Genome-wide footprints in the carob tree (Ceratonia siliqua) unveil a new domestication pattern of a fruit tree in the Mediterranean

Intense research efforts over the last two decades have renewed our understanding of plant phylogeography and domestication in the Mediterranean basin. Here we aim to investigate the evolutionary history and the origin of domestication of the carob tree (Ceratonia siliqua), which has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to delimit seven carob evolutionary units (CEUs). We investigated genome-wide diversity and evolutionary patterns of the CEUs with 3557 single nucleotide polymorphisms generated by restriction-site associated DNA sequencing (RADseq). To address the complex wild vs. cultivated status of sampled trees, we classified 56 sampled populations across the Mediterranean basin as wild, seminatural or cultivated. Nuclear and cytoplasmic loci were identified from RADseq data and separated for analyses. Phylogenetic analyses of these genomic-wide data allowed us to resolve west-to-east expansions from a single long-term refugium probably located in the foothills of the High Atlas Mountains near the Atlantic coast. Our findings support multiple origins of domestication with a low impact on the genetic diversity at range-wide level. The carob was mostly domesticated from locally selected wild genotypes and scattered long-distance westward dispersals of domesticated varieties by humans, concomitant with major historical migrations by Romans, Greeks and Arabs. Ex situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in southwest Morocco, south Spain and eastern Mediterranean. Our study highlights the relevance of wild and seminatural habitats in the conservation of genetic resources for cultivated trees

Conservation unit allows assessing vulnerability and setting conservation priorities for a Mediterranean endemic plant within the context of extreme urbanization

International audienceCurrent biodiversity patterns are a temporary state in a continuum of ecological and evolutionary changes. Conservation policies must incorporate this dynamic to ensure the long-term conservation of biodiversity which is particularly challenging in a context of extreme urbanization. An original approach, rarely used for plant conservation, is to define conservation units to set conservation priorities within species by combining ecological and evolutionary divergences. In the Maritime Alps (southern France), the ecological and evolutionary divergences between the populations of Acis nicaeensis has allowed us the determination of conservation units of this endemic plant threatened by severe urbanization and land-use changes. Phylogeographical data (cpDNA haplotype) were considered as a proxy for evolutionary legacy, and ecological data (multivariate analysis of habitat) were used as a proxy for ecological distinctiveness. Our goal was to explore the potential of this approach to assess vulnerability and set conservation priorities for narrow endemic species in the context of conflict between biodiversity and human activities. The results highlight five different conservation units within A. nicaeensis distribution. Genetic and ecological divergences are present at fine-scale. This pattern is highly endangered by urbanisation. This study highlights the vulnerability of conservation units near the coast whose originality and restricted distribution call for rapid conservation management to avoid the loss of species evolutionary and ecological distinctiveness

Biogeographic and genetic aspects on the relationship between two endemic Moehringia sp. (Caryophyllaceae) of Provence and Liguria.

This study analyses twoendemic species of the Southwest Italian and French Alps, Moehringia sp. in order to understand the glaciation's effect on speciationevents and or floristic and ecological patterns

Climate change and the future of endemic flora: a case study from the centre of endemism of South Western Alps

Climate change is a major threat to biodiversity, particularly in mountain ecosystems, which are often important centres of endemism. However, climate change effects are mainly studied on widely distributed taxa. Using species distribution model, we assessed the climate change impact on endemic flora of the richest centres of endemism in the Alps: South Western Alps. Assuming realistic dispersal abilities, we projected the species potential distributions (year 2070) using both an optimistic and a pessimistic scenario. Moreover, we explored the differences among vegetation belts and niche properties. Overall, high range loss and low range gain were predicted for all species, determining a strongly negative range change, mainly caused by dispersal limitation. Nevertheless, the predicted extinction rate was low. Mountain and subalpine species resulted more threatened by climate change than colline species, which are already experiencing dry and warm climate. Moreover, the relationship between range loss and niche properties vary among vegetation belts. The lowest range loss was predicted for specialist (termophilous) species in colline belt and for generalist species in mountain and subalpine belts. Altogether, these results suggest that the distribution pattern of this endemic flora will deeply change in the future, despite its overall species composition will be little affected by climate change. Particularly, those species that currently occupy environmental conditions toward which the climate of the study area is expected to move in the future seem less prone to climate change. These result underline the urgency of elaborating conservation strategies focused on mountain and subalpine taxa

Applying a hierarchisation method to a biodiversity hotspot: Challenges and perspectives in the South-Western Alps flora

