Allopolyploidy: An Underestimated Driver in Juniperus Evolution.

Allopolyploidy is considered as a principal driver that shaped angiosperms' evolution in terms of diversification and speciation. Despite the unexpected high frequency of polyploidy that was recently discovered in the coniferous genus Juniperus, little is known about the origin of these polyploid taxa. Here, we conducted the first study devoted to deciphering the origin of the only hexaploid taxon in Juniperus along with four of its closely related tetraploid taxa using AFLP markers with four primers combinations. Phylogenetic analysis revealed that the 10 studied species belong to 2 major clusters. J. foetidissima appeared to be more related to J. thurifera, J. sabina, and J. chinensis. The Bayesian clustering analysis showing a slight variation in genetic admixture between the studied populations of J. foetidissima, suggesting an allopolyploid origin of this species involving J. thurifera and J. sabina lineages, although a purely autopolyploidy origin of both J. thurifera and J. foetidissima cannot be ruled out. The admixed genetic pattern revealed for J. seravschanica showed that the tetraploid cytotypes of this species originated from allopolyploidy, whereas no clear evidence of hybridization in the origin of the tetraploid J. thurifera and J. chinensis was detected. This study provides first insights into the polyploidy origin of the Sabina section and highlights the potential implication of allopolyploidy in the evolution of the genus Juniperus. Further analyses are needed for a more in-depth understanding of the evolutionary scenarios that produced the observed genetic patterns.

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.

Intracellular reactive oxygen species trafficking participates in seed dormancy alleviation in Arabidopsis seeds.

Reactive oxygen species (ROS) release seed dormancy through an unknown mechanism. We used different seed dormancy-breaking treatments to decipher the dynamics and localization of ROS production during seed germination. We studied the involvement of ROS in the breaking of Arabidopsis seed dormancy by cold stratification, gibberellic acid (GA3 ) and light. We characterized the effects of these treatments on abscisic acid and gibberellins biosynthesis and signalling pathways. ROS, mitochondrial redox status and peroxisomes were visualized and/or quantified during seed imbibition. Finally, we performed a cytogenetic characterization of the nuclei from the embryonic axes during seed germination. We show that mitochondria participate in the early ROS production during seed imbibition and that a possible involvement of peroxisomes in later stages should still be analysed. At the time of radicle protrusion, ROS accumulated within the nucleus, which correlated with nuclear expansion and chromatin decompaction. Taken together, our results provide evidence of the role of ROS trafficking between organelles and of the nuclear redox status in the regulation of seed germination by dormancy.

Tapping into non-English-language science for the conservation of global biodiversity.

The widely held assumption that any important scientific information would be available in English underlies the underuse of non-English-language science across disciplines. However, non-English-language science is expected to bring unique and valuable scientific information, especially in disciplines where the evidence is patchy, and for emergent issues where synthesising available evidence is an urgent challenge. Yet such contribution of non-English-language science to scientific communities and the application of science is rarely quantified. Here, we show that non-English-language studies provide crucial evidence for informing global biodiversity conservation. By screening 419,679 peer-reviewed papers in 16 languages, we identified 1,234 non-English-language studies providing evidence on the effectiveness of biodiversity conservation interventions, compared to 4,412 English-language studies identified with the same criteria. Relevant non-English-language studies are being published at an increasing rate in 6 out of the 12 languages where there were a sufficient number of relevant studies. Incorporating non-English-language studies can expand the geographical coverage (i.e., the number of 2° × 2° grid cells with relevant studies) of English-language evidence by 12% to 25%, especially in biodiverse regions, and taxonomic coverage (i.e., the number of species covered by the relevant studies) by 5% to 32%, although they do tend to be based on less robust study designs. Our results show that synthesising non-English-language studies is key to overcoming the widespread lack of local, context-dependent evidence and facilitating evidence-based conservation globally. We urge wider disciplines to rigorously reassess the untapped potential of non-English-language science in informing decisions to address other global challenges. Please see the Supporting information files for Alternative Language Abstracts.

First mitochondrial genome of the Caucasian squirrel Sciurus anomalus (Rodentia, Sciuridae).

The Caucasian Squirrel, Sciurus anomalus, is the only representative of the Sciuridae family in the Eastern Mediterranean region. In this study, the mitochondrial genome of the Sciurus anomalus species was generated, and we investigate its phylogenetic position within the Sciuridae family. The generated mitogenome sequence is 16,234 bp. It is composed of a control region and a conserved set of 37 genes containing 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes.

