Vincent Bonhomme

Vincent Bonhomme
Université de Montpellier | UM1 · Institut des Sciences de l’Évolution Montpellier (ISEM)

About

69
Publications
33,661
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,248
Citations
Citations since 2017
49 Research Items
1091 Citations
2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250
Introduction
Grapevine domestication, domesticated plant evolution, geometric morphometrics, deep learning

Publications

Publications (69)
Chapter
Backed pieces became widespread in the Upper Pleistocene and Holocene and are part of the classic definitions for the Later Stone Age in many parts of Africa. However, the association of backed pieces with Later Stone Age is not clear in the Horn of Africa. These pieces are present in both Middle Stone Age (MSA) and Later Stone Age (LSA) contexts....
Article
Full-text available
Nut shape is an important trait in determining the value of a pecan (Carya illinoensis) nut crop. Nut shape influences attractiveness to consumers, nut filling, ease of mechanical cracking, and is distinctive enough that it is the primary means of cultivar identification. Narrow sense heritability (h²) of a trait is the fraction of phenotypic varia...
Article
Full-text available
Geometric morphometrics revolutionized domestication studies through the precise quantification of the phenotype of ancient plant and animal remains. Geometric morphometrics allow for an increasingly detailed understanding of the past agrobiodiversity and our ability to characterize large scale ancient phenotypes has led to what can be named archae...
Article
Full-text available
Quantifying the morphology of organisms remains fundamental in ecology given the form-function relationship. Morphology is quantifiable in traits, landmarks, and outlines, and the choice of approach may influence ecological conclusions to an unknown extent. Here, we apply these three approaches to 111 individual coral reef fish of 40 species common...
Preprint
Full-text available
Geometric morphometrics revolutionized domestication studies through the precise quantification of the phenotype of ancient plant and animal remains. Geometric morphometrics allow for an increasingly detailed understanding of the past agrobiodiversity and our ability to characterize large scale ancient phenotypes has led to what can be named archae...
Article
Full-text available
The use and socio-environmental importance of fruits dramatically changed after the emergence of arboriculture and fruit domestication in the eastern Mediterranean, between the 5th and the 3rd millennia BCE. Domesticated fruits together with cultivation techniques apparently reached the western Mediterranean via colonial activities during the 1st m...
Article
Full-text available
The pip, as the most common grapevine archaeological remain, is extensively used to document past viticulture dynamics. This paper uses state of the art morphological analyses to analyse the largest reference collection of modern pips to date, representative of the present-day diversity of the domesticated grapevine from Western Eurasia. We tested...
Article
Full-text available
The first exploited and domesticated olive forms are still unknown. The exceptionally wellpreserved stones from the submerged Hishuley Carmel site (Israel), dating from the middle of the 7th millennium BP, offer us the opportunity to study the oldest table olives discovered so far. We apply a geometrical morphometric analysis in reference to a coll...
Chapter
The development of agricultural societies is closely entangled with that of domestic animals and plants. Local and traditional domestic breeds and varieties are the result of millennia of selec- tion by farmers. DEMETER (2020-2025) is an international pro- ject which is aiming to characterize the changes in animal and plant agrobiodiversity (pigs,...
Article
Grapevine and olive are thought to have been intensively cultivated during the Hellenistic period, as part of an agrarian system which included agricultural choices specializing in the production of their secondary products. The discovery of large assemblages of carbonized grapes and olives at three sites in Pieria, Macedonia, Greece, provides a un...
Article
Full-text available
Opium poppy (Papaver somniferum L. subsp. somniferum) was likely domesticated in the Western Mediterranean, where its putative wild ancestor is indigenous, and then spread to central and northern Europe. While opium poppy seeds are regularly identified in archaeobotanical studies, the absence of morphological criteria to distinguish the seeds of wi...
Article
The present study aims to contribute to the investigation of the role of Phoenicians in the spreading and trade of the grapevine through the morphometric analysis of grape pips. Waterlogged and charred samples were selected from three Iron Age sites in the Western Mediterranean: Motya (Sicily, Italy), Nuraghe S’Urachi (Sardinia, Italy) and Huelva (...
Article
Full-text available
A crucial aspect of viticulture is finally unveiled as the historical dynamics of its agrobiodiversity are described in the Champagne region for the first time. Outline analyses were carried out to compare the morphology of archaeological grape seeds from Troyes and Reims (first c. AD to fifteenth c. AD) with that of a reference collection of moder...
