sci U S A 2016 08 15;113(31):E4437-8. Epub 2016 Jul 15.

School of Archaeology, University of Oxford, Oxford OX1 2PG, United Kingdom;

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http://dx.doi.org/10.1073/pnas.1609617113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978256PMC
August 2016

Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions.

Proc Natl Acad Sci U S A 2016 Jun;113(23):6388-96

School of Archaeology, University of Oxford, Oxford OX1 2PG, United Kingdom;

The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity-the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences.
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http://dx.doi.org/10.1073/pnas.1525200113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4988612PMC
June 2016

Ancient crops provide first archaeological signature of the westward Austronesian expansion.

Proc Natl Acad Sci U S A 2016 06 31;113(24):6635-40. Epub 2016 May 31.

School of Archaeology, University of Oxford, Oxford OX1 2PG, United Kingdom; Department of Archaeology, Max Planck Institute for the Science of Human History, D-07743 Jena, Germany.

The Austronesian settlement of the remote island of Madagascar remains one of the great puzzles of Indo-Pacific prehistory. Although linguistic, ethnographic, and genetic evidence points clearly to a colonization of Madagascar by Austronesian language-speaking people from Island Southeast Asia, decades of archaeological research have failed to locate evidence for a Southeast Asian signature in the island's early material record. Here, we present new archaeobotanical data that show that Southeast Asian settlers brought Asian crops with them when they settled in Africa. These crops provide the first, to our knowledge, reliable archaeological window into the Southeast Asian colonization of Madagascar. They additionally suggest that initial Southeast Asian settlement in Africa was not limited to Madagascar, but also extended to the Comoros. Archaeobotanical data may support a model of indirect Austronesian colonization of Madagascar from the Comoros and/or elsewhere in eastern Africa.
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http://dx.doi.org/10.1073/pnas.1522714113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914162PMC
June 2016
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