First mitochondrial genome of the marbled polecat Vormela peregusna (Carnivora, Mustelidae).

The marbled polecat, Vormela peregusna, is one of the least studied species in the Mustelidae family, especially with regard to phylogeography and genetic diversity. In this study, we determined the mitochondrial genome sequence of V. peregusna and investigated its position within the Mustelidae phylogeny. The generated mitogenome is 15,982 bp in length; it consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region.

First mitochondrial genome of the Egyptian mongoose Herpestes ichneumon (Carnivora, Herpestidae).

The Egyptian mongoose, Herpestes ichneumon, is the only extant mongoose in Europe, with populations still distributed in Africa and the Middle East. In this study, we present the first mitochondrial genome sequence of Herpestes ichneumon and we investigate its phylogenetic position within Feliformia suborder. The resultant mitogenome sequence is 16,775 bps, composed of a conserved set of 37 genes containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Our results represent a valuable resource for further phylogeographical studies.

First DNA sequence reference library for mammals and plants of the Eastern Mediterranean Region.

The Mediterranean region is identified as one of the world's 36 biodiversity hotspots, with the Earth's most biologically rich yet threatened areas. Lebanon is a hub for Eastern Mediterranean Region (EMR) biodiversity with 9116 characterized plant and animal species (4486 fauna and 4630 flora). Using DNA barcoding as a tool has become crucial in the accurate identification of species in multiple contexts. It can also complement species morphological descriptions, which will add to our understanding of the biodiversity and richness of ecosystems and benefit conservation projects for endangered and endemic species. In this study, we create the first reference library of standard DNA markers for mammals and plants in the EMR, with a focus on endemic and endangered species. Plant leaves were collected from different nature reserves in Mount Lebanon, and mammal samples were obtained from taxidermized museum specimens or road kills. We generated the 12S rRNA sequences of 18 mammal species from 6 orders and 13 different families. We also obtained the trnL and rbcL barcode sequences of 52 plant species from 24 different families. Twenty-five plant species and two mammal species included in this study were sequenced for the first time using these markers.

Polyploidy in the Conifer Genus Juniperus: An Unexpectedly High Rate.

Recent research suggests that the frequency of polyploidy may have been underestimated in gymnosperms. One notable example is in the conifer genus Juniperus, where there are already a few reports of polyploids although data are still missing for most species. In this study, we evaluated the extent of polyploidy in Juniperus by conducting the first comprehensive screen across nearly all of the genus. Genome size data from fresh material, together with chromosome counts, were used to demonstrate that genome sizes estimated from dried material could be used as reliable proxies to uncover the extent of ploidy diversity across the genus. Our analysis revealed that 16 Juniperus taxa were polyploid, with tetraploids and one hexaploid being reported. Furthermore, by analyzing the genome size and chromosome data within a phylogenetic framework we provide the first evidence of possible lineage-specific polyploidizations within the genus. Genome downsizing following polyploidization is moderate, suggesting limited genome restructuring. This study highlights the importance of polyploidy in Juniperus, making it the first conifer genus and only the second genus in gymnosperms where polyploidy is frequent. In this sense, Juniperus represents an interesting model for investigating the genomic and ecological consequences of polyploidy in conifers.

Identification and prioritization of areas with high environmental risk in Mediterranean coastal areas: A flexible approach.

Interdisciplinarity and transdisciplinarity are the cornerstone for the future management of coastal ecosystems with many vulnerability and hazard indexes developed for this purpose, especially in the engineering literature, but with limited studies that considered ecological implications within a risk assessment. Similarly, the concept of prioritization of sites has been widely examined in biodiversity conservation studies, but only recently as an instrument for territory management. Considering coastal plant diversity at the species and community levels, and their vulnerability to three main potential hazards threatening coastal areas (oil spills, Hazardous and Noxious Substances pollution, fragmentation of natural habitats), the objective of this paper is to define an easy-to-use approach to locate and prioritize the areas more susceptible to those stressors, in order to have a practical instrument for risk management in the ordinary and extra-ordinary management of the coastline. The procedure has been applied at pilot areas in four Mediterranean countries (Italy, France, Lebanon and Tunisia). This approach can provide policy planners, decision makers and local communities an easy-to-use instrument able to facilitate the implementation of the ICZM (Integrated Coastal Zone Management) process in their territory.

Unlocking the Karyological and Cytogenetic Diversity of Iris from Lebanon: Oncocyclus Section Shows a Distinctive Profile and Relative Stasis during Its Continental Radiation.

