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2. Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae)

Author

Herrando-Moraira, Sonia, Roquet, Cristina, Calleja, Juan-Antonio, Chen, You-Sheng, Fujikawa, Kazumi, Galbany-Casals, Mercè, Garcia-Jacas, Núria, Liu, Jian-Quan, López-Alvarado, Javier, López-Pujol, Jordi, Mandel, Jennifer R., Mehregan, Iraj, Sáez, Llorenç, Sennikov, Alexander N., Susanna, Alfonso, Vilatersana, Roser, and Xu, Lian-Sheng

Published
2023
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6. Generic boundaries in subtribe Saussureinae (Compositae: Cardueae) : Insights from Hyb-Seq data

Author

The Cardueae Radiations Group, Herrando-Moraira, Sonia, Calleja, Juan-Antonio, Chen, You-Sheng, Fujikawa, Kazumi, Galbany-Casals, Mercè, Garcia-Jacas, Núria, Kim, Seung-Chul, Liu, Jian-Quan, López-Alvarado, Javier, López-Pujol, Jordi, Mandel, Jennifer R., Mehregan, Iraj, Roquet, Cristina, Sennikov, Alexander N., Susanna, Alfonso, Vilatersana, Roser, and Xu, Lian-Sheng

Published
2020

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

Author

Moreyra, Lucía D., primary, Garcia-Jacas, Núria, additional, Roquet, Cristina, additional, Ackerfield, Jennifer R., additional, Arabacı, Turan, additional, Blanco-Gavaldà, Carme, additional, Brochmann, Christian, additional, Calleja, Juan Antonio, additional, Dirmenci, Tuncay, additional, Fujikawa, Kazumi, additional, Galbany-Casals, Mercè, additional, Gao, Tiangang, additional, Gizaw, Abel, additional, López-Alvarado, Javier, additional, Mehregan, Iraj, additional, Vilatersana, Roser, additional, Yıldız, Bayram, additional, Leliaert, Frederik, additional, Seregin, Alexey P., additional, and Susanna, Alfonso, additional

Published
2023
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9. European ornamental garden flora as an invasion debt under climate change

Author

Haeuser, Emily, Block, Svenja, Dawson, Wayne, Thuiller, Wilfried, Dullinger, Stefan, Bossdorf, Oliver, Carboni, Marta, Conti, Luisa, Dullinger, Iwona, Essl, Franz, Klonner, Günther, Moser, Dietmar, Kreft, Holger, Münkemüller, Tamara, Parepa, Madalin, Talluto, Matthew V., Pergl, Jan, Hermy, Martin, Pyšek, Petr, Weigelt, Patrick, Winter, Marten, Van der Veken, Sebastiaan, Roquet, Cristina, and van Kleunen, Mark

Published
2018

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

Author

Blanco-Gavaldà, Carme, primary, Galbany-Casals, Mercè, additional, Susanna, Alfonso, additional, Andrés-Sánchez, Santiago, additional, Bayer, Randall J., additional, Brochmann, Christian, additional, Cron, Glynis V., additional, Bergh, Nicola G., additional, Garcia-Jacas, Núria, additional, Gizaw, Abel, additional, Kandziora, Martha, additional, Kolář, Filip, additional, López-Alvarado, Javier, additional, Leliaert, Frederik, additional, Letsara, Rokiman, additional, Moreyra, Lucía D., additional, Razafimandimbison, Sylvain G., additional, Schmickl, Roswitha, additional, and Roquet, Cristina, additional

Published
2023
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13. Repeatedly Northwards and Upwards: Southern African Grasslands Fuel the Colonization of the African Sky Islands in Helichrysum (Compositae)