Article
Full-text available
This study applied size and shape analyses through traditional and geometric morphometrics to quantify the differences between three taxa: Lathyrus sativus (grass pea), Lens culinaris (lentil) and Vicia faba (broad bean). This analysis represents a pilot study in view of a wider future application of this technique to identify the role of legumes t...
Article
Full-text available
The Near East and the Caucasus are commonly regarded as the original domestication centres of Vitis vinifera (grapevine), and the region continues to be home to a high diversity of wild and cultivated grapevines, particularly within Georgia. The earliest chemical evidence for wine making was recorded in Georgian Neolithic sites (6000–5800 bc) and g...
Article
Full-text available
Grapevine (Vitis vinifera L.) is one of the emblematic crops of Greece. Despite evidence of early wine making in the Aegean since the Late Neolithic (ca 4500–4000 BC), the hypothesis of a local domestication of the grapevine in this area hasn't be thoroughly investigated. In order to date the first appearance of the domesticated grapevine and to ex...
Article
Full-text available
A classic example of phenotypic plasticity in plants is the set of traits that change in response to shade. There is widespread evidence that plants in low light conditions often avoid shade by growing taller or by increasing their photosynthetic efficiency, i.e. the shade avoidance syndrome. Whether this plasticity might evolve in response to natu...
Conference Paper
Full-text available
Grapevine (Vitis vinifera) is one of the most important fruit crops of the past and present world, both economically and culturally. The wild and domesticated forms, respectively Vitis vinifera subsp. sylvestris and V. vinifera subsp. vinifera , differ by an array of traits, including the form of their seeds that may be retrieved in archaeological...
Article
Full-text available
Quantifying phenotypes is a common practice for addressing questions regarding morphological variation. The time dedicated to data acquisition can vary greatly depending on methods and on the required quantity of information. Optimizing digitization effort can be done either by pooling datasets among users, by automatizing data collection, or by re...
Article
Full-text available
The phenotypic changes that occurred during the domestication and diversification of grapevine are well known, particularly changes in seed morphology, but the functional causes and consequences behind these variations are poorly understood. Wild and domesticate grapes differ, among others, in the form of their pips: wild grapes produce roundish pi...
Article
Despite reports of sexual dimorphism in extinct taxa, such claims in non-avian dinosaurs have been rare over the last decade and have often been criticized. Since dimorphism is widespread in sexually reproducing organisms today, under-reporting in the literature might suggest either methodological shortcomings or that this diverse group exhibited h...
Article
Full-text available
Backed pieces became widespread in the Upper Pleistocene and Holocene and are part of the classic definitions for the Later Stone Age in many parts of Africa. However, the association of backed pieces with Later Stone Age is not clear in the Horn of Africa. These pieces are present in both Middle Stone Age (MSA) and Later Stone Age (LSA) contexts....
Chapter
Full-text available
Des analyses de contours de pépins de raisin archéologiques des sites de Troyes et de Reims (France) dont les résultats ont été examinés au regard d'un vaste référentiel moderne, permettent d’inférer l’identité, les origines et l’histoire des anciennes variétés utilisées en Champagne. Cet article explore trois aspects de l’agrobiodiversité historiq...
Article
Full-text available
Despite reports of sexual dimorphism in extinct taxa, such claims in non-avian dinosaurs have been rare over the last decade and have often been criticized. Since dimorphism is widespread in sexually reproducing organisms today, under-reporting in the literature might suggest either methodological shortcomings or that this diverse group exhibited h...
Article
Full-text available
Phenotypic divergence among natural populations can be explained by natural selection or by neutral processes such as drift. Many examples in the literature compare putatively neutral (FST) and quantitative genetic (QST) differentiation in multiple populations to assess their evolutionary signature and identify candidate traits involved with local...
Article
Full-text available
Viticulture and wine making have been at the heart of discussions concerning the Mycenaean society with elite groups which emerged in the Mediterranean during the Bronze Age. In the south of Greece, in Crete and the Peloponnese, viticulture and wine consumption are mentioned in 2nd millennium bc Linear B texts. Despite the key role of the grapevine...
Article
Full-text available
Bere is a landrace of barley, adapted to the marginal conditions of northern Scotland, especially those of the Northern and Western Isles. The history of bere on these islands is long and, in an era of diminishing landrace cultivation, bere now represents one of the oldest cereal landraces in Europe still grown commercially. The longevity of bere r...
