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Grant, Jason

Nom
Grant, Jason
Affiliation principale
Fonction
Professeur.e ordinaire
Email
jason.grant@unine.ch
Identifiants
https://libra.unine.ch/handle/123456789/30709
_
0000-0002-1197-1131

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  • Publication
    Accès libre
    Evolutionary diversification in the hyper-diverse montane forests of the tropical Andes: radiation of Macrocarpaea (Gentianaceae) and the possible role of range expansion
    (2021-11-19)
    Kissling, Jonathan 
    ;
    Vieu, Julien 
    ;
    Hughes, Colin
    ;
    Grant, Jason 
    The humid mid-elevation montane forests (MMF) of the tropical Andes harbour high levels of plant species diversity, contributing to the exceptional overall diversity of the tropical Andean biodiversity hotspot. However, little is known about the diversification dynamics of MMF plant lineages compared to lineages in other Andean biomes. Here, we use Macrocarpaea (Gentianaceae) to investigate patterns of plant diversification in the MMF, using molecular dating with fossils and secondary calibration (from a family-wide phylogenetic analysis of Gentianaceae). We sequenced 76 of 118 recognized Macrocarpaea spp. for six markers to reconstruct a time-calibrated phylogenetic tree and infer the historical biogeography of Macrocarpaea using maximum-likelihood methods implemented in BioGeoBEARS, estimating diversification rates through time and among lineages with BAMM. We document a rapid radiation of Macrocarpaea in Andean MMF coinciding with rapid colonization and range expansion across the entire distribution of the genus in the Andes starting 7.2 Mya. Our results support allopatric founder-event speciation as the dominant process contributing to geographical phylogenetic structure across the genus. We propose that establishment of the MMF in the late Miocene, when the Andes attained critical elevation to modify regional climates, provided large new areas of suitable habitat for Macrocarpaea to quickly colonize and expand through repeated founder-events. We suggest that this wave of colonization and range expansion triggered rapid diversification, and, as the MMF became progressively occupied, the diversification rate slowed. Our study also supports the idea that MMF plant radiations are older and more slowly evolving than the quickly evolving lineages in the recent Andean high-elevation grasslands.
  • Publication
    Accès libre
    Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure
    (2021)
    Mossion, Vinciane 
    ;
    Benjamin Dauphin
    ;
    Grant, Jason 
    ;
    Michael Kessler
    ;
    Niklaus Zemp
    ;
    Croll, Daniel 
    AbstractFerns are the second most diverse group of land plants after angiosperms. Extant species occupy a wide range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources and within‐species studies based on high‐resolution markers are entirely lacking. The genus Botrychium belongs to the family Ophioglossaceae, which includes species with very large genomes and chromosome numbers (e.g., Ophioglossum reticulatum 2n = 1520). The genus has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome for Botrychium lunaria (L.) Sw., a diploid species with an extremely large genome of about ~19.0–23.7 Gb. We assembled 25,677 high‐quality transcripts with an average length of 1,333 bp based on deep RNA‐sequencing of a single individual. We sequenced 11 additional transcriptomes of individuals from two populations in Switzerland, including the population of the reference individual. Based on read mapping to reference transcript sequences, we identified 374,463 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kilobase. We found that all 12 transcriptomes were most likely from diploid individuals. The transcriptome‐wide markers provided unprecedented resolution of the population genetic structure, revealing substantial variation in heterozygosity among individuals. We also constructed a phylogenomic tree of 92 taxa representing all fern orders to ascertain the placement of the genus Botrychium. High‐quality transcriptomic resources and SNP sets constitute powerful population genomic resources to investigate the ecology, and evolution of fern populations.
