Alex Baumel

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.

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.

Genetic diversity and structure of a Mediterranean endemic plant in Corsica (Mercurialis corsica, Euphorbiaceae)

The island of Corsica is a Mediterranean hotspot of plant biodiversity characterized by a high rate of plant endemism, but also by a lack of studies combining genetic diversity and conservation. In Corsica, the dioecious and Corso-Sardinian endemic Mercurialis corsica Cosson (Euphorbiaceae) occurs across a wide ecological gradient, but the number of populations have decreased considerably over the last century. The main aim of this study was to examine the patterns of genetic diversity occurring in the Corsican populations of M. corsica, depending on their location and demographic structure. The rDNA sequences did not show the existence of any polymorphism, whereas the cpDNA sequences revealed the divergence of the western Corsican populations. By contrast, when the AFLP markers were examined, although significant levels of differentiation were detected between populations, no distinct geographical patterns were observed except for the pronounced isolation of the Cap Corse genotypes. No significant correlations were found to exist between population size and the genetic diversity indexes used. The results of this study suggest that M. corsica has undergone a complex gene flow history involving past population admixtures, followed by fragmentation processes resulting in population differentiation but no geographical patterns of isolation. These results support the existence of three evolutive conservation units which have to be monitored in priority to determine whether the current pattern of demographic structure is still declining or has stabilized.

Genomic DNA isolation and amplification from callus culture in succulent plants, Carpobrotus species (Aizoaceae)

Genomic DNA of high quality and quantity is needed to analyze genetic diversity with AFLP.Carpobrotus plant species, like most succulents, contain high amounts of polysaccharides and polyphenols, making PCR amplification difficult. Our protocol eliminates contaminants before DNA isolation by using leaf callus as plant material. This simple and inexpensive technique gives an average DNA yield of 1800 ng/g of callus and high reproducible profiles in AFLP. Our results indicate that no genetic variability is associated with callus culture conditions. This technique is suitable for studying genomic polymorphism in succulents and other plants when classic DNA extraction procedures fail.

The polyploid nature of Cenchrus ciliaris L. (Poaceae) has been overlooked: new insights for the conservation and invasion biology of this species – a review

Climate change, associated with increased aridity, and high grazing pressure by livestock results in the scarcity and loss of perennial Poaceae in arid ecosystems. The species threatened by this include Cenchrus ciliaris L., a native perennial grass of the tropical and sub-tropical arid rangelands of Africa and Western Asia and now introduced in Central and South America, and Australia. This species reproduces predominantly through aposporous apomixis although sexual individuals have been occasionally identified. Cenchrus ciliaris is characterised by a significant, heritable, phenotypic polymorphism and three ploidy levels including tetraploids (2n = 4x = 36), pentaploids (2n = 5x = 45) and hexaploids (2n = 6x = 54). Under water-deficit conditions, C. ciliaris shows plasticity in growth characteristics and aboveground biomass. This phenotypic plasticity has led to the identification of genotypic-associated responses conferring more productivity. This underlines the importance of conserving the genetic diversity of C. ciliaris in order to ensure the persistence of the vegetation cover in the arid ecosystems in which it occurs. Observations from cytogenetic and molecular data converge to underline the possibility of sexual reproduction, recombination and gene flow within and between populations of C. ciliaris. Genetic mechanisms, such as polyploidy, hybridisation between ploidy levels and apomixes, are generating and then maintaining the diversity of C. ciliaris. This review emphasises the role of polyploidy in the evolutionary development of C. ciliaris and how it may be a crucial factor for its conservation in some countries and its weedy nature in others.

Phylogenetic diversity and genome sizes of Astragalus (Fabaceae) in the Lebanon biogeographical crossroad

The Lebanese mountain range is an important zone of plant species richness and endemism where the genus Astragalus constitutes a principal component of plant biodiversity. Most of endemic Astragalus taxa, living in mountains and arid zones of Mounts Lebanon and anti-Lebanon, are characterized by a cushion, spiny vegetative form, named “tragacanthic”, which is a remarkable example of vegetative convergence evolution. Because of determination difficulties, taxonomic uncertainties, and discrepancy in the number of taxa listed according to authors, new data are hardly needed to improve systematics of Astragalus and to investigate the role of the Lebanese mountain range as refugia of biodiversity. Before this study only two values on the genome size of Astragalus were reported in the literature and no previous molecular studies had been carried out on Astragalus genus in Lebanon. We examined the utility of rDNA ITS molecular markers to distinguish Astragalus species of Lebanese mountain range and the variation range of their genome size. The main results revealed a striking diversity in Lebanese Astragalus species with the emphasis of a huge variation of genome sizes, an important inter-specific chromosome polymorphism and the existence of a high phylogenetic diversity. The strict endemic species of the Lebanese mountains are positioned throughout the phylogeny. These results confirm that the Lebanon and anti-Lebanon mounts constitute a third diversity center for Astragalus and that high altitude areas are important refugia of plant biodiversity despite centuries of exploitation by humans.

Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat

Positive species–genetic diversity correlations (SGDCs) are often thought to result from the parallel influence of neutral processes on genetic and species diversity. Yet, confounding effects of non‐neutral mechanisms have not been explored. Here, we investigate the impact of non‐neutral genetic diversity on SGDCs in high Andean wetlands. We compare correlations between plant species diversity and genetic diversity (GD) calculated with and without loci potentially under selection (outlier loci). The study system includes 2188 specimens from five species (three common aquatic macroinvertebrate and two dominant plant species) that were genotyped for 396 amplified fragment length polymorphism loci. We also appraise the importance of neutral processes on SGDCs by investigating the influence of habitat fragmentation features. Significant positive SGDCs were detected for all five species (mean SGDC = 0.52 ± 0.05). While only a few outlier loci were detected in each species, they resulted in significant decreases in GD and in SGDCs. This supports the hypothesis that neutral processes drive species–genetic diversity relationships in high Andean wetlands. Unexpectedly, the effects on genetic diversity GD of the habitat fragmentation characteristics in this study increased with the presence of outlier loci in two species. Overall, our results reveal pitfalls in using habitat features to infer processes driving SGDCs and show that a few loci potentially under selection are enough to cause a significant downward bias in SGDC. Investigating confounding effects of outlier loci thus represents a useful approach to evidence the contribution of neutral processes on species–genetic diversity relationships.

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

Current 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.

Habitat Suitability Assessment of the Rare Perennial Plant Armeria Arenaria (Pers.) Schult. (Plumbaginaceae) along the French Mediterranean Coastline

Abstract Baumel, A., S. Youssef, G. Ongamo & F. Médail (2013). Habitat suitability assessment of the rare perennial plant Armeria arenaria (Pers.) (Plumba ginaceae) Schult. along the French Mediterranean coastline. Candollea 68: 221–228. In English, English and French abstracts. A major challenge in conservation biology is to identify the factors driving abundance and demographic regeneration of rare species populations. We assess habitat suitability within a protected area for Armeria arenaria (Pers.) Schult. (Plumbaginaceae), a small perennial polycarpic plant and keystone species of a threatened plant community on the rocky crystalline coastline of South-East France. The factors associated with the occurrence and abundance of adult plants and juveniles of this species were investigated by an “Outlier Mean Index analysis” (OMI). A second census was conducted three years later to test the reliability of inferences about habitat suitability. The results underline the importance of fine scale habitat heterogeneity to understand the variation of abundance. Moreover only a portion of the habitat of Armeria arenaria is suitable for regeneration, underlying the necessity to consider both abundance and regeneration to set conservation and management priorities.