Author

Blanco-Gavaldà, C, Galbany-Casals, Mercè, Susanna de la Serna, Alfonso, Andrés-Sánchez, Santiago, Bayer, Randall J., Brochmann, Christian, Cron, Glynis V., Bergh, Nicola G., Garcia-Jacas, Núria, Gizaw, Abel, Kandziora, Martha, Kolář, Filip, López-Alvarado, Javier, Leliaert, Frederik, Letsara, Rokiman, Moreyra, Lucía D., Razafimandimbison, Sylvain G., Schmickl, Roswitha E., Roquet, Cristina, Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Universidad Autónoma de Barcelona, Czech Science Foundation, Czech Academy of Sciences, and Research Council of Norway

Subjects
Helichrysum, Biogeography, Long-distance dispersal, Evolution, Afromontane, Asteraceae, Afroalpine, Phylogeny, Target-enrichment
Abstract

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., 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 References

Published
2023

14. Filogenia de la flora Pirenaica a nivel de género

Author

Agencia Estatal de Investigación (España), Roquet, Cristina [0000-0001-8748-3743], García González, María Begoña [0000-0003-4231-6006], Roquet, Cristina [cristina.roquet@gmail.com], García González, María Begoña [mariab@ipe.csic.es], Roquet, Cristina, García González, María Begoña, Agencia Estatal de Investigación (España), Roquet, Cristina [0000-0001-8748-3743], García González, María Begoña [0000-0003-4231-6006], Roquet, Cristina [cristina.roquet@gmail.com], García González, María Begoña [mariab@ipe.csic.es], Roquet, Cristina, and García González, María Begoña

Published
2022

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

Author

Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Miranda, Héctor [0000-0002-0340-8373], Roquet, Cristina [0000-0001-8748-3743], Pizarro Gavilán, Manuel [0000-0002-6981-0154], García González, María Begoña [0000-0003-4231-6006], Miranda, Héctor, Font, Xavier, Roquet, Cristina, Pizarro Gavilán, Manuel, García González, María Begoña, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Miranda, Héctor [0000-0002-0340-8373], Roquet, Cristina [0000-0001-8748-3743], Pizarro Gavilán, Manuel [0000-0002-6981-0154], García González, María Begoña [0000-0003-4231-6006], Miranda, Héctor, Font, Xavier, Roquet, Cristina, Pizarro Gavilán, Manuel, and García González, María Begoña

Abstract

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 prote

Published
2022

16. Habitats hold an evolutionary signal of past climatic refugia

Author

Consejo Superior de Investigaciones Científicas (España), Conferencia de Rectores de las Universidades Españolas, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), García González, María Begoña [0000-0003-4231-6006], Miranda, Héctor [0000-0002-0340-8373], Pizarro Gavilán, Manuel [0000-0002-6981-0154], Roquet, Cristina [0000-0001-8748-3743], González-Sampériz, Penélope [0000-0002-5097-1468], García González, María Begoña, Miranda, Héctor, Pizarro Gavilán, Manuel, Font, Xavier, Roquet, Cristina, González-Sampériz, Penélope, Consejo Superior de Investigaciones Científicas (España), Conferencia de Rectores de las Universidades Españolas, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), García González, María Begoña [0000-0003-4231-6006], Miranda, Héctor [0000-0002-0340-8373], Pizarro Gavilán, Manuel [0000-0002-6981-0154], Roquet, Cristina [0000-0001-8748-3743], González-Sampériz, Penélope [0000-0002-5097-1468], García González, María Begoña, Miranda, Héctor, Pizarro Gavilán, Manuel, Font, Xavier, Roquet, Cristina, and González-Sampériz, Penélope

Abstract

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.

