L'intégration de l'ethnobotanique et de la génétique des populations met en évidence l'agrobiodiversité des palmiers dattiers de l'oasis de Siwa (Égypte) et leur importance pour l'histoire évolutive de l'espèce.

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)

Diversity of Algerian oases date palm (Phoenix dactylifera L., Arecaceae): Heterozygote excess and cryptic structure suggest farmer management had a major impact on diversity.

Date palm (Phoenix dactyliferaL.) is the mainstay of oasis agriculture in the Saharan region. It is cultivated in a large part of the Mediterranean coastal area of the Sahara and in most isolated oases in the Algerian desert. We sampled 10 oases in Algeria to understand the structure of date palm diversity from the coastal area to a very isolated desert location. We used 18 microsatellite markers and a chloroplast minisatellite to characterize 414 individual palm trees corresponding to 114 named varieties. We found a significant negative inbreeding coefficient, suggesting active farmer selection for heterozygous individuals. Three distinct genetic clusters were identified, a ubiquitous set of varieties found across the different oases, and two clusters, one of which was specific to the northern area, and the other to the drier southern area of the Algerian Sahara. The ubiquitous cluster presented very striking chloroplast diversity, signing the frequency of haplotypes found in Saudi Arabia, the most eastern part of the date palm range. Exchanges of Middle Eastern and Algerian date palms are known to have occurred and could have led to the introduction of this particular chlorotype. However, Algerian nuclear diversity was not of eastern origin. Our study strongly suggests that the peculiar chloroplastic diversity of date palm is maintained by farmers and could originate from date palms introduced from the Middle East a long time ago, which since then, hasbeen strongly introgressed. This study illustrates the complex structure of date palm diversity in Algerian oases and the role of farmers in shaping such cryptic diversity

Map showing the distribution of the 10 oases sampled in Algeria.

<p>The 414 samples came from the following sources: Biskra 13 cultivars; Oued Souf 22 cultivars; Touggourt 30 cultivars; Ouargla 5 cultivars; Ghardaia 17 cultivars; El Menia 10 cultivars; Timimoun 16 cultivars; Adrar 18 cultivars; Beni Abbes 14 cultivars, and Tamanrasset 4 cultivars.</p

Genetic distance between Structure populations (F_ST).

<p>Genetic distance between Structure populations (F_ST).</p

Summary data for 18 microsatellite loci.

<p>Summary data for 18 microsatellite loci.</p

Descriptive genetic parameters for 18 microsatellite loci analyzed on 192individual date palms.

<p>Descriptive genetic parameters for 18 microsatellite loci analyzed on 192individual date palms.</p

Bayesian cluster analysis using the STRUCTURE program: Results for K = 3.

<p>(A) Plots of (a) maximum log likelihood over the 10 runs and (b) delta k from the structure analysis was calculated according to the method of Evanno et al. (B) Estimated population structure inferred from all the individual date palms for K = 3. Each individual is represented by a thin vertical line divided into K colored segments representing the fraction of the individual’s estimated membership of the K clusters. Pie charts show the frequencies of the haplotypes belonging to the three structure groups. (C) Geographic distributions of the 10 oases and two haplotypes. The pie chart shows the proportions of haplotypes in each oasis. (D) Sampling location of the date palms. Pie charts show the proportion of membership of each sampled population inferred by structure analysis (K = 3).</p

Genetic distance between oases (F_ST).

<p>Genetic distance between oases (F_ST).</p

Sur la nécessité de combiner l'ethnobotanique et la génétique pour évaluer l'agrobiodiversité et son évolution des plantes cultivées : Une étude de cas sur les palmiers dattiers (Phoenix dactylifera L.) dans l'oasis de Siwa, Égypte

International audienceCrop 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 Greuter, 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).La diversité des plantes cultivées est façonnée par des processus biologiques et sociaux qui interagissent à différentes échelles spatiotemporelles. Nous avons ici combiné la génétique des populations et l’ethnobotanique pour étudier la diversité du palmier-dattier (Phoenix dactylifera L.) dans l’oasis de Siwa, en Égypte. Sur la base d’entretiens avec des agriculteurs et de l’observation des pratiques sur le terrain, nous avons collecté 149 palmiers dattiers de l’oasis de Siwa et 27 palmiers dattiers non cultivés provenant d’oasis abandonnées dans le désert environnant. En utilisant les données de génotypage de 18 loci microsatellites nucléaires et plastidiques, nous avons confirmé que certains types nommés constituent chacun une ligne clonale, c’est-à-dire un « cultivar vrai » (true-to-type). Nous avons également constaté que d’autres sont des collections de lignes clonales, c’est-à-dire des « ethnovariétés », voire même des échantillons non apparentés, c’est-à-dire des « catégories locales ». Cela modifie les évaluations existantes de l’agrobiodiversité, qui sont visiblement sous-estimées, et révèle l’impact des pratiques agricoles de faible intensité, mais très efficaces, sur la biodiversité. Ces pratiques difficilement observables, supposées par l’enquête ethnographique et confirmées par l’analyse génétique, sont rendues possibles par la façon dont les Isiwans conçoivent et classifient les êtres vivants dans leur oasis, qui ne correspond pas tout à fait à la façon dont les biologistes le font : une disparité classique des catégorisations étiques vs. émiques. En outre, nous avons établi que les palmiers dattiers de Siwa représentent un groupe génétique unique et très diversifié, plutôt qu’un sous-ensemble de la diversité des palmiers d’Afrique du Nord et du Moyen-Orient. Comme nous l’avons montré précédemment, les palmiers dattiers d’Afrique du Nord présentent des signes d’introgression par le parent sauvage Phoenix theophrasti Greuter, et nous avons constaté que les palmiers dattiers non cultivés des oasis abandonnées partagent encore plus d’allèles avec cette espèce que les palmiers cultivés de cette région. L’étude des palmiers dattiers de Siwa pourrait donc être une clé pour la compréhension de la diversification des palmiers dattiers en Afrique du Nord. L’intégration de l’ethnographie et de la génétique des populations a permis de comprendre l’interaction entre la gestion de la diversité dans l’oasis (l’échelle du court terme) et les origines et la dynamique de la diversité au travers de la domestication et de la diversification (l’échelle du long terme)