The South-Western Alps host a great diversity of vascular plants, and especially endemic taxa. Thus, setting up a hierarchisation of patrimonial taxa of this biogeographical territory is needed in order to determine the main conservation concerns of flora. We adapted a hierarchisation method which leans on two criteria representing different kinds of rarity, and a third criterion which incorporates potential threats. This hierarchisation goes further than the objectives assigned to red lists and protection lists because it assesses taxa by taking into account the territorial context, using a standardised method, objective and reproducible. The classification of 913 patrimonial taxa into four concern categories aims to improve the available financial and human resources allocation for conservation measures

Hierarchization of species and prioritization of conservation actions: towards a conservation strategy for flora, from biogeographical to regional level

The Maritime and Ligurian Alps, located at the interface between the Alps Mountains and the Mediterranean region, constitute one of the regional biodiversity hotspots of the Mediterranean basin. Biodiversity hotspots are areas where exceptional concentrations of endemic species undergo exceptional loss of habitat. In fact, with the population increase and tourism boom, many low altitude species are critically threatened of extinction. Refuge areas, containing a great biodiversity, are also threatened by human impacts because they are submitted to important pressures. Many of these endemic species have very restricted distribution areas shared between two countries, France and Italy. Most conservation actions are funded at the national or regional level; however, in most cases this doesn\u2019t match species distribution. Moreover, resources are usually limited and it is not possible to implement conservation actions for all species. This is why a hierarchisation of species and a prioritisation of their conservation actions are required, at both cross-border (or biogeographical) and administrative scales. The considered strategy can be synthesised in four steps: (1) list and hierarchise species; (2) list the different management projects; (3) prioritise management projects; and (4) choose a set of projects to implement. A hierarchisation of species was carried out according to three criteria: biogeographical rarity, local rarity and threats. This last criterion included two sub-criteria, habitat vulnerability and artificialisation. This hierarchisation enabled us to classify species into four conservation concerns: very high, high, medium and low. Then for each very high or high conservation concern species, a management project is assigned according to several criteria. Each project is then assessed in terms of costs, benefits and likelihood of success; which produce the project efficiency. Finally we choose a set of projects to implement, according to their efficiency, but also according to available financial and human resources, legislation, and other contextual factors. This strategy should enable us to head resources towards species which need them the most and towards projects with a high success probabilit

Priority species and sites for plant conservation in the Mediterranean Alps: an example of a cross-border approach

Conservation challenges are particularly important within regional hotspots of biodiversity. This is the case of the south-western Alps (France \u2013 Italy) situated at the interface of the Alpine and Mediterranean ecoregions. A key objective here is to perform practical and biogeographical analyses in order to create a hierarchy of species in terms of their conservation importance, and thus the identification of small but key areas to prevent biodiversity loss. First, we made the rank of 914 species with criteria related to rarity and vulnerability using a standardized repeatable method to define and prioritize conservation actions. Second, we analyzed the spatial patterns of species richness for endemic, threatened, and high conservation priority species. in the dataset. Third, we investigated whether current protected areas include a sufficient proportion of these indicators of species

A strong east–west Mediterranean divergence supports a new phylogeographic history of the carob tree (Ceratonia siliqua, Leguminosae) and multiple domestications from native populations

Aim: Phylogeography of fruit trees is challenging due to recurrent exchanges between domesticated and wild populations. Here we tested the eastern refugium hypothesis (ERH) for the carob tree, Ceratonia siliqua, which supports its natural and domestication origins in the eastern Mediterranean and a feral origin in the west. Location: Mediterranean basin. Taxon: Ceratonia siliqua L., Leguminosae. Methods: A phylogenetic reconstruction based on two nuclear and one plastid sequences was performed to estimate the divergence time between the carob tree and its sister species, Ceratonia oreothauma. Variation from four plastid regions and 17 nuclear microsatellite loci were used to decipher genetic structure in the carob tree and to test coalescent-based models by an Approximate Bayesian computation (ABC) approach. We assessed our hypotheses by examining palaeobotanical records and hindcasting the past distribution of the carob tree at Mid-Holocene, Last Glacial Maximum (LGM) and Last Interglacial (LIG) using species distribution modelling. Results: The split between C. oreothauma and C. siliqua was estimated at 6.4 Ma, and a first divergence within C. siliqua at 1.3 Ma. After a continuous presence since the Oligocene, Ceratonia was rarely found in the fossil record during the Pleistocene but present in the western and the eastern Mediterranean. Plastid and nuclear markers, characterized by low allelic richness, revealed a strong west-east genetic structuring. ABC analyses rejected the ERH. Main conclusions: Our study supports a severe population decline during LIG. The strong west–east divergence and the occurrence of four lineages within C. siliqua provided support for a new hypothesis of multiple domestications of the carob tree from native populations throughout the Mediterranean basin