Published
2022

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

Author

Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Universidad Autónoma de Barcelona, Czech Science Foundation, Czech Academy of Sciences, Research Council of Norway, Blanco-Gavaldà, C, Galbany-Casals, Mercè, Susanna de la Serna, Alfonso, Andrés-Sánchez, Santiago, Bayer, Randall J., Brochmann, Christian, Cron, Glynis V., Bergh, Nicola G., Garcia-Jacas, Núria, Gizaw, Abel, Kandziora, Martha, Kolář, Filip, López-Alvarado, Javier, Leliaert, Frederik, Letsara, Rokiman, Moreyra, Lucía D., Razafimandimbison, Sylvain G., Schmickl, Roswitha E., Roquet, Cristina, Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Universidad Autónoma de Barcelona, Czech Science Foundation, Czech Academy of Sciences, Research Council of Norway, Blanco-Gavaldà, C, Galbany-Casals, Mercè, Susanna de la Serna, Alfonso, Andrés-Sánchez, Santiago, Bayer, Randall J., Brochmann, Christian, Cron, Glynis V., Bergh, Nicola G., Garcia-Jacas, Núria, Gizaw, Abel, Kandziora, Martha, Kolář, Filip, López-Alvarado, Javier, Leliaert, Frederik, Letsara, Rokiman, Moreyra, Lucía D., Razafimandimbison, Sylvain G., Schmickl, Roswitha E., and Roquet, Cristina

Abstract

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.

Published
2023

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

Author

Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, National Natural Science Foundation of China, Universidad Autónoma de Barcelona, Moreyra, Lucía D., Garcia-Jacas, Núria, Roquet, Cristina, Ackerfield, Jennifer, Arabaci, Turan, Blanco-Gavaldà, C., Brochmann, Christian, Calleja, Juan A., Dirmenci, Tuncay, Fujikawa, Kazumi, Galbany-Casals, Mercè, Gao, Tian-Gang, Gizaw, Abel, López-Alvarado, Javier, Mehregan, Iraj, Vilatersana, Roser, Yildiz, Bayram, Leliaert, Frederik, Seregin, Alexey P., Susanna de la Serna, Alfonso, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, National Natural Science Foundation of China, Universidad Autónoma de Barcelona, Moreyra, Lucía D., Garcia-Jacas, Núria, Roquet, Cristina, Ackerfield, Jennifer, Arabaci, Turan, Blanco-Gavaldà, C., Brochmann, Christian, Calleja, Juan A., Dirmenci, Tuncay, Fujikawa, Kazumi, Galbany-Casals, Mercè, Gao, Tian-Gang, Gizaw, Abel, López-Alvarado, Javier, Mehregan, Iraj, Vilatersana, Roser, Yildiz, Bayram, Leliaert, Frederik, Seregin, Alexey P., and Susanna de la Serna, Alfonso

Abstract

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.

Published
2023

25. Habitats hold a phylogenetic signal of past climatic refugia in the Pyrenean range, a biogeographical crossroad

Author

García González, María Begoña [0000-0003-4231-6006], Miranda, Héctor [0000-0002-0340-8373], Pizarro Gavilán, Manuel [0000-0002-6981-0154], Font, Xavier [0000-0002-7253-8905], Roquet, Cristina [0000-0001-8748-3743], González-Sampériz, Penélope [0000-0002-5097-1468], García González, María Begoña [mariab@ipe.csic.es], González-Sampériz, Penélope, Font, Xavier, Pizarro, Manuel, García González, María Begoña, Miranda, Héctor, Roquet, Cristina, Pizarro Gavilán, Manuel, García González, María Begoña [0000-0003-4231-6006], Miranda, Héctor [0000-0002-0340-8373], Pizarro Gavilán, Manuel [0000-0002-6981-0154], Font, Xavier [0000-0002-7253-8905], Roquet, Cristina [0000-0001-8748-3743], González-Sampériz, Penélope [0000-0002-5097-1468], García González, María Begoña [mariab@ipe.csic.es], González-Sampériz, Penélope, Font, Xavier, Pizarro, Manuel, García González, María Begoña, Miranda, Héctor, Roquet, Cristina, and Pizarro Gavilán, Manuel

Abstract

Habitats hold a phylogenetic signal of past climatic refugia in the Pyrenean range, a biogeographical crossroad. This set of data come from the SIVIM database, and original data produced from our analysis. Used to test refugial locations in the Pyrenees

Published
2021

26. Scale decisions can reverse conclusions on community assembly processes

Author

Münkemüller, Tamara, Gallien, Laure, Lavergne, Sébastien, Renaud, Julien, Roquet, Cristina, Abdulhak, Sylvain, Dullinger, Stefan, Garraud, Luc, Guisan, Antoine, Lenoir, Jonathan, Svenning, Jens-Christian, Van Es, Jérémie, Vittoz, Pascal, Willner, Wolfgang, Wohlgemuth, Thomas, Zimmermann, Niklaus E., and Thuiller, Wilfried

Published
2014
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29. ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications

Author

Pouchon, Charles, Boyer, Frédéric, Roquet, Cristina, Denoeud, France, Chave, Jérome, Coissac, Eric, Alsos, Inger Greve, Lavergne, Sébastien, Smyčka, J, Boleda, M, Thuiller, W, Gielly, L, Taberlet, P, Rioux, D, Hombiat, A, Bzeznick, B, Alberti, A, Wincker, P, Orvain, C, Perrier, C, Douzet, R, Rome, M, Valay, Jg, Aubert, S, Zimmermann, N, Wüest, Ro, Latzin, S, Wipf, S, van Es, J, Garraud, L, Villaret, Jc, Abdulhak, S, Bonnet, V, Huc, S, Fort, N, Legland, T, Sanz, T, Pache, G, Mikolajczak, A, Noble, V, Michaud, H, Offerhaus, B, Pires, M, Morvant, Y, Dentant, C, Salomez, P, Bonet, R, Delahaye, T, Leccia, Mf, Perfus, M, Eggenberg, S, Möhl, A, Hurdu, B, Pușcaș, M, Slovák, M, Alsos, Ig, Merkel, F, Lammers, Y, Coissac, E, Pouchon, C, Denoeud, F, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Paris Cité (UPCité), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), National Centre for Biosystematics [Oslo], Natural History Museum [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Cellule Terroirs Viticoles, Partenaires INRAE, Istituto per la Microelettronica e Microsistemi [Catania] (IMM), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université d'Angers (UA), Centre National de la Propriété Forestière (CNPF-IDF), and ANR-16-CE93-0004,Origin-Alps,Origins, assembly and conservation of plant diversity in the European Alps(2016)

Subjects
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, DNA, Chloroplast, Genomics, Sequence Analysis, DNA, Genome, Chloroplast, Transcriptome, DNA, Mitochondrial, DNA, Ribosomal, Ecology, Evolution, Behavior and Systematics, Phylogeny, Biotechnology
Abstract

Low-coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost-effective method for acquiring genomic data in nonmodel organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over-represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: (i) global sequence assembly, (ii) mapping against reference sequences and (iii) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and noncoding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g., ultraconserved elements) or collections of single-copy orthologue genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome-skimming libraries and four RNA sequencing libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well-known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL-3 licence and is available at: https://github.com/cpouchon/ORTHOSKIM.

Published
2022

31. The Earth BioGenome Project 2020: Starting the clock

Author

Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, and Zhang, Guojie

Published
2022

32. Assessing the vulnerability of habitats through plant rarity patterns in the Pyrenean range

Author

Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), Gobierno de Aragón, Miranda, Héctor, Font, Xavier, Roquet, Cristina, Pizarro Gavilán, Manuel, García González, María Begoña, Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), Gobierno de Aragón, Miranda, Héctor, Font, Xavier, Roquet, Cristina, Pizarro Gavilán, Manuel, and García González, María Begoña

Abstract

Biodiversity is being severely affected by global change worldwide, but consequences differ across individual species and environments. Since rarity is a condition associated with vulnerability and extinction risk, it is a concerning factor itself that can also amplify the detrimental impact of global change drivers. Here, we assess differences in vulnerability derived from species rarity across environments in a South European mountain range, the Pyrenees, a complex landscape sheltering more than 3400 vascular plants. We first analyzed patterns of alpha taxonomic (richness) and phylogenetic diversity (standardized phylogenetic diversity, sesPD) from more than 18,000 plant surveys across 14 different habitats to find out which ones shelter the highest diversity. Then, we classified plant species according to four criteria of rarity (Pyrenean endemic, regional geographic range, ecological specialization and local abundance) and estimated their frequency among habitats and their contribution to PD. Generalized linear models were used to compare richness and sesPD among habitats, and the relationship between each diversity metric and rare species proportion was assessed. Grasslands harbor the greatest number of species but are poor in sesPD, while inland surface waters contain fewer species but are the most phylogenetically diverse. Deciduous, evergreen and Mediterranean forests show both high species richness and sesPD. Rare species account for half of the regional species pool, and are more abundant in habitats with fewer species and higher sesPD. Diversity metrics showed opposite tendencies between them and with rare species proportion, emphasizing that they are not interchangeable. Our results highlight the vulnerability of rocky and water-related habitats due to the rarity of the species they shelter, but only the latter match other assessments of habitat vulnerability to global change drivers. The analysis of rarity patterns can guide conservation efforts by iden

Published
2022

33. The Earth BioGenome Project 2020:Starting the clock

Author

Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., and Zhang, Guojie

Published
2022

40. The Earth BioGenome Project 2020: Starting the clock

Author

Lewin, Harris A., primary, Richards, Stephen, additional, Lieberman Aiden, Erez, additional, Allende, Miguel L., additional, Archibald, John M., additional, Bálint, Miklós, additional, Barker, Katharine B., additional, Baumgartner, Bridget, additional, Belov, Katherine, additional, Bertorelle, Giorgio, additional, Blaxter, Mark L., additional, Cai, Jing, additional, Caperello, Nicolette D., additional, Carlson, Keith, additional, Castilla-Rubio, Juan Carlos, additional, Chaw, Shu-Miaw, additional, Chen, Lei, additional, Childers, Anna K., additional, Coddington, Jonathan A., additional, Conde, Dalia A., additional, Corominas, Montserrat, additional, Crandall, Keith A., additional, Crawford, Andrew J., additional, DiPalma, Federica, additional, Durbin, Richard, additional, Ebenezer, ThankGod E., additional, Edwards, Scott V., additional, Fedrigo, Olivier, additional, Flicek, Paul, additional, Formenti, Giulio, additional, Gibbs, Richard A., additional, Gilbert, M. Thomas P., additional, Goldstein, Melissa M., additional, Graves, Jennifer Marshall, additional, Greely, Henry T., additional, Grigoriev, Igor V., additional, Hackett, Kevin J., additional, Hall, Neil, additional, Haussler, David, additional, Helgen, Kristofer M., additional, Hogg, Carolyn J., additional, Isobe, Sachiko, additional, Jakobsen, Kjetill Sigurd, additional, Janke, Axel, additional, Jarvis, Erich D., additional, Johnson, Warren E., additional, Jones, Steven J. M., additional, Karlsson, Elinor K., additional, Kersey, Paul J., additional, Kim, Jin-Hyoung, additional, Kress, W. John, additional, Kuraku, Shigehiro, additional, Lawniczak, Mara K. N., additional, Leebens-Mack, James H., additional, Li, Xueyan, additional, Lindblad-Toh, Kerstin, additional, Liu, Xin, additional, Lopez, Jose V., additional, Marques-Bonet, Tomas, additional, Mazard, Sophie, additional, Mazet, Jonna A. K., additional, Mazzoni, Camila J., additional, Myers, Eugene W., additional, O’Neill, Rachel J., additional, Paez, Sadye, additional, Park, Hyun, additional, Robinson, Gene E., additional, Roquet, Cristina, additional, Ryder, Oliver A., additional, Sabir, Jamal S. M., additional, Shaffer, H. Bradley, additional, Shank, Timothy M., additional, Sherkow, Jacob S., additional, Soltis, Pamela S., additional, Tang, Boping, additional, Tedersoo, Leho, additional, Uliano-Silva, Marcela, additional, Wang, Kun, additional, Wei, Xiaofeng, additional, Wetzer, Regina, additional, Wilson, Julia L., additional, Xu, Xun, additional, Yang, Huanming, additional, Yoder, Anne D., additional, and Zhang, Guojie, additional

Published
2022
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41. Tempo and drivers of plant diversification in the European mountain system

Author

Smycka, Jan, primary, Roquet, Cristina, additional, Boleda, Martí, additional, Alberti, Adriana, additional, Boyer, Frédéric, additional, Douzet, Rolland, additional, Perrier, Christophe, additional, Rome, Maxime, additional, Valay, Jean-Gabriel, additional, Denoeud, France, additional, Šemberová, Kristýna, additional, Zimmermann, Niklaus, additional, Thuiller, Wilfried, additional, Wincker, Patrick, additional, Alsos, Inger, additional, Coissac, Eric, additional, and Lavergne, Sebastien, additional

Published
2021
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44. Evolutionary origins and species delineation of the two Pyrenean endemics Campanula jaubertiana and C. andorrana (Campanulaceae): evidence for transverse alpine speciation

Author

Roquet, Cristina, primary, Smyčka, Jan, additional, Alberti, Adriana, additional, Boleda, Martí, additional, Coissac, Eric, additional, Denoeud, France, additional, Komac, Benjamin, additional, Lavergne, Sébastien, additional, Pladevall, Clara, additional, and Sáez, Llorenç, additional

Published
2021
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45. Dos ejemplos de radiaciones en las Cardueas (Compuestas): los géneros Saussurea y Jurinea

Author

Susanna de la Serna, Alfonso, Calleja, Juan Antonio, Galbany, Mercè, Garcia-Jacas, Núria, Herrando Moraira, Sonia, López-Alvarado, Javier, López-Pujol, Jordi, Roquet, Cristina, Sáez, Llorenç, and Vilatersana, Roser

Abstract

Trabajo presentado en el Primer Congreso Español de Botánica organizado por Sociedad Española de Botánica

Published
2021

46. A biogeographical analysis of Muhlenbergia (Poaceae: Chloridoideae: Cynodonteae: Muhlenbergiinae)

Author

Smithsonian Institution, National Geographic Society, Peterson, Paul M., Roquet, Cristina, Romaschenko, Konstantin, Herrera Arrieta, Yolanda, Susanna de la Serna, Alfonso, Smithsonian Institution, National Geographic Society, Peterson, Paul M., Roquet, Cristina, Romaschenko, Konstantin, Herrera Arrieta, Yolanda, and Susanna de la Serna, Alfonso

Abstract

A phylogeny based on the analysis of six DNA sequence markers (ITS, ndhA intron, rpl32-trnL, rps3, rps16 intron, and rps16-trnK) is used to infer ancestral areas and divergence times, and reconstruct the biogeographical history and evolution of 150 of the 183 (82%) species of Muhlenbergia. Our results suggest that the genus originated 9.3 mya in the Sierra Madre (Occidental and Oriental) in Mexico, splitting into six lineages: M. ramulosa diverging 8.2 mya, M. subg. Muhlenbergia at 5.9 mya, M. subg. Pseudosporobolus at 5.9 mya, M. subg. Clomena at 5.4 mya, M. subg. Bealia at 4.3 mya, and M. subg. Trichochloa at 1 mya, each of these with a high probability of Sierra Madrean origin. Our results further suggest that founder-event speciation from Sierra Madre to South America occurred independently multiple times in all five subgenera during the Pleistocene and late Pliocene. One long-distance dispersal event most likely originating from Central or Eastern North America to East and Central Asia occurred 1.6-1 mya in M. subg. Muhlenbergia. In our cladogram, members of M. subg. Trichochloa show little genetic resolution, suggesting very low levels of divergence among the species, and this may be a consequence of rapid radiation

Published
2021

47. Consequences of climate change on the tree of life in Europe

Author

Thuiller, Wilfried, Lavergne, Sebastien, Roquet, Cristina, Boulangeat, Isabelle, Lafourcade, Bruno, and Araujo, Miguel. B.

Subjects
Conservation of natural resources -- Forecasts and trends -- Management -- Europe, Endangered species -- Forecasts and trends, Climatic changes -- Influence -- Forecasts and trends -- Management, Company business management, Market trend/market analysis, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Many species are projected to become vulnerable to twenty-first-century climate changes (1,2), with consequent effects on the tree of life. If losses were not randomly distributed across the tree of [...]

Published
2011
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49. A biogeographical analysis of Muhlenbergia (Poaceae: Chloridoideae: Cynodonteae: Muhlenbergiinae).

Author

Peterson, Paul M., Roquet, Cristina, Romaschenko, Konstantin, Herrera Arrieta, Yolanda, and Susanna, Alfonso

Subjects
*DNA sequencing, *GRASSES, *GENETIC markers, *MOLECULAR phylogeny, *PHYLOGENY
Abstract

A phylogeny based on the analysis of six DNA sequence markers (ITS, ndhA intron, rpl32‐trnL, rps3, rps16 intron, and rps16‐trnK) is used to infer ancestral areas and divergence times, and reconstruct the biogeographical history and evolution of 150 of the 183 (82%) species of Muhlenbergia. Our results suggest that the genus originated 9.3 mya in the Sierra Madre (Occidental and Oriental) in Mexico, splitting into six lineages: M. ramulosa diverging 8.2 mya, M. subg. Muhlenbergia at 5.9 mya, M. subg. Pseudosporobolus at 5.9 mya, M. subg. Clomena at 5.4 mya, M. subg. Bealia at 4.3 mya, and M. subg. Trichochloa at 1 mya, each of these with a high probability of Sierra Madrean origin. Our results further suggest that founder‐event speciation from Sierra Madre to South America occurred independently multiple times in all five subgenera during the Pleistocene and late Pliocene. One long‐distance dispersal event most likely originating from Central or Eastern North America to East and Central Asia occurred 1.6–1 mya in M. subg. Muhlenbergia. In our cladogram, members of M. subg. Trichochloa show little genetic resolution, suggesting very low levels of divergence among the species, and this may be a consequence of rapid radiation. [ABSTRACT FROM AUTHOR]

Published
2022
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50. The Treasure Vault Can be Opened : Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

Author

Alsos, Inger Greve, Lavergne, Sebastien, Merkel, Marie Kristine Føreid, Boleda, Marti, Lammers, Youri, Alberti, Adriana, Pouchon, Charles, Denoeud, France, Pitelkova, Iva, Pușcaș, Mihai, Roquet, Cristina, Hurdu, Bogdan-Iuliu, Thuiller, Wilfried, Zimmermann, Niklaus E., Hollingsworth, Peter M., Coissac, Eric, Alsos, Inger Greve, Lavergne, Sebastien, Merkel, Marie Kristine Føreid, Boleda, Marti, Lammers, Youri, Alberti, Adriana, Pouchon, Charles, Denoeud, France, Pitelkova, Iva, Pușcaș, Mihai, Roquet, Cristina, Hurdu, Bogdan-Iuliu, Thuiller, Wilfried, Zimmermann, Niklaus E., Hollingsworth, Peter M., and Coissac, Eric

Abstract

Altres ajuts: The Sixth European Framework Programme (GOCE-CT-2007-036866), 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.

Published
2020

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