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. We used several ecoinformatics and phylogenetic comparative analyses to quantify differences in the ecological niche of each cytotype and to evaluate alternative models of niche evolution. Each cytotype in this complex occupied a distinct ecological niche. The distributions were mainly constrained by soil characteristics, temperature and drought stress imposed by the Mediterranean climate. Tetraploids had the highest niche breadth and overlap due to their multiple origins, whereas the higher ploidy cytotypes were found in different, restricted, nonoverlapping niches. Niche evolution analyses suggested a scenario with one niche optimum for each ploidy, including the two independent tetraploid lineages.Our results suggest that the fate of nascent polyploids could not be predicted without accounting for phylogenetic relatedness, recurrent origins or the niche occupied by ancestors.Aridos La Melera S.L. (FIUS project 2234/0724

Using rubrics as a self-assessment tool in Botany learning

Las rúbricas o matrices de evaluación son una herramienta educativa para la evaluación del proceso de aprendizaje. En la rúbrica se identifican ciertos criterios en la realización de un trabajo y también se define la gradación de calidad para cada criterio, desde un rendimiento pobre hasta la excelencia. Las rúbricas ayudan a estudiantes y profesores a juzgar la calidad de la tarea realizada por los estudiantes y pueden utilizarse además como herramienta de autoevaluación, mostrándose muy eficaces en algunos estudios previos. La realización de un herbario personal o en grupo ha sido un recurso utilizado para el aprendizaje de la Botánica desde hace años. Los herbarios permiten que el alumno conozca la terminología adecuada de la Taxonomía Botánica, aprenda a preparar, conservar e identificar las plantas con la bibliografía adecuada, y adquiera un conocimiento de visu de la flora local. Asimismo, otras competencias transversales, como la capacidad de trabajo en grupo, pueden ser potenciadas con la realización de dicho herbarios. La evaluación de los herbarios es compleja debido a la diversidad de competencias necesarias para la correcta realización del trabajo. Aquí presentamos una rúbrica desarrollada para que el alumno pueda autoevaluarse según diferentes criterios que se agrupan en tres grandes bloques: (i) Contenido, (ii) Presentación y Documentación, y (iii) Destrezas de trabajo colaborativas (trabajo en grupo). Esta autoevaluación tiene como finalidad la mejora en la presentación de los herbarios y con ello una mejora del rendimiento académico del alumno.A rubric (evaluation matrix) is an educational tool designed to evaluate the learning process. In an evaluation matrix, specific expectations are identified as well as a grade of fulfillment for each criterion, from a poor to an excellent performance. Rubrics make easier the evaluation task carried out by teachers and students, improving its quality, and can be used for self-assessment as its efficiency is proved by previous studies. An individual or collective herbarium is a learning tool that has been used for many years. Herbaria allow that students can familiarize with the Botanical Taxonomy terminology, learn to prepare, preserve and identify plant specimens (with the necessary bibliography), and acquire visual knowledge of local flora. In addition, several transversal competences, like teamwork related skills, are boosted in its construction. The evaluation of a herbarium is complex due to the diversity of necessary competences involved. Here, we bring a rubric to let students self-assess different criteria (grouped in three blocks): (i) Content, (ii) Presentation and Documentation, and (iii) Teamwork skills. The purpose of this self-assessment is to improve the presentation of the herbarium and hence the student's academic performance

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. This package can simulate dominant markers in hybridizing populations and implements genome scan methods for detecting outlier dominant loci in hybrids. In addition, it includes tools for further manipulating the results, plotting them and other tasks. We describe and tabulate the major functions implemented in AFLPsim. In addition, we provide some demonstration of its use and we perform a comparative study with other software. Finally, we conclude by briefly describing the input and output formats. Conclusions The R package AFLPsim application provides several useful tools in the context of hybridization studies. It can simulate dominant markers in hybridizing populations and predict their demographic evolution. In addition, we implement a new genome scan method for detecting outlier dominant loci in hybrids, which shows a rather high sensitivity and is very conservative in comparison with Gagnaire et al.’s, bayescan and introgress. The application is downloadable at http://cran.r-project.org/web/packages/AFLPsim/

Polyploidy promotes divergent evolution across the leaf economics spectrum and plant edaphic niche in the Dianthus broteri complex

The evolution of the leaf economics spectrum (LES) is known to be constrained by genetic relatedness but also promoted at small geographical and phylogenetic scales. In those cases, we hypothesized that polyploidy would play a prominent role as an outstanding source of functional divergence and adaptive potential. We registered leaf-level nutrient, water- and light-economy-related traits from the LES as well as edaphic properties in the four cytotypes of the autopolyploid Dianthus broteri complex (2×, 4×, 6× and 12×). We analysed the effect of ploidy level on the integration of the LES network, checked if concerted evolution occurred between LES and soil niche and tested the influence of phylogeny on the variables. Alternative evolutionary models for both sets of traits were compared. We found higher divergence of polyploids (especially 6× and 12×) compared to diploids in the LES and soil niche, but these traits are not coevolving. 6× and 12× showed opposite ecological strategies regarding resource use and higher uncoupling of the LES network. Early divergence of traits prevailed in both LES and edaphic niche (supported by better fitted evolutionary models with one optimum per cytotype), but post-polyploidization processes played an important role for the photochemical behaviour. Synthesis. Our results indicated shifts in ecological strategies across Dianthus broteri cytotypes and suggested a powerful role of polyploidy in overcoming constraints for the evolution of plant functional traits.PGC2018-098358-B-I00 from the Spanish MICINNÁridos La Melera S.L. (FIUS project 2234/0724

