L'origen de la diversitat de les campanetes

Les campanulàcies són una família de plantes difoses arreu del món. Principalment es troben en àrees muntanyoses, així com en regions de climes freds i àrids de l'hemisferi nord. Bona part de les espècies que en formen part presenten típicament flors d'un color blau violaci amb forma de campana. El present article se centra en estudiar com ha evolucionat aquesta família de plantes tant a l'espai com al temps, i quins processos climàtics, geològics i biogeogràfics han portat a la distribució actual de les campanulàcies. Aquest estudi s'ha dut a terme mitjançant anàlisis genètiques combinades amb dades fòssils i geològiques.Las campanuláceas son una familia de plantas difundidas por cualquier parte del mundo. Principalmente, se encuentran en áreas montañosas, así como en regiones de climas fríos y áridos del hemisferio norte. Muchas especies que forman parte de ellas, presentan típicamente flores de un color azul violáceo con forma de campana. El presente artículo se centra en estudiar cómo ha evolucionado esta familia de plantas tanto en el espacio como en el tiempo, y qué procesos climáticos, geológicos y biogeográficos han llevado a la distribución actual de las campanuláceas. Este estudio se ha llevado a cabo mediante análisis genéticos combinados con datos fósiles y geológicos

Directional biases in phylogenetic structure quantification: a Mediterranean case study

Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, using a large plant community and elevational dataset, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure; and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well-resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that sensitivity of phylogenetic structure measures to low phylogenetic resolution can strongly differ depending on phylogenetic tree shape

Systematics of the narrow endemic species Brimeura duvigneaudii (Hyacinthaceae)

We carried out a morphological study of Brimeura duvigneaudii (Hyacinthaceae), a narrow endemic species limited to northeastern Mallorca (Balearic Islands). Morphological analyses showed noticeably variability which is correlated with geographic distribution and some ecological factors. These data led us to propose a new subspecies of Brimeura duvigneaudii, which is described from the middle range of Serra de Tramuntana. The new taxon (Brimeura duvigneaudii subsp. occultata) differs from B. duvigneaudii subsp. duvigneaudii in several vegetative (leaf anatomy and leaf width) and flower features (corolla size, corolla lobe length and shape, scape length). Data on the local distribution and ecology of the new taxon are reported. The new subspecies is restricted to a karst gorge and it is in danger of extinction, due to its small population size. In adition, controversial taxonomy of Brimeura amethystina and B. fontqueri (= B. amethystina subsp. fontqueri) is clarified, and they are confirmed as synonyms on the basis of morphological analyses.Se ha realizado un estudio morfológico de Brimeura duvigneaudii (Hyacinthaceae), una especie endémica restringida al noreste de Mallorca (Islas Baleares). Los análisis basados en caracteres morfológicos indican que existe una variabilidad destacable que se relaciona con una distribución geográfica y algunos factores ecológicos. Estos datos permiten proponer una nueva subespecie de Brimeura duvigneaudii, restringida de la zona central de la Sierra de Tramuntana. El nuevo taxon (Brimeura duvigneaudii subsp. occultata) difiere de B. duvigneaudii subsp. duvigneaudii tanto en caracteres vegetativos (anatomía foliar y anchura de las hojas) como florales (tamaño de la corola, longitud y forma de los lóbulos de la corola, longitud del escapo). Se aportan datos de la distribución local y la ecología del nuevo taxon. La nueva subespecie se encuentra restringida a un profundo barranco cárstico y está en peligro de extinción como consecuencia de su exiguo tamaño poblacional. Por otro lado se clarifica la controversia taxonómica relativa a Brimeura amethystina y B. fontqueri (= B. amethystina subsp. fontqueri), y se confirma que se trata de sinónimos, sobre la base de los análisis morfológicos realizado

Phylogenetic patterns of rarity and vulnerability in the flora of a temperate mountain range

Species rarity has puzzled ecologists for decades owing to its theoretical fundamentals and practical implications. The main concern that rarity raises from a conservation standpoint is that rare species tend to have higher extinction risk. Understanding the underlying phylogenetic patterns of rarity can shed light on the evolutionary processes yielding rarity, contribute to forecasting potential vulnerable species or lineages, and assess the consequences of the loss of rare species. Here, we apply Rabinowitz's rarity classification scheme and explore phylogenetic patterns in the flora of the Pyrenees, a temperate mountain range. We first categorized species according to their geographic range (endemicity and regional geographic range), habitat specialization and local abundance. Then we analyzed the phylogenetic signal of each rarity type, along with the phylogenetic association between species according to their rarity, and decomposed the variation of rarity among taxonomic levels to better understand its diversification through time. Finally, we estimated the expected loss of phylogenetic diversity (PD) in the regional flora if rare species go extinct. All rarity types showed a certain degree of phylogenetic signal, with endemics, species of limited regional geographic range and habitat specialists forming groups of phylogenetically close species. The decomposition of variation supported these results, as the rarity types with the strongest signal had more variation explained by higher taxonomic levels. The loss of these groups of species had different consequences based on the type of rarity, with the disappearance of habitat specialists having the strongest, negative effect on PD. Our results show a general pattern of phylogenetic association in rarity among the flora of the Pyrenees, which leads to increased vulnerability along certain branches of the Tree of Life. Phylogenetic patterns should be taken into account in conservation planning to effectively protect all facets of biodiversity

Habitats hold an evolutionary signal of past climatic refugia

Climatic refugia have often been associated with hotspots of richness and endemism, and identified on the basis of molecular or paleobotanical information. Here, we apply a phylogenetic analysis to 18,000 plant communities distributed across the Pyrenees, a south European mountain range, to identify climatic refugia from imprints of relictuality inferred from species' evolutionary distinctiveness (ED). We produced a genus-level phylogenetic tree to calculate the standardized mean ED value of plant communities (cED). Then, we explored which habitats concentrate the plant communities with the highest cED and the interrelated effect of past (long-term climatic stability) and present (topographic and spatial position) factors. Results show strong differences of cED among habitats: forests ranked first, followed by some open habitats like high altitude wetlands. Climate stability and roughness positively influenced cED. A weak negative association resulted between the two diversity measurements (richness and endemism rate) and also with cED. We propose that forests acted as 'mobile refugia' during the glacial-interglacial periods, supported by paleoenvironmental reconstructions revealing continuous presence at regional scale of key broadleaved trees at that time. Azonal habitats like the endemic-poor humid communities at high elevation would have also played an important role as more permanent microrefugia. Our approach identifies a variety of habitats and plant assemblages that have successfully withstood past climate change in different ways, and therefore would hold an important evolutionary potential to cope with current climate change. Given their potential role in preserving biodiversity, they should be integrated in future conservation agendas

Tempo and drivers of plant diversification in the European mountain system

There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras

The treasure vault can be opened: large-scale genome skimming works well using herbarium and silica gel dried material

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications

Generic boundaries in subtribe Saussureinae (Compositae: Cardueae): Insights from Hyb-Seq data

The subtribe Saussureinae is a highly speciose group with more than 600 species distributed in the Northern Hemisphere and is particularly species-rich at the high mountains of central and eastern Asia. Saussurea and Jurinea are the two main genera described within the subtribe. However, up to 15 satellite genera are recognized in some recent taxonomic treatments with an analytical viewpoint. For the first time, we carried out a complete sampling to clarify generic boundaries based on a well-resolved phylogeny of Saussureinae. We employed a Hyb-Seq technique that targets 1061 nuclear conserved ortholog loci designed for Compositae. After a filtering of potential paralogs, 588 loci were retained to infer phylogenetic trees under concatenation and coalescence approaches. High branch support resolution was recovered at the generic level, but a non-monophyletic pattern was detected for most of the genera as they are currently circumscribed. Accordingly, we propose a new generic delimitation based on the three main clades recovered in the backbone tree, which are also in agreement with morphological evidence: Dolomiaea, Saussurea, and Jurinea. Following this classification into three genera, 18 new combinations are proposed. This new genus delineation will be used as a basis for future evolutionary studies in the Saussureinae.Financial support from the Ministerio de Ciencia e Innovación (Project CGL2015-66703-P MINECO/FEDER, UE and Ph.D. grant to Sonia Herrando-Moraira) and the Catalan government (“Ajuts a grups consolidats” 2017-SGR1116) is also greatly acknowledged. This study has been performed under the Ph.D. program “Plant Biology and Biotechnology” of the Autonomous University of Barcelona (UAB)INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION TAXONOMIC IMPLICATIONS NOTE ADDED IN PROOF AUTHOR CONTRIBUTIONS ACKNOWLEDGMENT

African Mountain Thistles: Three New Genera in the Carduus-Cirsium Group

The floras on the highest mountains in tropical eastern Africa are among the most unique floras in the world. Despite the exceptionally high concentration of endemic species, these floras remain understudied from an evolutionary point of view. In this study, we focus on the Carduus-Cirsium group (subtribe Carduinae) to unravel the evolutionary relationships of the species endemic to the tropical Afromontane and Afroalpine floras, aiming to improve the systematics of the group. We applied the Hyb-Seq approach using the Compositae1061 probe set on 190 samples (159 species), encompassing representatives of all genera of Carduinae. We used two recently developed pipelines that enabled the processing of raw sequence reads, identification of paralogous sequences and segregation into orthologous alignments. After the implementation of a missing data filter, we retained sequences from 986 nuclear loci and 177 plastid regions. Phylogenomic analyses were conducted using both concatenated and summary-coalescence methods. The resulting phylogenies were highly resolved and revealed three distinct evolutionary lineages consisting of the African species traditionally referred to as Carduus and Cirsium. Consequently, we propose the three new genera Afrocarduus, Afrocirsium and Nuriaea; the latter did notably not belong to the Carduus-Cirsium group. We detected some incongruences between the phylogenies based on concatenation vs. coalescence and on nuclear vs. plastid datasets, likely attributable to incomplete lineage sorting and/or hybridization

Repeatedly Northwards and Upwards: Southern African Grasslands Fuel the Colonization of the African Sky Islands in Helichrysum (Compositae)

The Afromontane and Afroalpine areas constitute some of the main biodiversity hotspots of Africa. They are particularly rich in plant endemics, but the biogeographic origins and evolutionary processes leading to this outstanding diversity are poorly understood. We performed phylogenomic and biogeographic analyses of one of the most species-rich plant genera in these mountains, Helichrysum (Compositae-Gnaphalieae). Most previous studies have focused on Afroalpine elements of Eurasian origin, and the southern African origin of Helichrysum provides an interesting counterexample. We obtained a comprehensive nuclear dataset from 304 species (≈50% of the genus) using target-enrichment with the Compositae1061 probe set. Summary-coalescent and concatenation approaches combined with paralog recovery yielded congruent, well-resolved phylogenies. Ancestral range estimations revealed that Helichrysum originated in arid southern Africa, whereas the southern African grasslands were the source of most lineages that dispersed within and outside Africa. Colonization of the tropical Afromontane and Afroalpine areas occurred repeatedly throughout the Miocene-Pliocene. This timing coincides with mountain uplift and the onset of glacial cycles, which together may have facilitated both speciation and intermountain gene flow, contributing to the evolution of the Afroalpine flora.This work received financial support from the Spanish Ministry of Science, Innovation and Universities (PID2019-105583GB-C22/AEI/10.13039/501100011033) and the Catalan government (“Ajuts a grups consolidats” 2021SGR00315 and FI grant to C.B.-G. 2022FI_B 00150). The Ph.D. thesis was carried out under the Ph.D. program “Plant Biology and Biotechnology” of the Autonomous University of Barcelona (UAB). Additional support was provided by the Czech Science Foundation GAČR project no. 20-10878S to R.S. and F.K. and long-term research development project (RVO 67985939) of the Czech Academy of Sciences. Additional funds were obtained from the Norwegian Programme for Development, Research and Higher Education (NUFU; project AFROALP-II, no 2007/1058) and the Research Council of Norway (project SpeciationClock, no 274607) to C.B.Abstract 1. Introduction 2. Materials and Methods 2.1. Taxon Sampling 2.2. DNA Extraction, Library Preparation, Target Capture, and Sequencing 2.3. Molecular Data Processing and Phylogenetic Analyses 2.4. Divergence Time Estimation 2.5. Ancestral Range Estimation 3. Results 3.1. Alignment Processing and Filtering 3.2. Phylogenetic Analyses 3.3. Divergence Time and Ancestral Range Estimation 3.4. Number, Type, and Directionality Estimation of Biogeographical Events 4. Discussion 4.1. Utility of Target-Enrichment Strategies in Reconstructing the Radiation of Helichrysum 4.2. The Early History of Helichrysum and Colonization of Madagascar 4.3. Repeatedly Northwards 4.4. Repeatedly Upwards 5. Conclusions Supplementary Materials Author Contributions Funding Data Availability Statement Acknowledgments Conflicts of Interest Reference