Kjellberg, F. | bioRxiv Science

bioRxiv2025

Diffuse and regionally structured domestication of the common fig (Ficus carica L.) in the Mediterranean Basin

Understanding domestication in perennial crops is crucial for unraveling the evolutionary trajectories that have shaped crop genetic diversity and for guiding future conservation and breeding efforts. The domestication of perennial Mediterranean fruit trees is less studied than that of annual crops. The common fig (Ficus carica L.) is thought to have been domesticated in the Levant before dispersion across the Mediterranean. However, pre-human fossils of F. carica in Europe suggest an ancient wild presence, challenging the assumption of a single eastern origin. We used microsatellite markers to genotype 949 fig accessions comprising cultivated and spontaneous individuals collected from 14 Mediterranean and Near Eastern countries representing F. carica sensu stricto and its two close relatives, F. carica subsp. rupestris, and, F. colchica. Principal component analysis revealed that F. carica sensu stricto forms a cohesive genetic group distinct from its two relatives, which are actually different species. Bayesian clustering revealed three major gene pools within F. carica sensu stricto -- Moroccan-Algerian, Northern Mediterranean, and Levantine--each containing both cultivated and spontaneous individuals. The Levantine group was the most differentiated, while the other two were closer genetically, together reflecting a longitudinal Mediterranean structure. Cultivated and spontaneous figs were genetically indistinguishable within each region, supporting a model of diffuse, regionally independent domestication rather than a single Levantine origin. These results highlight spontaneous populations and local landraces as key reservoirs of genetic variation, particularly in Morocco, Algeria, and the Levant. Our study provides a foundation for future genomic work to identify the genetic basis of key traits, emphasizing that practical breeding and conservation strategies should rely on regional biodiversity rather than a narrow set of elite cultivars to enhance fig resilience and productivity in the face of climate change and emerging disease pressures.

evolutionary biology↗

bioRxiv2020

Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)

Despite their ecological and evolutionary importance as key components of tropical ecosystems, the phylogeny of fig trees is still unresolved. We use restriction-site-associated DNA (RAD) sequencing (ca 420kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus representing all known subgenera and sections and five outgroups. We compare morphological and molecular results to highlight discrepancies and reveal possible inference bias. We analyse marker and taxon properties that may bias molecular inferences, with existing softwares and a new approach based on iterative principal component analysis to reduce variance between clusters of samples. For the first time, with both molecular and morphological data, we recover a monophyletic subgenus Urostigma and a clade with all gynodioecious fig trees. However, our analyses show that it is not possible to homogenize evolutionary rates and GC content for all taxa prior to phylogenetic inference and that four competing positions for the root of the molecular tree are possible. The placement of the long-branched section Pharmacosycea as sister to all other fig trees is not supported by morphological data and considered as a result of a long branch attraction artefact to the outgroups. Regarding morphological features and indirect evidence from the pollinator tree of life, the topology that divides the genus Ficus into monoecious versus gynodioecious species appears most likely. Active pollination is inferred as the ancestral state for all topologies, ambiguity remains for ancestral breeding system including for the favored topology, and it appears most likely that the ancestor of fig trees was a freestanding tree. Increasing sampling may improve results and would be at least as relevant as maximizing the number of sequenced regions given the strong heterogeneity in evolutionary rates, and to a lesser extent, base composition among species. Despite morphological plasticity and frequent homoplasy of multiple characters, we advocate giving a central role to morphology in our understanding of the evolution of Ficus, especially as it can help detect insidious systematic errors that tend to become more pronounced with larger molecular data sets.

evolutionary biology↗