  • Publication
    Accès libre
    Rapid allopolyploid radiation of moonwort ferns (Botrychium; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions
    (2018)
    Dauphin, Benjamin
    ;
    Grant, Jason 
    ;
    Farrar, Donald R
    ;
    Rothfels, Carl J
    Polyploidy is a major speciation process in vascular plants, and is postulated to be particularly important in shaping the diversity of extant ferns. However, limitations in the availability of bi-parental markers for ferns have greatly limited phylogenetic investigation of polyploidy in this group. With a large number of allopolyploid species, the genus Botrychium is a classic example in ferns where recurrent polyploidy is postulated to have driven frequent speciation events. Here, we use PacBio sequencing and the PURC bioinformatics pipeline to capture all homeologous or allelic copies of four long (∼1 kb) low-copy nuclear regions from a sample of 45 specimens (25 diploids and 20 polyploids) representing 37 Botrychium taxa, and three outgroups. This sample includes most currently recognized Botrychium species in Europe and North America, and the majority of our specimens were genotyped with co-dominant nuclear allozymes to ensure species identification. We analyzed the sequence data using maximum likelihood (ML) and Bayesian inference (BI) concatenated-data (“gene tree”) approaches to explore the relationships among Botrychium species. Finally, we estimated divergence times among Botrychium lineages and inferred the multi-labeled polyploid species tree showing the origins of the polyploid taxa, and their relationships to each other and to their diploid progenitors. We found strong support for the monophyly of the major lineages within Botrychium and identified most of the parental donors of the polyploids; these results largely corroborate earlier morphological and allozyme-based investigations. Each polyploid had at least two distinct homeologs, indicating that all sampled polyploids are likely allopolyploids (rather than autopolyploids). Our divergence-time analyses revealed that these allopolyploid lineages originated recently—within the last two million years—and thus that the genus has undergone a recent radiation, correlated with multiple independent allopolyploidizations across the phylogeny. Also, we found strong parental biases in the formation of allopolyploids, with individual diploid species participating multiple times as either the maternal or paternal donor (but not both). Finally, we discuss the role of polyploidy in the evolutionary history of Botrychium and the interspecific reproductive barriers possibly involved in these parental biases.
  • Publication
    Accès libre
    Evolution of moonwort ferns ("Botrychium", Ophioglossaceae) on local to global scales
    (2017)
    Dauphin, Benjamin
    ;
    Grant, Jason 
    Les plantes ont depuis longtemps fasciné les biologistes par leur capacité à former des espèces cryptiques, des hybrides entre des espèces distinctes, de grandes tailles de génomes stables, et une large variété de systèmes reproducteurs parmi les taxons qui ont conduit à l’actuelle biodiversité des plantes. Il y a plus de 450 millions d’années, les plantes vasculaires ont émergé et colonisé la terre. Rapidement, elles se sont dispersées pour explorer de nouveaux habitats et se sont diversifiées dans des environnements favorables pour former plus de 300 000 espèces vivantes. Une meilleure compréhension des forces évolutives passées qui ont mené aux morphologies, aux écologies, et aux diversités génétiques actuelles des plantes est essentielle pour prédire leur évolution, particulièrement dans le contexte des changements globaux. Ainsi, les objectifs principaux de cette thèse consistaient à étudier les relations phylogénétiques parmi les taxons de Botrychium et comment l’allopolyploïdie et l’alternance des systèmes reproducteurs ont mené à la spéciation de ces espèces.
    Dans un cadre multidisciplinaire, nous avons combiné la phylogénétique avec la génétique des populations et la cytométrie en flux pour produire des données cellulaires et moléculaires pertinentes pour l’exploration des mécanismes biologiques clefs prenant place à des échelles locales ou globales. Etant les fondements de notre projet, nous avons reconstruit la phylogénie chloroplastique du genre Botrychium basée sur un échantillonnage mondiale pour examiner les relations de parentés parmi les taxons diploïdes et les origines maternelles des allopolyploïdes. Dans une seconde étape, nous avons estimé les tailles de génome des Botrychium diploïdes et polyploïdes pour comparer les variations du contenu en ADN après l’allopolyploïdisation et entre les niveaux de ploïdie. Ensuite, nous avons utilisé le séquençage PacBio pour inférer une phylogénie moléculaire dans le but de révéler l’histoire évolutive des deux, les lignées maternelles et paternelles des allopolyploïdes, et d’établir l’échelle temporelle de leur héritage bi-parentale basée sur les estimations des temps de divergence. Travaillant à une échelle régionale et locale, nous avons génotypé des populations de B. lunaria des alpes en utilisant des variants enzymatiques co-dominants et des données de séquençage ddRAD pour caractériser le mode prédominant de reproduction ainsi que leur histoire démographique durant le dernier maximum glaciaire.
