Biology subjects

Ivorra, S.

Publications and source records attributed to Ivorra, S..

4 recordsLinked to original sources

bioRxiv2023

Deep learning versus geometric morphometrics for archaeobotanical domestication study and subspecific identification

The identification of archaeological fruits and seeds is crucial for understanding the relationships between humans and plants within the cultural and biological history of both wild and cultivated species. We compared the relative performance of a deep learning approach, namely convolutional neural networks (CNN), and outline analyses via geometric morphometrics using elliptical Fourier transforms (EFT) at identifying pairs of plant taxa. We used their seeds and fruit stones that are the most abundant organs in archaeobotanical assemblages, and whose morphological identification, chiefly between wild and domesticated types, allows to document their domestication and biogeographical history. We used existing modern datasets of four plant taxa (barley, olive, date palm and grapevine) corresponding to photographs of two orthogonal views of their seeds that were analysed separately to offer a larger spectrum of shape diversity. Sample sizes ranged from 473 to 1,769 seeds per class, which constitute a relatively small dataset for training CNNs models yet typical within archaeobotanical research. On these eight datasets, we compared the performance of CNN and EFT coupled with linear discriminant analyses. Our objectives were twofold: i) to test whether CNN can beat geometric morphometrics in taxonomic identification and if so, ii) to test which minimal sample size is required. We ran simulations on the full datasets and also on subsets, starting from 50 images in each binary class. For the CNN network, we deliberately used a candid approach relying on pre-parameterised VGG19 network. For EFT, we used a state-of-the art morphometrical pipeline. The main difference rests in the data used by each model: our CNN used bare photographs where EFT used outline coordinates. This "pre-distilled" geometrical description of seed outlines is often the most time-consuming part of morphometric studies. Results show that our CNN beats EFT in most cases, even for very small datasets. We finally discuss the potential of CNNs for archaeobotany, and how bioarchaeological studies could embrace both approaches, used in a complementary way, to better assess and understand the past history of species.

bioinformatics↗

bioRxiv2019

Integration of ethnobotany and population genetics uncovers the agrobiodiversity of date palms of Siwa Oasis (Egypt) and their importance to the evolutionary history of the species

Crop diversity is shaped by biological and social processes interacting at different spatiotemporal scales. Here we combined population genetics and ethnobotany to investigate date palm (Phoenix dactylifera L.) diversity in Siwa Oasis, Egypt. Based on interviews with farmers and observation of practices in the field, we collected 149 date palms from Siwa Oasis and 27 uncultivated date palms from abandoned oases in the surrounding desert. Using genotyping data from 18 nuclear and plastid microsatellite loci, we confirmed that some named types each constitute a clonal line, i.e. a true-to-type cultivar. We also found that others are collections of clonal lines, i.e. ethnovarieties, or even unrelated samples, i.e. local categories. This alters current assessments of agrobiodiversity, which are visibly underestimated, and uncovers the impact of low-intensity, but highly effective, farming practices on biodiversity. These hardly observable practices, hypothesized by ethnographic survey and confirmed by genetic analysis, are enabled by the way Isiwans conceive and classify living beings in their oasis, which do not quite match the way biologists do: a classic disparity of etic vs. emic categorizations. In addition, we established that Siwa date palms represent a unique and highly diverse genetic cluster, rather than a subset of North African and Middle Eastern palm diversity. As previously shown, North African date palms display evidence of introgression by the wild relative Phoenix theophrasti, and we found that the uncultivated date palms from the abandoned oases share even more alleles with this species than cultivated palms in this region. The study of Siwa date palms could hence be a key to the understanding of date palm diversification in North Africa. Integration of ethnography and population genetics promoted the understanding of the interplay between diversity management in the oasis (short-time scale), and the origins and dynamic of diversity through domestication and diversification (long-time scale).

evolutionary biology↗

bioRxiv2019

Berry and pip form covariation in wild and domesticated grapevines: eco-evo-devo implications and archaeobotanical perspectives

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 pips with short stalks and cultivated varieties have more elongated pips with longer stalks. Such variations of form are of first importance for archaeobotany since the pip form is, most often, the only remaining information in archaeological settings. This study aims to enlight archaeobotanical record and grapevine pip development by better understanding how size and shape (co)variates between pip and berry in both wild and domesticated Vitis vinifera. The covariation of berry size, number of seeds per berry ("piposity"), pip size and pip shape were explored on 49 grapevine accessions sampled among Euro-Mediterranean traditional cultivars and wild grapevines. We show that for wild grapevine, the higher the piposity, the bigger the berry and the more elongated the pip. For both wild and domesticated grapevine, the longer is the pip, the more it has a "domesticated" shape. Consequences for archaeobotanical studies are tested and discussed, and these covariations allowed the inference of berry dimensions from archaeological pips from a Southern France Roman site. This systematic exploration sheds light on new aspects of pip-berry relationship, in both size and shape, on grapevine eco-evo-devo changes during domestication, and invites to explore further the functional ecology of grapevine pip and berry and notably the impact of cultivation practices and human selection on grapevine morphology.

plant biology↗

bioRxiv2017

The Date Palm (Phoenix dactylifera L.) In Siwa Oasis (Egypt): How Ethnographic, Morphometric, And Genetic Analyses Together Explain The Local Agrobiodiversity

The agrobiodiversity of the Siwa oasis (in Egypt), located at the crossroads of ancient Trans-Saharan routes, is evaluated in this article focusing on the date palm (Phoenix dactylifera L.), the oasis \"ecosystem engineer\". This assessment confronts different ontologies: diversity as expressed and maintained by the folk categorization system of the Siwa inhabitants (through the results of an ethnographical analysis) and diversity described by genetic sciences and a morphometric tool based on the size and geometry of the seeds. This work is also an opportunity to evaluate this tool intended for archaeobotany. Beyond a simple instrumentalization of one discipline by another, this study offers a space of mutual enrichment: on the relative importance of the feral and cultivated date palms, the local relevance of the concept of \"cultivar\" and the confirmation of the existence of \"ethnovarieties\".

plant biology↗