Potential of combining morphometry and ancient DNA information to investigate grapevine domestication

Baciliéri, Roberto; Bouby, Laurent; Figueiral, Isabel; Schaal, Caroline; Terral, Jean‐Frédéric; Breton, Catherine; Picq, Sandrine; Weber, Audrey; Schlumbaum, Angela

doi:10.1007/s00334-016-0597-4

Cited by 24 publications

(24 citation statements)

References 48 publications

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“…All specimens in the UCL archaeobotanical reference collection; scale bars 1 cm that wild and domesticated populations fall towards different ends of a morphological spectrum seems clear. Indeed, studies employing geometric morphometrics (GMM) on grapes (Vitis vinifera) (Pagnoux et al 2015;Bacilieri et al 2017), as well as on other taxa such as olives (Olea europaea) (Terral et al 2004;Newton et al 2014), plums (Prunus domestica) (Ucchesu et al 2017) and dates (Phoenix dactylifera) (Rivera et al 2014;Gros-Balthazard et al 2016), which factor out size and focus instead on shape, demonstrate statistically shape differences between wild and cultivated forms of these fruits, as well as among different cultivar groups. Domesticated forms have higher L:W ratios and tend to have more pointed (acute to acuminate) ends.…”

Section: Introductionmentioning

confidence: 99%

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

Fuller

2017

Veget Hist Archaeobot

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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 (Castanea crenata), Neolithic China (Prunus persica) and the later Neolithic of the Near East (Olea europaea, Phoenix dactylifera) to estimate rates of change. More limited data allow us to also compare Mesoamerica avocado (Persea americana) and western Pacific Canarium sp. nuts and Spondias sp. fruits. Data from modern Indian jujube (Ziziphus mauritiana) 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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Section: Introductionmentioning

confidence: 99%

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

Fuller

2017

Veget Hist Archaeobot

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“…Evidence for the start of systematic cultivation remains elusive. Morphological change in terms of grape pip lengthening would certainly be indicative but may only evolve later in the domestication process, and is yet to be systematically studied for West Asian Vitis (see Bacilieri et al 2017 ). Nevertheless, what is clear is the period when grapes expanded beyond their natural wild distribution, which can be taken as indicative of cultivation, if not domestication (Fig.…”

Section: Results: West Asia—the Domestication and Dispersal Of Fig Gmentioning

confidence: 99%

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

Fuller

Stevens

2019

Veget Hist Archaeobot

114

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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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“…An automated stereoscopic microscope is an available tool found in many labs, making our method of using the full data set gained by 3D data for separating the varieties by their morphological trait, available and approachable. This new approach is the next step in the journey for grape variety identification for agriculture and archaeobotanical purposes, started by the development of the traditional morphometric methods and the elliptic Fourier transform method [18][19][20]43 later applied for charred and archaeological findings by analysis of surface morphology [44][45][46][47][48][49] using ICP from A to B might differ in every iteration. Concerning the above mentioned possible introduced errors, we implemented the following steps: 1.…”

Section: Discussionmentioning

confidence: 99%

“…Also, a significant correlation between pip morphology and the taxonomic relationship was demonstrated. Furthermore, an innovative approach for the investigation of archaeological remains by combined 2D morphometric and genetic methods was recently developed, showing promising results in melon seeds 20,21 .…”

Section: Introductionmentioning

confidence: 99%

Utilizing machine-learning-based 3D image analysis for classifying charred grape seeds to the varietal level

Landa

Shapira

David

et al. 2020

Preprint

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Grapevine (Vitis vinifera L.) is an essential part of the oldest group of fruit trees around which horticulture evolved, currently includes thousands of cultivars, grown at numerous climatic conditions. Discrimination between these varieties has been traditionally conducted using ampelography, and in recent decades mostly by genetic analysis. However, when aiming to identify archaeobotanical remains, which are mostly charred- with extremely low genomic preservation, the application of the genomic approach is rarely successful. As a result, variety-level identification of most grape remains is currently prevented. Because grape pips are highly polymorphic, several attempts were made to utilize their morphological diversity as a classification tool, mostly using 2D image analysis technics, aiming to utilize these methods for the identification of fresh and archaeological specimens. Here, we present for the first time a highly accurate varietal classification tool, using an innovative and accessible approach for 3D seed scanning. The suggested classification methodology is machine-learning-based, using a complete set of 3D data obtained for each seed, applied with the Iterative Closest Point (ICP) registration algorithm and the Linear Discriminant Analysis (LDA) technique. This methodology achieved classification results of ca. 90-99% accuracy when trained by fresh seeds to test unknown fresh seeds. Moreover, the classification of charred seeds reached up to 100% accuracy when trained by charred seeds. Based on this approach, our long-term aim is to develop a computerized classification tool for the identification of grape and possibly other species and varieties. Such a tool can significantly improve the fields of archaeobotany, as well as general taxonomy.

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Potential of combining morphometry and ancient DNA information to investigate grapevine domestication

Cited by 24 publications

References 48 publications

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

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

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

Utilizing machine-learning-based 3D image analysis for classifying charred grape seeds to the varietal level

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