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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
    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.
  • Publication
    Accès libre
    Monophyly and relationships of the tribe Exaceae (Gentianaceae) inferred from nuclear ribosomal and chloroplast DNA sequences
    (2003)
    Yuan, Yong-Ming
    ;
    Wohlhauser, Sébastien
    ;
    Moller, Michael
    ;
    Chassot, Philippe
    ;
    Mansion, Guilhem
    ;
    Grant, Jason 
    ;
    Küpfer, Philippe 
    ;
    Klackenberg, Jens
    Both chloroplast trnL (UAA) intron and nuclear ribosomal ITS sequences highly confirmed the monophyly of the tribes of the Gentianaceae defined by the recent classification, and revealed the tribe Exaceae as a basal clade just next to the basal-most lineage, the tribe Saccifolieae. Within the tribe Exaceae, Sebaea (except Sebaea madagascariensis) appeared as the most basal clade as the sister group to the rest of the tribe. The Madagascan endemic genera Gentianothamnus and Tachicrdenus were very closely related to each other, together standing as sister to a clade comprising Sebaea madagascariensis, Ornichia, and Exacum. The saprophytic genus Cotylanthera nested deeply inside Exacum. Sebaea madagascariensis was shown closer to the Madagascan endemic genus Ornichia than to any other sampled Sebaea species. Exacum appeared as the most derived taxon within this tribe. The topology of the phylogenetic trees conform with the Gondwana vicariance hypothesis regarding the biogeography of Exaceae. However, no evidence for matching the older relationships within the family to the tectonic history could be corroborated with various divergence time analyses. Divergence dating estimated a post-Gondwana diverging of the Gentianaceae about 50 million years ago (MYA), and the tribe Exaceae as about 40 MYA. The Mozambique Channel land-bridge could have played an important role in the biogeographic history of the tribe Exaceae. (C) 2003 Elsevier Science (USA). All rights reserved.
  • Publication
    Accès libre
    Convergent Vessel Diameter–Stem Diameter Scaling across Five Clades of New and Old World Eudicots from Desert to Rain Forest
    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
    Molecular phylogeny and systematics of the tribe Chorisporeae (Brassicaceae)
    German, Dmitry A
    ;
    Grant, Jason 
    ;
    Lysak, Martin A
    ;
    Al-Shehbaz, Ihsan A
    Sequence data from nuclear (ITS) and chloroplast (trnL-F) regions for 89 accessions representing 56 out of 64 species from all five genera of the tribe Chorisporeae (plus Dontostemon tibeticus) have been studied to test the monophyly of the tribe and its component genera, clarify its boundaries, and elucidate its phylogenetic position in the family. Both data sets showed strong support for the monophyly of the Chorisporeae as currently delimited, though the position of its tentative member D. tibeticus was not resolved by ITS. Parrya and Pseudoclausia are poly- and paraphyletic with regard to each other, and Chorispora is either polyphyletic or at least paraphyletic (comprising Diptychocarpus) within a weakly supported monophyletic clade. The incongruence in branching pattern among the markers was most likely caused by hybridization and possibly influenced by incomplete lineage sorting. The present results suggest uniting Pseudoclausia, Clausia podlechii, and Achoriphragma with Parrya and transferring P. beketovii and P. saposhnikovii to Leiospora (Euclidieae). We also obtained support for splitting Chorispora into two geographically defined groups, one of which is closer to Diptychocarpus. Both data sets revealed a close relationship of the Chorisporeae to Dontostemoneae, while ITS also indicated affinity to Hesperideae. Therefore, the position of Chorisporeae needs further verification. KeywordsBrassicaceae–Chorisporeae–Generic delimitation–Phylogeny–Parrya.
  • Publication
    Accès libre
    A Revision of Neotropical Bonyunia (Loganiaceae: Antonieae)
    Grant, Jason 
    A revision of the Neotropical genus Bonyunia M. R. Schomb. ex Progel (Loganiaceae, Antonieae) is provided, including a key to species, description, distribution, IUCN Red List status, and discussion. Bonyunia is morphologically and ecologically diverse with taxonomically informative characters that include habit, seed and leaf morphology, and the shape and indument of the calyx, bracts, and bracteoles. Bonyunia occurs in lowland regions of the Amazon River watershed (Brazil and Bolivia), the Orinoco River watershed (Colombia and Venezuela), tepuis of the Guayana region and outliers (Brazil, Guyana, Venezuela, and Colombia), and lowland regions of Amazon Basin–facing Andes in Peru, throughout on white sands. Ten species are recognized, including four established species: B. antoniifolia Progel, B. aquatica Ducke, B. minor N. E. Br. (including B. cinchonoides Gleason & Standl.), and B. superba M. R. Schomb. ex Progel. Six species are newly described: B. excelsa J. R. Grant (Colombia), B. magnifica J. R. Grant (Brazil), B. nobilis J. R. Grant (Colombia), B. pulchra Ricketson, J. R. Grant & Liesner (Peru), B. spectabilis J. R. Grant (Guyana), and B. venusta J. R. Grant (Brazil).
  • Publication
    Accès libre
    Andean Speciation and Vicariance in Neotropical Macrocarpaea (Gentianaceae-Helieae)
    Struwe, Lena
    ;
    Haag, Scott
    ;
    Heiberg, Einar
    ;
    Grant, Jason 
    The genus Macrocarpaea (Griseb.) Gilg (Gentianaceae, Helieae) is among the largest woody genera of tropical gentians, with most of its species occurring in the wet mountainous forests of the Andes. Phylogenetic and dispersal-vicariance analyses (DIVA) of 57 of the 105 currently recognized species in the genus, using two data sets from nuclear DNA (ITS and 5S-NTS sequences) and morphology, show a single origin of the Andean species from an ancestral distribution that includes southeastern Brazil. Within the Andes, species divide into two major clades: (1) northern species from the cordilleras of northern Ecuador, Colombia, and Venezuela; and (2) southern species of the Andean Amotape–Huancabamba Zone in Ecuador and Peru, as well as the Andes of central and southern Peru and Bolivia. The Amotape–Huancabamba Zone is supported as the ancestral area for Macrocarpaea within the Andes. There are repeated speciation patterns within the Andes, and three Mesoamerican species derive from the northern clade, as is the single sampled species from the Guayana Shield. The position of the subclade of the three Caribbean species is less certain, but it currently nests among Andean species. An Atlantic coastal Brazilian clade is placed as sister group to all other Macrocarpaea, providing further support for an ancestral refuge in southeastern Brazil for the Helieae. The biogeographic analysis showed that local speciation is more common than long-distance dispersal, and allopatric speciation is more common than sympatric speciation. Using detailed, georeferenced herbarium collection data, patterns in environmental characteristics between clades and sister species were analyzed with Spatial Evolutionary and Ecological Vicariance Analysis (SEEVA), utilizing geographic information system (GIS) and statistical methods. Sister clades and taxa were evaluated for statistical significance in variables such as annual rainfall and temperature, elevation, temperature and rainfall seasonality, geological bedrock age, and soil type to evaluate ecological vicariance between sister groups. The results indicate that there are no general patterns for each variable, but that there are many significant divergences in ecological niches between both larger sister groups and sister species, and ecological niche conservation was also observed when subsequent nodes in the phylogeny were compared.
  • Publication
    Accès libre
    Molecular phylogenetics supports widespread cryptic species in moonworts (Botrychium s.s., Ophioglossaceae)
    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.