Genomic-Guided Conservation Actions to Restore the Most Endangered Conifer in the Mediterranean Basin.

Species with extremely small population sizes are critically endangered because of reduced genetic diversity, increased inbreeding and hybridisation threats. Genomic tools significantly advance conservation by revealing genetic insights into endangered species, notably in monitoring frameworks. Sicilian fir (Abies nebrodensis) is the most endangered conifer in Europe with only 30 adult trees in an 84-ha area.

Long-term methylome changes after experimental seed demethylation and their interaction with recurrent water stress in Erodium cicutarium (Geraniaceae).

The frequencies and lengths of drought periods are increasing in subtropical and temperate regions worldwide. Epigenetic responses to water stress could be key for plant resilience to these largely unpredictable challenges. Experimental DNA demethylation, together with application of a stress factor is an appropriate strategy to reveal the contribution of epigenetics to plant responses to stress.

Physiology, gene expression, and epiphenotype of two Dianthus broteri polyploid cytotypes under temperature stress.

Increasing evidence supports a major role for abiotic stress response in the success of plant polyploids, which usually thrive in harsh environments. However, understanding the ecophysiology of polyploids is challenging due to interactions between genome doubling and natural selection. Here, we investigated physiological responses, gene expression, and the epiphenotype of two related Dianthus broteri cytotypes-with different genome duplications (4× and 12×) and evolutionary trajectories-to short extreme temperature events (42/28 °C and 9/5 °C).

Recurrent allopolyploidizations diversify ecophysiological traits in marsh orchids (Dactylorhiza majalis s.l.).

Whole-genome duplication has shaped the evolution of angiosperms and other organisms, and is important for many crops. Structural reorganization of chromosomes and repatterning of gene expression are frequently observed in allopolyploids, with physiological and ecological consequences. Recurrent origins from different parental populations are widespread among polyploids, resulting in an array of lineages that provide excellent models to uncover mechanisms of adaptation to divergent environments in early phases of polyploid evolution.

Spatially explicit assessment of genetic variation to inform conservation effort for an endangered Mediterranean conifer, .

Preserving the genetic diversity of forest species is critical for maintaining their adaptive potential and allowing for generation turnover in forest ecosystems. Considering an uncertain future, it is necessary to establish reliable genetic conservation strategies to optimize the genetic variation preserved within populations in a spatially explicit context to assist decision-makers. Hence, we aimed to incorporate genetic information into spatially designed conservation actions.

Evaluation of Reference Genes in the Polyploid Complex (Caryophyllaceae) Using qPCR.

is an endemic complex which is considered the largest polyploid series within the Dianthus genus. This polyploid species involves four cytotypes (2×, 4×, 6× and 12×) with spatial and ecological segregation. The study of gene expression in polyploid species must be very rigorous because of the effects of duplications on gene regulation.

Phenotypic diploidization in plant functional traits uncovered by synthetic neopolyploids in Dianthus broteri.

Whole-genome duplication and post-polyploidization genome downsizing play key roles in the evolution of land plants; however, the impact of genomic diploidization on functional traits still remains poorly understood. Using Dianthus broteri as a model, we compared the ecophysiological behaviour of colchicine-induced neotetraploids (4xNeo) to diploids (2x) and naturally occurring tetraploids (4xNat). Leaf gas-exchange and chlorophyll fluorescence analyses were performed in order to asses to what extent post-polyploidization evolutionary processes have affected 4xNat.

Plant Volatile Organic Compounds Evolution: Transcriptional Regulation, Epigenetics and Polyploidy.

Volatile organic compounds (VOCs) are emitted by plants as a consequence of their interaction with biotic and abiotic factors, and have a very important role in plant evolution. Floral VOCs are often involved in defense and pollinator attraction. These interactions often change rapidly over time, so a quick response to those changes is required.

Diving in uncharted waters: An updated genetics toolkit highlights the challenges of polyploidy in landscape genomics analyses.

As molecular ecologists, we have by necessity become adept at working across computational platforms. A diverse community of scientists has developed a broad array of analytical resources spanning command line to graphical user interface across Linux, Mac, and Windows environments and a dizzying array of program-specific input formats. In light of this, we often explore our data like free divers - filling our lungs with air and descending for a short period of time into one part of our data set before resurfacing, reformatting, and preparing for our next analysis.

Early diversification and permeable species boundaries in the Mediterranean firs.

Background And Aims: Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate.

Methods: We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status.

Niche divergence and limits to expansion in the high polyploid Dianthus broteri complex.

Niche evolution in plant polyploids remains controversial and evidence for alternative patterns has been reported. Using the autopolyploid Dianthus broteri complex (2×, 4×, 6× and 12×) as a model, we aimed to integrate three scenarios - competitive exclusion, recurrent origins of cytotypes and niche filling - into a single framework of polyploid niche evolution. We hypothesized that high polyploids would tend to evolve towards extreme niches when low ploidy cytotypes have nearly filled the niche space.

Uncovering the contribution of epigenetics to plant phenotypic variation in Mediterranean ecosystems.

