In defence of the entity of Macaronesia as a biogeographical region.

Since its coinage ca. 1850 AD by Philip Barker Webb, the biogeographical region of Macaronesia, consisting of the North Atlantic volcanic archipelagos of the Azores, Madeira with the tiny Selvagens, the Canaries and Cabo Verde, and for some authors different continental coastal strips, has been under dispute. Herein, after a brief introduction on the terminology and purpose of regionalism, we recover the origins of the Macaronesia name, concept and geographical adscription, as well as its biogeographical implications and how different authors have positioned themselves, using distinct terrestrial or marine floristic and/or faunistic taxa distributions and relationships for accepting or rejecting the existence of this biogeographical region. Four main issues related to Macaronesia are thoroughly discussed: (i) its independence from the Mediterranean phytogeographical region; (ii) discrepancies according to different taxa analysed; (iii) its geographical limits and the role of the continental enclave(s), and, (iv) the validity of the phytogeographical region level. We conclude that Macaronesia has its own identity and a sound phytogeographical foundation, and that this is mainly based on three different floristic components that are shared by the Macaronesian core (Madeira and the Canaries) and the outermost archipelagos (Azores and Cabo Verde). These floristic components are: (i) the Palaeotropical-Tethyan Geoflora, formerly much more widely distributed in Europe and North Africa and currently restricted to the three northern archipelagos (the Azores, Madeira and the Canaries); (ii) the African Rand Flora, still extant in the coastal margins of Africa and Arabia, and present in the southern archipelagos (Madeira, the Canaries and Cabo Verde), and (iii) the Macaronesian neoendemic floristic component, represented in all the archipelagos, a result of allopatric diversification promoted by isolation of Mediterranean ancestors that manage to colonize Central Macaronesia and, from there, the outer archipelagos. Finally, a differentiating floristic component recently colonized the different archipelagos from the nearest continental coast, providing them with different biogeographic flavours.

Microrefugia and microclimate: Unraveling decoupling potential and resistance to heatwaves.

Microrefugia, defined as small areas maintaining populations of species outside their range margins during environmental extremes, are increasingly recognized for their role in conserving species in the face of climate change. Understanding their microclimatic dynamics becomes crucial with global warming leading to severe temperature and precipitation changes. This study investigates the phenomenon of short-term climatic decoupling within microrefugia and its implications for plant persistence in the Mediterranean region of southeastern France. We focus on microrefugia's ability to climatically disconnect from macroclimatic trends, examining temperature and Vapor Pressure Deficit (VPD) dynamics in microrefugia, adjacent control plots, and weather stations. Our study encompasses both "normal" conditions and heatwave episodes to explore the role of microrefugia as thermal and moisture insulators during extreme events. Landscape attributes such as relative elevation, solar radiation, distance to streams, and vegetation height are investigated for their contribution to short-term decoupling. Our results demonstrate that microrefugia exhibit notable decoupling from macroclimatic trends. This effect is maintained during heatwaves, underscoring microrefugia's vital role in responding to climatic extremes. Importantly, microrefugia maintain lower VPD levels than their surroundings outside and during heatwaves, potentially mitigating water stress for plants. This study advances our understanding of microclimate dynamics within microrefugia and underscores their ecological importance for plant persistence in a changing climate. As heatwaves become more frequent and severe, our findings provide insights into the role of microrefugia in buffering but also decoupling against extreme climatic events and, more generally, against climate warming. This knowledge emphasizes the need to detect and protect existing microrefugia, as they can be integrated into conservation strategies and climate change adaptation plans.

Tree biodiversity of warm drylands is likely to decline in a drier world.

Warm drylands represent 19% of land surfaces worldwide and host ca. 1100 tree species. The risk of decline due to climate aridification of this neglected biodiversity has been overlooked despite its ecological and societal importance. To fill this gap, we assessed the risk of decline due to climate aridification of tree species in warm drylands based on spatialized occurrence data and climate models. We considered both species vulnerability and exposure, compared the risk of tree species decline across five bioregions and searched for phylogenetic correlates. Depending on the future climate model, from 44% to 88% of warm drylands' tree species will undergo climate aridification with a high risk of decline even under the most optimistic conditions. On a regional scale, the rate of species that will undergo climate aridification in the future varies from 21% in the Old World North, to 90% in Australia, with a risk of decline confirming the high level of risk predicted at the global scale. Using generalized linear mixed models, we found that, species more exposed to climate aridification will be more at risk, but also that species vulnerability is a key driver of their risk of decline. Indeed, the warm drylands specialist species will be less at risk due to climate aridification than species being marginal in warm drylands. We also found that the risk of decline is widespread across the main clades of the phylogeny and involves several evolutionary distinct species. Estimating a high risk of decline for numerous tree species in all warm drylands, including emblematic dryland endemics, our work warns that future increase in aridity could result in an extensive erosion of tree biodiversity in these ecosystems.