    Nous avons trouvé des résultats inattendus et des découvertes majeures pour la compréhension de la biologie des plantes vasculaires précoces. Pour la diversité spécifique elle-même, nous avons identifié treize nouveaux taxons potentiels et caractérisé la diversité exceptionnelle d’haplotypes survenant dans le complexe d’espèce Lunaria. De plus, nous avons présenté des évidences pour l’origine multiple de plusieurs taxons allopolyploïdes et révélé des cas incontestables de dipersion intercontinentale d’amérique du nord vers l’europe et l’asie. Avec la cytométrie en flux, nous avons rapporté un nouveau taxa hexploïde chez Botrychium et avons décrit différentes tailles de génome entre espèces diploïdes des deux clades majeurs, Lanceolatum et Lunaria. Par ailleurs, nos résultats ont supporté le scénario de stabilité des tailles de génome après l’allopolyploidization, rejetant ainsi l’hypothèse de la réduction des tailles de génome largement acceptée chez les angiospermes. Le résultat le plus frappant dans nos investigations phylogénétiques est probablement la récurrence de l'allopolyploïdie dans ce genre et les contributions asymétriques des donneurs parentaux dans la formation des taxons allopolyploïdes. De plus, nos estimations du temps de divergence ont révélé la spéciation récente et rapide par allopolyploïdie au cours des deux derniers millions d'années, ce qui constitue un premier cas de radiation dans l'ancienne lignée des Ophioglossaceae. Pour notre étude sur la génétique des populations, nous avons trouvé une diversité génétique sans précédent dans les populations de B. lunaria avec un grand nombre d'hétérozygotes qui soutient la prédominance pour la fécondation croisée. Ainsi, nous avons présenté les capacités de dispersion et de diversification des espèces de Botrychium afin de mieux comprendre le système d'accouplement des plantes vasculaires ancestrales. En tant qu'élément clef de ce modèle de spéciation, nous avons trouvé une signature génétique indicative d'un refuge pour B. lunaria dans les alpes centrales lors du dernier maximum glaciaire, lequel a abrité des individus ayant une richesse allélique élevée, qui se sont ensuite dispersés durant la déglaciation tout en maintenant la fécondation croisée.
    Indéniablement, le genre Botrychium offre une occasion unique d'aborder le rôle de l'allopolyploïdie et l'importance de l'alternance des systèmes d'accouplement dans la spéciation des plantes. Ce travail est destiné à être le point de départ pour d'autres études en biologie évolutive, lesquelles permettront peut-être de mieux comprendre le cycle de vie de ces espèces de fougères énigmatiques., Plants have long fascinated biologists by their ability to form cryptic species, hybrids between distinct species, large and stable genome sizes, and a wide variety of mating systems among taxa that have driven to the current plant biodiversity. More than 450 million year ago, vascular plants emerged and colonized the land. Rapidly, they dispersed to explore new habitats and diversified in suitable environments to form over 300,000 extant species. A better understanding of past evolutionary forces that led to the current plant morphologies, ecologies, and genetic diversity is critical for predicting their evolution, especially with the global changes ongoing. In this context, the main goals of this thesis were to investigate the phylogenetic relationships among the early divergent Botrychium taxa and how allopolyploidy and the alternation of mating systems have led to the speciation of these species.
    In a multidisciplinary framework, we combined phylogenetics with population genetics and flow cytometry to provide relevant cellular and molecular data for exploring key biological mechanisms taking place at local or global scale. As the backbone of our project, we reconstructed the plastid phylogeny of the genus Botrychium based on a worldwide sampling to investigate relationships among diploid taxa and the maternal origins of allopolyploids. As a second step, we estimated the genome sizes of Botrychium diploids and polyploids to study fluctuations of DNA amounts after allopolyploidization and between ploidy levels. Then, we applied PacBio sequencing to infer a nuclear phylogeny for revealing the evolutionary history for both, the maternal and the paternal lineages of allopolyploids, and drawing the timescale of their bi-parental inheritance based on divergence time estimates. Focusing at a local and regional scale, we genotyped B. lunaria populations in Alps using co-dominant allozymes and ddRADseq data to identify the predominant mode of reproduction as well as its demographic history during the last glacial maximum.