Despite being an important target of conservation concern and horticultural interest, Lebanese irises yet have a confusing taxonomic history and species' delimitation is often considered problematic, more especially among royal irises (Iris section Oncocyclus). Indeed, these irises of exceptionally large and spectacular flowers have radiated across Caucasus and eastern Mediterranean giving rise to a number of strict endemic taxa, many of them being considered under threat. Whilst efforts have mostly focused on clarifying the evolutionary relationships in the group based on morphological and molecular data, karyological and cytogenetic characters have been comparatively overlooked. In this study, we established for the first time the physical mapping of 35S rDNA loci and heterochromatin, and obtained karyo-morphological data for ten Lebanese Iris species belonging to four sections (Iris, Limniris, Oncocyclus and Scorpiris). Our results evidenced distinctive genomic profiles for each one of the sections, where Oncocyclus irises, while having the lowest chromosome numbers, exhibit both the highest number of 35S loci and CMA3+ sites. The continental radiation of royal irises has been accompanied by a relative karyological and cytogenetic stasis, even though some changes were observed regarding karyotype formula and asymmetry indexes. In addition to that, our results enabled taxonomic differentiation between I. germanica and I. mesopotamica-two taxa currently considered as synonyms-and highlighted the need for further studies on populations of I. persica and I. wallasiae in the Eastern Mediterranean Region.

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.

Morphological versus molecular markers to describe variability in Juniperus excelsa subsp. excelsa (Cupressaceae).

BACKGROUND AND AIMS: Juniperus excelsa M.-Bieb. is a major forest element in the mountains of the eastern part of Mediterranean and sub-Mediterranean regions. This study comprises the first morphological investigation covering a large part of the geographical range of J. excelsa and aims to verify the congruency between the morphological results and molecular results of a previous study. METHODOLOGY: We studied 14 populations sampled from Greece, Cyprus, Ukraine, Turkey and Lebanon, 11 of which have previously been investigated using molecular markers. Three hundred and ninety-four individuals of J. excelsa were examined using nine biometric features characterizing cones, seeds and shoots, and eight derived ratios. Statistical analyses were conducted in order to evaluate the intra- and inter-population morphological variability. PRINCIPAL RESULTS: The level of intra-population variability observed did not show any geographical trends. The total variation mostly depended on the ratios of cone diameter/seed width and seed width/seed length. The discrimination analysis, the Ward agglomeration method and barrier analysis results showed a separation of the sampled populations into three main clusters. These results confirmed, in part, the geographical differentiation revealed by molecular markers with a lower level of differentiation and a less clear geographical pattern. The most differentiated populations using both markers corresponded to old, isolated populations in the high altitudes of Lebanon (>2000 m). Moreover, a separation of the northern Turkish population from the southern Turkish populations was observed using both markers. CONCLUSIONS: Morphological variation together with genetic and biogeographic studies make an effective tool for detecting relict plant populations and also populations subjected to more intensive selection.

High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region.

BACKGROUND AND AIMS: Juniperus excelsa is an important woody species in the high mountain ecosystems of the eastern Mediterranean Basin where it constitutes the only coniferous species found at the tree line. The genetic diversity within and among J. excelsa populations of the eastern Mediterranean Basin is studied in the light of their historical fragmentation. METHODOLOGY: Nuclear microsatellites originally developed for Juniperus communis and J. przewalskii were tested on 320 individuals from 12 different populations originating from Lebanon, Turkey, Cyprus, Greece and the Ukraine. PRINCIPAL RESULTS: Among the 31 nuclear microsatellite primers tested, only three produced specific amplification products, with orthology confirmed by sequence analysis. They were then used for genetic diversity studies. The mean number of alleles and the expected heterozygosity means were N(a)=8.78 and H(e)=0.76, respectively. The fixation index showed a significant deviation from Hardy-Weinberg equilibrium and an excess of homozygotes (F(IS)=0.27-0.56). A moderate level of genetic differentiation was observed among the populations (F(ST)=0.075, P<0.001). The most differentiated populations corresponded to old vestigial stands found at the tree line (>2000 m) in Lebanon. These populations were differentiated from the other populations that are grouped into three sub-clusters. CONCLUSIONS: High levels of genetic diversity were observed at species and population levels. The high level of differentiation in the high-mountain Lebanese populations reflects a long period of isolation or possibly a different origin. The admixture observed in other populations from Lebanon suggests a more recent separation from the Turkish-southeastern European populations.