Epigenetic signals can affect plant phenotype and fitness and be stably inherited across multiple generations. Epigenetic regulation plays a key role in the mechanisms of plant response to the environment, without altering DNA sequence. As plants cannot adapt behaviourally or migrate instantly, such dynamic epigenetic responses may be particularly crucial for survival of plants within changing and challenging environments, such as the Mediterranean-Type Ecosystems (MTEs).

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima.

The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and Dactylorhiza fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage-specific adaptive evolution of protein-coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores.

Is the diversification of Mediterranean Basin plant lineages coupled to karyotypic changes?

The Mediterranean Basin region, home to 25,000 plant species, is included in the worldwide list of hotspots of biodiversity. Despite the indisputably important role of chromosome transitions in plant evolution and diversification, no reference study to date has dealt with the possible relationship between chromosome evolution and lineage diversification in the Mediterranean Basin. Here we study patterns of diversification, patterns of chromosome number transition (either polyploidy or dysploidy) and the relationship between the two for 14 Mediterranean Basin angiosperm lineages using previously published phylogenies.

Deciphering the ecophysiological traits involved during water stress acclimation and recovery of the threatened wild carnation, Dianthus inoxianus.

Dianthus inoxianus is an endangered species endemic from a small littoral area in the SW Spain, with an unusual flowering season under the adverse conditions of dry Mediterranean summer. A greenhouse experiment was designed to assess the physiological traits involved in drought acclimation and recovery of 3-month-old plants. The evolution of plant water status, leaf gas exchange, chlorophyll fluorescence, photosynthetic pigments concentrations and a quantitative analysis of photosynthesis limitations were followed during water stress and re-watering.

Epigenetic contribution to successful polyploidizations: variation in global cytosine methylation along an extensive ploidy series in Dianthus broteri (Caryophyllaceae).

Polyploidization is a significant evolutionary force in plants which involves major genomic and genetic changes, frequently regulated by epigenetic factors. We explored whether natural polyploidization in Dianthus broteri complex resulted in substantial changes in global DNA cytosine methylation associated to ploidy. Global cytosine methylation was estimated by high-performance liquid chromatography (HPLC) in 12 monocytotypic populations with different ploidies (2×, 4×, 6×, 12×) broadly distributed within D.

Phylogeography above the species level for perennial species in a composite genus.

In phylogeography, DNA sequence and fingerprint data at the population level are used to infer evolutionary histories of species. Phylogeography above the species level is concerned with the genealogical aspects of divergent lineages. Here, we present a phylogeographic study to examine the evolutionary history of a western Mediterranean composite, focusing on the perennial species of Helminthotheca (Asteraceae, Cichorieae).

Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex.

Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.

A test of phenotypic selection on petal form in the wild carnation, Dianthus inoxianus.

Floral phenotypes are considered a product of pollinator-mediated selection, which also has the side effect of decreasing floral variation within species. Correlates of flower visibility and function were studied in a carnation species (Dianthus inoxianus), which has crepuscular anthesis and scent-based pollination by the hawkmoth Hyles livornica. We also assessed constancy of flower form in nature and in cultivation and, using fruit set as an estimate of plant relative fitness, tested whether the main pollinator exerted phenotypic selection on floral traits.

Big thistle eats the little thistle: does unidirectional introgressive hybridization endanger the conservation of Onopordum hinojense?

Hybridization is known to have a creative role in plant evolution. However, it can also have negative effects on parental species. Onopordum is a large genus whose species frequently hybridize.

Effects of tree architecture on pollen dispersal and mating patterns in Abies pinsapo Boiss. (Pinaceae).

Plant architecture is crucial to pollination and mating in wind-pollinated species. We investigated the effect of crown architecture on pollen dispersal, mating system and offspring quality, combining phenotypic and genotypic analyses in a low-density population of the endangered species Abies pinsapo. A total of 598 embryos from three relative crown height levels (bottom, middle and top) in five mother plants were genotyped using eleven nuclear microsatellite markers (nSSRs).

Do chromosome numbers reflect phylogeny? New counts for Bombacoideae and a review of Malvaceae s.l.

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Premise Of The Study: Whole genome duplication (WGD) and specific polyploidy events marked turning points for angiosperm genome structure and evolution. Therefore, cytogenetic studies of polyploidy-prone groups such as the tropical Malvaceae and plant formations such as as the Brazilian Cerrado have gained further importance. We present new chromosome counts for Cerrado Bombacoideae and revised chromosome numbers for the Malvaceae s.

Phylogeography of SW Mediterranean firs: different European origins for the North African Abies species.

The current distribution of Western Mediterranean Abies species is a result of complex geodynamic processes and climatic oscillations that occurred in the past. Abies sect. Piceaster offers a good study model to explore how geo-climatic oscillations might have influenced its expansion and diversification on both sides of the W Mediterranean basin.

AFLPsim: an R package to simulate and detect dominant markers under selection in hybridizing populations.

Background: In spite of a large diversity of approaches to investigate loci under selection from a population genetic perspective, very few programs have been specifically designed to date to test selection in hybrids using dominant markers. In addition, simulators of dominant markers are very scarce and they do not usually take into account hybridization.

Results: Here, we present a new, multifunctional, R package for dominant genetic markers, AFLPsim.