    We found unexpected results and major discoveries for the understanding of the biology of early vascular plants. For the species diversity itself, we identified thirteen possibly new taxa and characterized the exceptional haplotype diversity occurring in the Lunaria complex. Also, we presented evidence for multiple origins of several polyploid taxa and highlighted incontestable cases of inter-continental dispersal from North America to Europe and Asia. With flow cytometry, we reported a new hexaploid in Botrychium and described different genome sizes between diploid species of the two major clades Lanceolatum and Lunaria. Besides, our results supported the genome size stability after allopolyploidization, therefore rejecting the scenario of genome downsizing widespread accepted for angiosperms. Probably the most striking outcome of our phylogenetic investigations is the recurrent allopolyploidy in that genus and the strong bias of parental donors in the formation of allopolyploid taxa. Furthermore, our divergence time estimates revealed the recent and rapid speciation via allopolyploidy in the last two million years, which constitutes a first case of radiation in the old lineage of Ophioglossaceae. For our population genetics study, we found unprecedented genetic diversity within B. lunaria populations with a large number of heterozygotes that supports the outcrossing mating system. Thus, we presented the capabilities of dispersion and diversification of these Botrychium species to better understand the ancestral vascular plant mating system. Being a key element of this speciation model, we found a genetic signature indicative of a refuge for B. lunaria in the central Alps during the last glacial maximum, which has hosted individuals having a high allele richness that was secondarily dispersed after deglaciation with the maintenance of outcrossing in alpine grasslands.
    Undeniably, the genus Botrychium offers a unique opportunity to address the role of allopolyploidy and the importance of alternation of mating systems in plant speciation. This work is intended to be the starting point for further studies in evolutionary biology that ultimately will provide a better understanding of the life style of these enigmatic fern species.
  • Publication
    Accès libre
    Molecular phylogenetics supports widespread cryptic species in moonworts (Botrychium s.s., Ophioglossaceae)
    (2014)
    Dauphin, Benjamin
    ;
    Vieu, Julien 
    ;
    Grant, Jason 
    Premise of the study: Previous phylogenetic studies of moonworts (Botrychium sensu stricto (s.s.)) included few taxa from outside of North America. This low geographical representation limited interpretations of relationships of this group rich in cryptic species. With 18 out of 30 species in the genus being polyploid, understanding their evolutionary history remains a major challenge.
    Methods: A new molecular phylogeny was reconstructed using Maximum Likelihood (ML) and Bayesian Inference (BI) analyses based on multiple accessions of the most wide- ranging Arctic taxa of Botrychium in North America and Europe using three noncoding plastid DNA regions (psbA-trnHGUG, trnLUAA- trnFGAA intergenic spacer, and rpL16 intron).
    Key results: The new phylogeny confirms the identity of several recently described species and proposed new taxa. Nine subclades are newly identified within the two major clades in Botrychium s.s.: Lanceolatum and Lunaria. Chloroplast DNA was variable enough to separate morphologically cryptic species in the Lunaria clade. On the contrary, much less variation is seen within the morphologically variable Lanceolatum clade despite sampling over the same broad geographic range. The chloroplast region psbA-trnHGUG is identified as an efficient DNA barcode for the identification of cryptic taxa in Botrychium s.s.
    Conclusions: The combined increase in species representation, samples from throughout the geographic range of each species, and sequencing of multiple plastid DNA regions supports morphologically cryptic species in Botrychium s.s.
  • Publication
    Accès libre
    DE MACROCARPAEAE GRISEBACH (EX GENTIANACEIS) SPECIEBUS NOVIS XI: FIVE NEW SPECIES FROM THE ANDES OF ECUADOR AND COLOMBIA
    (2014)
    Grant, Jason 
    Five new species are described from Andean regions of Colombia and Ecuador including M. catherineae, M. cortinae, M. illuminata, M. pacifica, and M. umbellata. Macrocarpaea stenophylla is reported as a range extension from Peru to Ecuador.
  • Publication
    Accès libre
    DE MACROCARPAEAE GRISEBACH (EX GENTIANACEIS) SPECIEBUS NOVIS XII: THREE NEW SPECIES FROM THE ANDES OF PERU
    (2014)
    Grant, Jason 
    ;
    Vieu, Julien 
    Three new species from Peru, Macrocarpaea abiseo, M. felicitata, and M. huamantanga, are described and illustrated.
  • Publication
    Accès libre
    Convergent Vessel Diameter–Stem Diameter Scaling across Five Clades of New and Old World Eudicots from Desert to Rain Forest
    (2013)
    Olson, Mark E
    ;
    Rosell, Julieta A
    ;
    León, Calixto
    ;
    Zamora, Salvador
    ;
    Weeks, Andrea
    ;
    Alvarado-Cardenas, Leonardo O
    ;
    Ivalu Cacho, N
    ;
    Grant, Jason 
    Premise of research. Variation in average xylem vessel diameter across species has important functional consequences, but the causes of this variation remain unclear. Average vessel diameter is known to scale with stem size within and across species. Vessel diameter also seems to differ between clades and across environments, with dryland plants having narrower, more cavitation-resistant vessels. As a result, it is not clear to what extent phylogenetic affinity and environment are associated with differences in the vessel diameter–stem size relationship.
    Methodology. With linear models and correlations, we explored the influence of environment and phy- logeny on the vessel diameter–stem diameter relationship in a molecular phylogenetic context across 83 species in four families spanning desert to rain forest in the Americas, Africa, Asia, and Madagascar.
    Pivotal results. Mean species vessel diameter was strongly predicted by trunk diameter (slope ∼ 0.33), and this slope was not affected by either phylogenetic affinity or environment. Clades differed only slightly in mean vessel diameter when controlling for stem size, and there was no tendency for plants of moist environments to have wider vessels. Of four climate indexes, only the temperature index contributed to explaining vessel diameter, although very weakly.
    Conclusions. Our results are congruent with models suggesting that natural selection should maximize vessel conductivity while minimizing cavitation risk via vessel taper in the context of conductive path length. Because neither environment nor phylogeny contributed to explaining vessel diameter–stem diameter scaling across species, our results appear congruent with the notion that selection favoring cavitation resistance via narrow vessels should lead to shorter statures independently of ancestry or habitat. The repeated finding of narrow vessels in dryland plants might therefore reflect the smaller average stem size of plants in drylands rather than the plants having vessels that are narrow for their stem diameters.
  • Publication
    Accès libre
    Two new species of Gentianella (Gentianaceae) from Peru
    (2012)
    Pringle, James S
    ;
    Grant, Jason 
    Two new species of Gentianella (Gentianaceae, Gentianeae, Swertiinae), G. grantii and G. wayqecha, are described from Departamento Cusco, Peru. These two species differ from other Peruvian species of Gentianella in a combination of stems 10–100 cm long; no rosette of basal leaves; cauline leaves 10– 75 mm long; flowers in thyrses; and corollas 14–26 mm long, campanulate, and adaxially glabrous. The leaves of G. grantii consist of an appressed pseudopetiole and a spreading, narrowly elliptic-oblong to linear blade; the corollas are lavender; and the corolla lobes are 0.6–0.7× as long as the tube. Gentianella grantii is similar to G. lythroides, of Bolivia, but differs in having more closely spaced leaves and less deeply lobed corollas. The leaves of G. wayqecha are sessile, lanceolate to ovate; the corollas are rose-violet; and the corolla lobes are 0.75–1.35× as long as the tube. Gentianella wayqecha is similar to G. rapunculoides, of Colombia and Ecuador, and G. ruizii, of Peru, but differs from both in its adaxially glabrous corollas and from G. rapunculoides in its less deeply lobed corollas. Both G. grantii and G. wayqecha grow in moist habitats near tree line, and are known only from a area northeast of the city of Cusco.