Genomic, spatial and morphometric data for discrimination of four species in the Mediterranean Tamus clade of yams (Dioscorea, Dioscoreaceae).

BACKGROUND AND AIMS: Among the numerous pantropical species of the yam genus, Dioscorea, only a small group occurs in the Mediterranean basin, including two narrow Pyrenean endemics (Borderea clade) and two Mediterranean-wide species (D. communis and D. orientalis, Tamus clade). However, several currently unrecognized species and infraspecific taxa have been described in the Tamus clade due to significant morphological variation associated with D. communis. Our overarching aim was to investigate taxon delimitation in the Tamus clade using an integrative approach combining phylogenomic, spatial and morphological data. METHODS: We analysed 76 herbarium samples using Hyb-Seq genomic capture to sequence 260 low-copy nuclear genes and plastomes, together with morphometric and environmental modelling approaches. KEY RESULTS: Phylogenomic reconstructions confirmed that the two previously accepted species of the Tamus clade, D. communis and D. orientalis, are monophyletic and form sister clades. Three subclades showing distinctive geographic patterns were identified within D. communis. These subclades were also identifiable from morphometric and climatic data, and introgression patterns were inferred between subclades in the eastern part of the distribution of D. communis. CONCLUSIONS: We propose a taxonomy that maintains D. orientalis, endemic to the eastern Mediterranean region, and splits D. communis sensu lato into three species: D. edulis, endemic to Macaronesia (Canary Islands and Madeira); D. cretica, endemic to the eastern Mediterranean region; and D. communis sensu stricto, widespread across western and central Europe. Introgression inferred between D. communis s.s. and D. cretica is likely to be explained by their relatively recent speciation at the end of the Miocene, disjunct isolation in eastern and western Mediterranean glacial refugia and a subsequent westward recolonization of D. communis s.s. Our study shows that the use of integrated genomic, spatial and morphological approaches allows a more robust definition of species boundaries and the identification of species that previous systematic studies failed to uncover.

Bridging the gap between microclimate and microrefugia: A bottom-up approach reveals strong climatic and biological offsets.

In the context of global warming, a clear understanding of microrefugia-microsites enabling the survival of species populations outside their main range limits-is crucial. Several studies have identified forcing factors that are thought to favor the existence of microrefugia. However, there is a lack of evidence to conclude whether, and to what extent, the climate encountered within existing microrefugia differs from the surrounding climate. To investigate this, we adopt a "bottom-up" approach, linking marginal disconnected populations to microclimate. We used the southernmost disconnected and abyssal populations of the circumboreal herbaceous plant Oxalis acetosella in Southern France to study whether populations in sites matching the definition of "microrefugia" occur in particularly favorable climatic conditions compared to neighboring control plots located at distances of between 50 to 100 m. Temperatures were recorded in putative microrefugia and in neighboring plots for approximately 2 years to quantify their thermal offsets. Vascular plant inventories were carried out to test whether plant communities also reflect microclimatic offsets. We found that current microclimatic dynamics are genuinely at stake in microrefugia. Microrefugia climates are systematically colder compared to those found in neighboring control plots. This pattern was more noticeable during the summer months. Abyssal populations showed stronger offsets compared to neighboring plots than the putative microrefugia occurring at higher altitudes. Plant communities demonstrate this strong spatial climatic variability, even at such a microscale approach, as species compositions systematically differed between the two plots, with species more adapted to colder and moister conditions in microrefugia compared to the surrounding area.

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.

When ecological marginality is not geographically peripheral: exploring genetic predictions of the centre-periphery hypothesis in the endemic plant Lilium pomponium.