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

Dianthus broteri 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. In these cases, real-time polymer-ase chain reaction (qPCR) is the most appropriate technique for determining the gene expression profile because of its high sensitivity. The relative quantification strategy using qPCR requires genes with stable expression, known as reference genes, for normalization. In this work, we evaluated the stability of 13 candidate genes to be considered reference genes in leaf and petal tissues in Dianthus broteri. Several statistical analyses were used to determine the most stable candidate genes: Bayesian analysis, network analysis based on equivalence tests, geNorm and BestKeeper algorithms. In the leaf tissue, the most stable candidate genes were TIP41, TIF5A, PP2A and SAMDC. Similarly, the most adequate reference genes were H3.1, TIP41, TIF5A and ACT7 in the petal tissue. Therefore, we suggest that the best reference genes to compare different ploidy levels for both tissues in D. broteri are TIP41 and TIF5A.Ministerio de Ciencia e Innovación PGC2018-098358-B-I00Junta de Andalucía US-138123

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. Genomic diploidization and phenotypic novelty were evident. Distinct patterns of variation revealed that post-polyploidization processes altered the phenotypic shifts directly mediated by genome doubling. The photosynthetic phenotype was affected in several ways but the main effect was phenotypic diploidization (i.e. 2x and 4xNat were closer to each other than to 4xNeo). Overall, our results show the potential benefits of considering experimentally synthetized versus naturally established polyploids when exploring the role of polyploidization in promoting functional divergence.España Ministerio de Ciencia e Innovación project POLYTRANSECO (PGC2018-098358-B-I00)Spanish Ministerio de Universidades (FPU19/02936

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. In turn, a substantial regulatory divergence between the two species appears linked to adaptation/acclimation to abiotic conditions. Several of the pathways affected by differential expression are also targeted by deviating post-transcriptional regulation via sRNAs. Finally, D. incarnata appears to suffer from insufficient sRNA control over the activity of RNA-dependent DNA polymerase, resulting in increased activity of class I transposable elements and, over time, in larger genome size than that of D. fuchsii. The extensive molecular divergence between the two species suggests significant genomic and transcriptomic shock in their hybrids and offers insights into the difficulty of coexistence at the homoploid level. Altogether, biological response to selection, accumulated during the history of these orchids, appears governed by their microenvironmental context, in which biotic and abiotic pressures act synergistically to shape transcriptome structure, expression and regulation.OP and a Marie Curie IEF Fellowship PERG-GA2011-299608-TRANSADAPTATIO

Anthropogenic deforestation and climate dryness as drivers of demographic decline and genetic erosion in the southernmost European fir forests

A better understanding of long-term effects of climate and historical anthropogenic changes is needed to define effective conservation measures of endangered forest inhabiting managed landscapes. Diversification and distribution of Mediterranean firs are attributed to the global climate change during the Miocene and Quaternary as well as to the effects of human-driven deforestation. We evaluated the impact of climate change and anthropogenic activities in shaping the genetic diversity and structure of Abies pinsapo Boiss. (Pinaceae), a relict fir endemic from SW Spain. We genotyped a total of 440 individuals from 44 populations by using two different molecular markers (cpSSRs and nSSRs). Overall, low genetic structure was found; however, incipient differentiation appeared within mountain ranges. Analyses suggest that the effects of isolation by distance and lithological or topographical diversity were not enough to structure the populations of the different mountain ranges. The combined role of genetic drift in the small populations and the anthropogenic action associated with forest management has shaped the current genetic pattern of this fir species in the study area. Demographic inference analyses pointed to a very recent synchronic divergence (eleventh–sixteenth century) of the ancestral A. pinsapo population into its current scattered distribution range. Although population bottlenecks were supported by several analyses, the conservation of this endangered species seems not to be limited by lacking genetic diversity, while threats of current climate change and habitat loss must be regarded.Ministerio de Economía y Competitividad P08-RNM-03703, P18-RT-1170, CGL2013-45463-PJunta de Andalucía IF/01375/2012, PTDC/BIA-BIC/5233/2014, POCI-01-0145- FEDER-01681

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 (CMF) 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. KEY RESULTS: Based on thousands of genome-wide SNPs, we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMF. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of A. tazaotana and A. marocana. An unexpectedly early pulse of speciation in the Oligocene-Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. CONCLUSIONS: Our phylogenomic results contribute to shed light on conifers' diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolutio