Search

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.

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background and aims - Conserving threatened biodiversity needs a robust knowledge and delineation of the taxonomical entities targeted for in or ex situ conservation. In the genus Armeria (Plumbaginaceae), the frequent correlation between geographical isolation and morphological differentiation led to the delineation of some taxa consisting of few populations. Armeria belgenciensis is a narrow endemic represented by one population in southern France, which recently experienced a strong demographic decline caused by repeated disturbances of its habitat and was the object of a demographic rescue. Within two kilometres of A. belgenciensis, the presence of A. arenaria subsp. peirescii, also represented by one small population, poses the question whether the two populations are genetically isolated and should be considered as separated taxa for conservation. Material and methods - The genetic structure of Armeria belgenciensis and the geographically close populations of Armeria arenaria were analysed based on 328 AFLP markers using model-based and model-free clustering methods. In addition, flowering phenology was estimated to address the possibility of pre-zygotic isolation between A. belgenciensis and A. arenaria subsp. peirescii. Key results - The genetic structure supported a close relationship between A. belgenciensis and A. arenaria subsp. peirescii, compared to other populations of A. arenaria. Despite its recent decline, the genetic diversity of A. belgenciensis was not particularly low compared to the other studied populations or other rare species in this genus. The existence of gene flow between these two populations is likely given their moderate differentiation and the detection of admixture by one of the clustering methods. The phenological study showed that cross-pollination is possible during a short time period. Conclusion - We propose to place these two populations under the name A. belgenciensis, but to keep them as two different management units until there is no evidence of a harmful effect due to small effective sizes. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Rare and vulnerable narrow endemic species represent distinct evolutionary units emerging from various temporal processes, and the preservation of such species is a key issue in biological conservation. Phylogeography has proven to be a relevant tool for distinguishing evolutionary units within species resulting from contrasted biogeographical events, and it can be leveraged to obtain historical and evolutionary perspectives. Yet, despite its usefulness, it is curiously underutilized in plant conservation genetics. Here we provide a comprehensive review of the available case studies on the structure of genetic diversity in the Mediterranean narrow endemic plants (MNEs) of the Mediterranean Basin hotspot. The use of genetic diversity structure for phylogeographical inference and for defining conservation units was examined in eighty-four studies dealing with eighty-three distinct taxa, most of which are perennial herbs occupying a narrow ecological niche. In addition, some 91.5% of the analyzed MNEs are located in the north-western part of the Mediterranean region, and this results in a geographical coverage that is heavily biased. Half of the studied species have moderate to high genetic diversity, and genetic differentiation is geographically structured in 56% of the case studies, indicating that MNEs are not “evolutionary dead-ends,” but rather represent species that have a strong evolutionary legacy. Taken at face value, this would imply conservation planning at the population level. However, it was only a minority of the studies that used these genetic structures to define conservation units. The main insight of the present review is that phylogeography is generally overlooked in conservation genetics. In fact, the design of conservation units has not often been the main goal of these studies, which more commonly is simply to enhance the scope of genetic diversity analyses of rare plants. Nevertheless, the strong phylogeographic structure revealed by several studies of MNEs underlines the relevance of phylogeography. We argue that comparative phylogeography across several co-occurring taxa could greatly improve the proactive conservation planning for threatened endemic plants within biodiversity hotspots. [ABSTRACT FROM AUTHOR]

The simultaneous application of species distribution modelling (SDM) and study of genetic imprints left by range dynamics is appropriate when examining the biogeographical processes that have favoured the survival of plants through past climate changes. Nevertheless, such an approach is rarely performed on the scale of the entire Mediterranean and almost never concerns widespread thermophilous plants. Here, we examine the biogeographical responses of an important Mediterranean shrub, Myrtus communis (Myrtaceae), to severe Quaternary climate conditions. Our analysis combines SDM and phylogeography based on plastid/nuclear DNA sequences and AFLP data. Palaeoclimatic models using MaxEnt and levels of genetic diversity in M. communis are used to infer drastic changes in areas of climatic suitability during the last 130000 years, with a southward range contraction during the Last Glacial Maximum. Modelling of past areas of suitability for M. communis identifies a few relatively small long-term refugia, suggesting that it survived in temporary refugia during glacial periods. Myrtus communis is characterized by a higher genetic diversity and distinctiveness in the southern part of its range, where it was less impacted by glaciations. The structure of genetic diversity reveals stronger range expansions in the western part of the range, whereas migration processes remained much more restricted in the eastern Mediterranean. [ABSTRACT FROM AUTHOR]

The monophyletic Anemone section Anemone (Ranunculaceae) includes predominantly diploid and outbreeding geophytic perennials. A revised taxonomy of the section with 16 species (and some infraspecific taxa) is proposed on the basis of a critical morphological analysis of living populations and extensive herbarium material, together with karyological, cytogenetical and DNA-analytical data. A key, descriptions, figures illustrating some type specimens and differential characters, examples of seedling development and pollen grain micromorphology (scanning electron microscopy) and distribution maps are presented. The position of A. section Anemone within the family is illustrated by a plastid DNA phylogram from sequences of the atpB-rbcL intergenic region. A penalized likelihood approach permitted the approximate dating of the origin and major differentiation phases of the section. The analysis of 20 morphological characters from all species of A. section Anemone with A. blanda ( A. section Tuberosa) as an outgroup resulted in a morphology-based phylogram which supports the recognition of four subsections, i.e. Somalienses (one species, northern Somalia), Anemone (three species, Mediterranean area), Biflorae (five species, South-West and Central Asia) and Carolinianae (seven species, North and South America). These data allow a discussion of the phylogenetic diversification and stepwise expansion of the section since the late Miocene ( c. 9 Mya). Partly by long distance dispersion, section Anemone has developed from a palaeo-Mediterranean ancestor to its present transcontinental distribution. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160, 312–354. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]