BACKGROUND: Quantifying variation of genetic traits over the geographical range of species is crucial for understanding the factors driving their range dynamics. The center-periphery hypothesis postulates, and many studies support, the idea that genetic diversity decreases and genetic differentiation increases toward the geographical periphery due to population isolation. The effects of environmental marginality on genetic variation has however received much less attention. METHODS: We tested the concordance between geographical and environmental gradients and the genetic predictions of center-periphery hypothesis for endemic Lilium pomponium in the southern Alps. RESULTS: We found little evidence for concordance between genetic variation and both geographical and environmental gradients. Although the prediction of increased differentiation at range limits is met, genetic diversity does not decrease towards the geographical periphery. Increased differentiation among peripheral populations, that are not ecologically marginal, may be explained by a decrease in habitat availability that reduces population connectivity. In contrast, a decrease of genetic diversity along environmental but not geographical gradients may be due to the presence of low quality habitats in the different parts of the range of a species that reduce effective population size or increase environmental constraints. As a result, environmental factors may affect population dynamics irrespective of distance from the geographical center of the range. In such situations of discordance between geographical and environmental gradients, the predictions of decreasing genetic diversity and increasing differentiation toward the geographical periphery may not be respected.

WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees.

Trees play a key role in the structure and function of many ecosystems worldwide. In the Mediterranean Basin, forests cover approximately 22% of the total land area hosting a large number of endemics (46 species). Despite its particularities and vulnerability, the biodiversity of Mediterranean trees is not well known at the taxonomic, spatial, functional, and genetic levels required for conservation applications. The WOODIV database fills this gap by providing reliable occurrences, four functional traits (plant height, seed mass, wood density, and specific leaf area), and sequences from three DNA-regions (rbcL, matK, and trnH-psbA), together with modelled occurrences and a phylogeny for all 210 Euro-Mediterranean tree species. We compiled, homogenized, and verified occurrence data from sparse datasets and collated them on an INSPIRE-compliant 10 × 10 km grid. We also gathered functional trait and genetic data, filling existing gaps where possible. The WOODIV database can benefit macroecological studies in the fields of conservation, biogeography, and community ecology.

Effects of environmental heterogeneity on phenotypic variation of the endemic plant Lilium pomponium in the Maritime and Ligurian Alps.

Geographical limits of species' distributions are assumed to be coincident with ecological margins, although this assumption might not always be true. Indeed, harsh environments such as Alpine and Mediterranean ecosystems may favour high phenotypic variability among populations, especially those in peripheral sites. Floral traits are often found to be less variable and less affected by environmental heterogeneity than vegetative traits because variation in the former may have negative effects on fitness. For this reason, it is important to quantify variation in floral traits and plant fecundity in study range limits. The objective of the study is to examine phenotypic variation and differences in reproduction in endemic Lilium pomponium in the Maritime and Ligurian Alps in relation to environmental variation across its distribution range. In this species, marginal climatic populations occur both in the peripheral and central geographical locations of the distribution range; hence, geographical and ecological gradients are not concordant. Floral trait variation is related to local environmental conditions with an array of interactions among resource availability, potential pollen limitation and population size that are differentially related to floral traits. Contrary to the general expectation, all central and peripheral populations had similar, moderate seed production with each group limited by different factors acting on different stages of the life-history strategy. Our results are in line with the idea that general expectations are confirmed only when its assumptions are met and that the differences in pollination environment along an environmental gradient may not be the main determinant of the distribution limit.

Recent Anthropogenic Plant Extinctions Differ in Biodiversity Hotspots and Coldspots.

During the Anthropocene, humans are changing the Earth system in ways that will be detectable for millennia to come [1]. Biologically, these changes include habitat destruction, biotic homogenization, increased species invasions, and accelerated extinctions [2]. Contemporary extinction rates far surpass background rates [3], but they seem remarkably low in plants [4, 5]. However, biodiversity is not evenly distributed, and as a result, extinction rates may vary among regions. Some authors have contentiously argued that novel anthropic habitats and human-induced plant speciation can actually increase regional biodiversity [6, 7]. Here, we report on one of the most comprehensive datasets to date, including regional and global plant extinctions in both biodiversity hotspots (mostly from Mediterranean-type climate regions) and coldspots (mostly from Eurasian countries). Our data come from regions covering 15.3% of the Earth's surface and span over 300 years. With this dataset, we explore the trends, causes, and temporal dynamics of recent plant extinctions. We found more, and faster accrual of, absolute numbers of extinction events in biodiversity hotspots compared to coldspots. Extinction rates were also substantially higher than historical background rates, but recent declines are evident. We found higher levels of taxonomic uniqueness being lost in biodiversity coldspots compared to hotspots. Causes of plant extinctions also showed distinct temporal patterns, with agriculture, invasions, and urbanization being significant drivers in hotspots, while hydrological disturbance was an important driver in coldspots. Overall, plant extinctions over the last three centuries appear to be low, with a recent (post-1990) and steady extinction rate of 1.26 extinctions/year.

Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae).

PREMISE OF THE STUDY: Simple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected. METHODS: In this study, we implemented a next-generation sequencing-based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, Ceratonia siliqua. Our aim was to evaluate the effect of three different methods of scoring molecular variation present within microsatellite markers on the genetic diversity and structure results. RESULTS: The analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single-nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates. DISCUSSION: Next-generation sequencing allows the detection and scoring of SSRs, single-nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies.

Geographical isolation caused the diversification of the Mediterranean thorny cushion-like Astragalus L. sect. Tragacantha DC. (Fabaceae).

Understanding the origin and evolution of Mediterranean vascular flora within the long-term context of climate change requires a continuous study of historical biogeography supported by molecular phylogenetic approaches. Here we provide new insights into the fascinating but often overlooked diversification of Mediterranean xerophytic plants. Growing in some of the most stressing Mediterranean environments, i.e. coastal and mountainous opened habitats, the circum-Mediterranean Astragalus L. sect. Tragacantha DC. (Fabaceae) gathers several thorny cushion-like taxa. These have been the subjects of recent taxonomical studies, but they have not yet been investigated within a comprehensive molecular framework. Bayesian phylogenetics applied to rDNA ITS sequences reveal that the diversification of A. sect. Tragacantha has roots dating back to the Pliocene, and the same data also indicate an eastern-western split giving rise to the five main lineages that exist today. In addition, AFLP fingerprinting supports an old east-west pattern of vicariance that completely rules out the possibility of a recent eastern origin for western taxa. The observed network of genetic relationships implies that contrary to what is widely claimed in the taxonomic literature, it is range fragmentation, as opposed to a coastal-to-mountain ecological shift, that is likely the main driver of diversification.

Eradications as scientific experiments: progress in simultaneous eradications of two major invasive taxa from a Mediterranean island.

BACKGROUND: Black rats, Rattus rattus, and mat-forming iceplants, Carpobrotus aff. acinaciformis and Carpobrotus edulis, are pervasive pests on Mediterranean islands. Their cumulative impacts on native biotas alter the functioning of island ecosystems and threaten biodiversity. A report is given here of the first attempt to eradicate both taxa from a protected nature reserve in south-eastern France (Bagaud Island). In order to minimise unwanted hazardous outcomes and produce scientific knowledge, the operations were embedded in a four-step strategy including initial site assessment, planning, restoration and monitoring. RESULTS: Trapping, which resulted in the removal of 1923 rats in 21 045 trap-nights, made it possible to eliminate a substantial proportion of the resident rat population and to reduce the amount of rodenticide delivered in the second stage of the operation. Forty tons of Carpobrotus spp. were manually uprooted from a total area of 18 000 m(2) ; yet careful monitoring over a decade is still required to prevent germinations from the seed bank. CONCLUSION: Two years after the beginning of the interventions, both eradication operations are still ongoing. Biosecurity measures have been implemented to reduce reinvasion risks of both taxa. With the long-term monitoring of various native plants and animals, Bagaud Island will become a reference study site for scientific purposes.

Surviving in mountain climate refugia: new insights from the genetic diversity and structure of the relict shrub Myrtus nivellei (Myrtaceae) in the Sahara Desert.

The identification of past glacial refugia has become a key topic for conservation under environmental change, since they contribute importantly to shaping current patterns of biodiversity. However, little attention has been paid so far to interglacial refugia despite their key role for the survival of relict species currently occurring in climate refugia. Here, we focus on the genetic consequences of range contraction on the relict populations of the evergreen shrub Myrtus nivellei, endemic in the Saharan mountains since at least the end of the last Green Sahara period, around 5.5 ka B.P. Multilocus genotypes (nuclear microsatellites and AFLP) were obtained from 215 individuals collected from 23 wadis (temporary rivers) in the three main mountain ranges in southern Algeria (the Hoggar, Tassili n'Ajjer and Tassili n'Immidir ranges). Identical genotypes were found in several plants growing far apart within the same wadis, a pattern taken as evidence of clonality. Multivariate analyses and Bayesian clustering revealed that genetic diversity was mainly structured among the mountain ranges, while low isolation by distance was observed within each mountain range. The range contraction induced by the last episode of aridification has likely increased the genetic isolation of the populations of M. nivellei, without greatly affecting the genetic diversity of the species as a whole. The pattern of genetic diversity observed here suggests that high connectivity may have prevailed during humid periods, which is consistent with recent paleoenvironmental reconstructions.

Phylogeography sheds light on the central-marginal hypothesis in a Mediterranean narrow endemic plant.

BACKGROUND AND AIMS: Understanding the factors that shape variation in genetic diversity across the geographic ranges of species is an important challenge in the effort to conserve evolutionary processes sustaining biodiversity. The historical influences leading to a central-marginal organization of genetic diversity have been explored for species whose range is known to have expanded from refugia after glacial events. However, this question has rarely been addressed for Mediterranean endemic plants of azonal habitats such as rocky slopes or screes. In this context, this comprehensive study examined molecular and field data from Arenaria provincialis (Caryophyllaceae), a narrow endemic plant of south-eastern France. METHODS: Across the whole geographic range, an investigation was made of whether high levels of abundance and genetic diversity (estimated from amplified fragment length polymorphism markers) are centrally distributed, to evaluate the relevance of the central-marginal hypothesis. Phylogeographic patterns inferred from chloroplast DNA (cpDNA) were used, applying Bayesian methods to test the influence of past biogeographic events. Multivariate analysis combining phylogeographic and ecological data was used to reveal the historical and ecological distinctiveness of populations. KEY RESULTS: Despite the narrow distribution of A. provincialis, a high level of nucleotide variation is found within cpDNA loci, supporting its persistence throughout the Pleistocene period. The area characterized by the highest genetic diversity is centrally located. Structured phylogeography and Bayesian factor analysis supported the hypothesis that the central area of the distribution was the source of both westward and eastward migrations, probably during arid periods of the Pleistocene, and more recently was a crossroads of backward migrations. By contrast, the two areas located today at the range limits are younger, have reduced genetic diversity and are marginal in the ecological gradients. CONCLUSIONS: This study highlights a case of strong population distinctiveness within a narrow range. Phylogeography sheds light on the historical role of the areas centrally situated in the distribution. The current range size and abundance patterns are not sufficient to predict the organization of genetic diversity.

Unexpected morphological and karyological changes in invasive Carpobrotus (Aizoaceae) in Provence (S-E France) compared to native South African species.

Hybridization processes can lead to evolutionary changes, particularly in co-introduced congeneric plant species, such as Carpobrotus spp. which are recognized as invasive in Mediterranean climate regions. Morphological and karyological comparisons have therefore been made between native Carpobrotus edulis and C. acinaciformis in South Africa and their invasive counterparts in Provence (C. edulis and C. aff. acinaciformis). Morphological data exhibited the most significant differences in invasive C. aff. acinaciformis that forms a new phenotypic variant. Unexpected chromosomal restructuring has been highlighted for both taxa in Provence, with in particular a clear decrease in asymmetry, an increase in the intraspecific variability, and an interspecific convergence of karyotypes. These changes suggest a drift that has facilitated various crosses, and has been amplified through hybridization/introgression. Furthermore, several morphological and karyological transgressive characters have been found in the two invasive taxa. These results stress the important role and the rapidity of karyological changes in invasive processes.

The origins of the domestication of the olive tree.

The present diversity of the olive (crop) and oleaster (wild) tree was investigated with nuclear and cytoplasm markers. Patterns of diversity of the wild form inferred eleven ancestral populations in the East and the West of the Mediterranean basin. Patterns of diversity for cultivars are less clear, but we showed that cultivars admixed to nine groups that corresponded to oleaster ancestral populations. We inferred that nine domestication events took place in the olive, but these origins were blurred by gene flow from oleaster and by human displacements. These origins of domestication probably reflected different reasons and uses to domesticate the oleaster.

Fire as a control agent of demographic structure and plant performance of a rare Mediterranean endemic geophyte.

We examine the effects of fire and/or surrounding vegetation cover on demographic stage densities and plant performance for a rare endemic geophyte, Acis nicaeensis (Alliaceae), in Mediterranean xerophytic grasslands of the 'Alpes-Maritimes' French 'département', through sampling plots in unburned and burned treatments. Fire increases density of flowering individuals and seedling emergence, as well as clump densities and number of individuals per clump, per limiting vegetation height and cover, and increasing bare soil cover. In contrast, fire has no effect on reproductive success. Nevertheless, two growing seasons after fire, all parameters of demographic stages and plant performance do not significantly differ between the two treatments. Small-scale fire is beneficial for the regeneration of this threatened geophyte at a short-time scale. In this context, a conservation planning with small and controlled fires could maintain the regeneration window for populations of rare Mediterranean geophytes.