Article
Full-text available
Archaeobotanical evidence from southwest Asia is often interpreted as showing that the spectrum of wild plant foods narrowed during the origins of agriculture, but it has long been acknowledged that the recognition of wild plants as foods is problematic. Here, we systematically combine compositional and contextual evidence to recognise the wild pla...
Preprint
Full-text available
If grapevine phenotypic changes occurred during domestication and diversification processes are quite well known, particularly seed morphology used in archaeobiological studies, the functional causes and consequences behind these variations are still poorly understood. This study clarifies many aspects of size and shape (co)variation between pip an...
Preprint
Full-text available
Phenotypic differentiation among natural populations can be explained by natural selection or by neutral processes such as drift. There are many examples in the literature where comparing the effects of these processes on multiple populations has allowed the detection of local adaptation. However, these studies rarely identify the agents of selecti...
Article
Full-text available
This article examines the impact of charring on the possibility to characterize grape pips, at compartment (wild versus domesticated) and cultivar level, using morphometrics. Two morphometric methods have been used, one based on linear measurements (traditional morphometrics) and one on elliptic Fourier transforms (EFT; morphogeometrics). Charring...
Preprint
Full-text available
A classical example of phenotypic plasticity in plants is the set of trait changes in response to shade, i.e. the shade avoidance syndrome. There is widespread evidence that plants in low light conditions often avoid shade by growing taller or by increasing their photosynthetic efficiency. This plastic response is expected to have evolved in respon...
Article
Full-text available
Birds, particularly raptors, are believed to forage primarily using visual cues. However, raptor foraging tactics are highly diverse - from chasing mobile prey to scavenging - which may reflect adaptations of their visual systems. To investigate this, we studied the visual field configuration of 15 species of diurnal Accipitriformes that differ in...
Article
Full-text available
During the excavations of a Roman amphora workshop and oil mill of the 1st–4th century ad in Las Delicias, Genil valley, Ecija, Spain, large quantities of charred olive stones were recovered. The assemblages discovered in the pottery kilns demonstrate the use as fuel of olive residues, which were obtained from the extraction of the oil in the nearb...
Article
Full-text available
Trait‐based approaches are increasingly popular in ecology to describe communities and their responses to natural or anthropogenic changes. Morphology is an integrative trait that combines functional and evolutionary information. However, the objective and quantitative description of the morphological diversity is quite challenging. Modern morphome...
Article
Dental morphological differences in the first two mandibular molars of domestic equids have been claimed to possess unique species characteristics and are commonly used to identify archaeological equids to a species level. However, the intraspecific and intra-teeth variability of this morphological trait seems to be largely underestimated and the e...
Presentation
Full-text available
Presentation slides. Video courtesy of Palaeocast is available through the following link: https://www.youtube.com/watch?v=ezzEISCDRB8
Article
This paper introduces dynamic configurational changes for patchy mosaics, parameterizable dilationand/or erosion processes of units in a vectorial landscape. Patchy-based models are rare although thisconceptual framework could yield insights to the functioning and dynamics of agricultural and naturallandscapes. Compared to common raster-based model...
Article
The application of morphometric analysis in archaeobotany has the potential to refine quantitatively identifications of ancient plant material recovered from archaeological sites, most commonly preserved through charring due to exposure to heat. This paper uses geometric morphometrics, first, to explore variation in grain shape between three domest...
Article
Complex ecosystems are difficult to model and are still poorly understood. In spite of the long lasting efforts to predict them, we still lack a real integrated framework to grasp their behaviours. In this paper, the concept of ecosystem development is proposed to understand the sharp regime shifts they cumulate over the long term. To handle regime...
Article
Feeding habits, diet overlap and morphological correlates of four juvenile species of the genus Diplodus were investigated during their settlement periods, along the Tyrrhenian coast. Stomach content analysis showed that the diets of D. sargus and D. puntazzo mainly comprised benthic prey such as harpacticoid copepods, amphipods and polychaetes. On...
Article
Traditional explanations of Rapa Nui history invoke environmental degradation and warfare to explain the ‘collapse’ of the island’s social and economic structure. One element in these reconstructions are the stemmed obsidian points known as mata’a, which some have envisaged as spearheads produced in the context of endemic warfare. Morphometric anal...
Article
Full-text available
Nepenthes pitcher plants display interspecific diversity in pitcher form and diets. This species-rich genus might be a conspicuous candidate for an adaptive radiation. However, the pitcher traits of different species have never been quantified in a comparative study, nor have their possible adaptations to the resources they exploit been tested. In...
Article
Full-text available
The transition from a mobile hunter-gatherer lifestyle to one of settled agriculture is arguably the most fundamental change in the development of human society (Lev-Yadun et al., 2000). The establishment of agricultural economies, emerging initially in the Fertile Crescent of the Near East (Nesbitt, 2002), required the domestication of crops; anci...
Presentation
This study aims to understand the past and present diversity of olive trees in Greece, according to the shape of modern and archaeological stones from various sites. It is based on a modern set of reference, which includes cultivars and wild populations from Greece and other countries around the Mediterranean Sea where olives trees grow spontaneous...
Article
This paper introduces the vectorial Kappa (κv) that one can utilize to assess congruence between two vectorial mosaics. The vectorial Kappa extends for vectorial mosaics the approach of the so-called Cohen's Kappa index, commonly used to compare raster mosaics. By comparing both approaches, we aim to demonstrate how efficient and convenient a vecto...
Article
Full-text available
We present a case for using Global Community Innovation Platforms (GCIPs), an approach to improve innovation and knowledge exchange in international scientific communities through a common and open online infrastructure. We highlight the value of GCIPs by focusing on recent efforts targeting the ecological sciences, where GCIPs are of high relevanc...
Preprint
Full-text available
We present a case for using global community innovation platforms (GCIPs), an approach to improve innovation and knowledge exchange in international scientific communities through a common and open online infrastructure. We highlight the value of GCIPs by focusing on recent efforts targeting the ecological sciences, where GCIPs are of high relevanc...
Article
Full-text available
The aim of the study was to use melissopalynology to delineate the foraging preferences of bees in tropical environs. This was done by comparing pollen spectra obtained from the same hives every three months for three years at four sampling locations (in two sites) within a confined landscape mosaic. If melissopalynology is highly replicable, the s...
Data
We introduce here Momocs, a package intended to ease and popularize modern mor-phometrics with R, and particularly outline analysis, which aims to extract quantitative variables from shapes. It mostly hinges on the functions published in the book entitled Modern Morphometrics Using R by Claude (2008). From outline extraction from raw data to multiv...
Article
Full-text available
We introduce here Momocs, a package intended to ease and popularize modern mor- phometrics with R, and particularly outline analysis, which aims to extract quantitative variables from shapes. It mostly hinges on the functions published in the book entitled Modern Morphometrics Using R by Claude (2008). From outline extraction from raw data to multi...
Book
Full-text available
Connaitre la biodiversité d’un campus universitaire peut paraître bizarre voire inutile. Cependant, la vie est partout et dans n’importe quel milieu, même au sein d’une ville comme Montpellier. L’inventaire de la biodiversité de la Faculté de Sciences et Techniques est un projet innovant qui s’inscrit dans une politique de développement durable. Il...
Article
The shape of watersheds is linked to its geomorphological origin and its hydrological behavior. The present study uses elliptical Fouri-er analysis to describe shapes of watershed outlines. With two successive analyses, considering or not the outlet position, on a case study in Haiti, we identify on these shapes more than the classical shape descri...
Article
Pollen grains have long fascinated biologists who used their remarkable interspecific diversity as a marker to infer profiles of past and present vegetations and environment. This study addresses the question of the diversity of the morphology of pollen grains at the intraspecific level: how different are pollen grains of the same species sampled i...
Article
The pitcher-shaped leaves of Nepenthes carnivorous plants have been considered as pitfall traps that essentially rely on slippery surfaces to capture insects. But a recent study of Nepenthes rafflesiana has shown that the viscoelasticity of the digestive fluid inside the pitchers plays a key role. Here, we investigated whether Nepenthes species exh...
Article
Full-text available
The Bornean climber, Nepenthes bicalcarata, is unique among plants because it is both carnivorous and myrmecophytic, bearing pitcher-shaped leaves and the ant Camponotus schmitzi within tendrils. We explored, in the peat swamp forests of Brunei, the hypothesis that these ants contribute to plant nutrition by catching and digesting its prey.Wefirst...
Article
Full-text available
Divergent adaptation to host plant species may be the major mechanism driving speciation and adaptive radiations in phytophagous insects. Host plants can differ intrinsically in a number of attributes, but the role of natural enemies in host plant specialization is often underappreciated. Here, we report behavioural divergence between the European...