GCG 2017 - Notes from lectures

From systematics

Jump to: navigation, search

Notes from lectures presented Thursday morning will be posted after review by each presenter.


Martin, Santiago, Pablo de Olavide University (Spain): Rhynchocycstis

Notes currently under review

Ford, Bruce, University of Manitoba (Canada) -- Sedges of Vietnam

With Julian Star and Etienne Leveille-Bourret Notes currently under review

Starr, Julian, University of Ottawa (Canada) -- Traditional molecular markers, anchored phylogenomics, morphology and embryology support a new tribal and subtribal classification of the CDS clade (Cariceae, Dulichieae, Scirpeae)

With Etienne Leveille-Bourret Notes currently under review

Hayat, Muhammad Qasim, National University of Sciences and Technology, Islamabad (Pakistan) -- The Importance, Biodiversity and and Phytogeography of Cyperacae in Pakistan with special emphasis on Carex

Notes currently under review

Hoffmann, Matthias, Martin-Luther-Universität Halle-Wittenberg (Germany) -- Using the Global Carex Groups Megaphylogeny: The evolution and recruitment of Arctic Carex species


  • Arctic checklist
  • GCG phylogeny 2016
  • WCM -- cyperaceae
  • Ecological data from text mining, 8 floras and ca. 90 manually added spp
  • Arctic spp mapped onto tree, with strong


  1. origins of arcic sedges
  2. altitudinal origin
  3. habitat origins


  • 46 origins, at least 46 independent origins
  • diversity centers: quite variable
  • Habitat: most arctic spp are from wet regions, though some are from drier habitats
  • Altitude: most clades are from high mountains, some from lower elevation
  • Open vs forested: mostly from open conditions, but some are from forested conditions
  • In sum, alpine sedges are a community assembled from disparate habitats and areas

Uzma, National University of Sciences and Technology, Islamabad (Pakistan) [via Skype] -- Biogeography of Himalayan Carex

Introduction: Himalaya

  • Derives from Sanskrit, meaning Abode of snow. It's the world's highest range, spread across Pakistan, China, India, Nepal and Bhutan
  • Flora varies depending on altitude and climate

Himalayan Carex

  • 209 spp, 47 sections (10% of total Carex species)
  • one study with phylogeny using matK, plus morphological and taxonomy work
  • why so few? taxonomy, difficulty of collection, complex morphology
  • Research gaps: phylogeny, origins of Himalayan Carex

Research objectives

  1. Phylogeny
  2. Divergence times and ancestral areas analysis

Research work

  • sampling
  • sequencing of ITS, ETS, matK
  • GCG data from Dryad, aligned using muscle
  • phylogeny using RAxML, 3 genes with gaps
  • Coding of biogeographical regions
  • BEAST analysis for dated analysis
  • DEC analysis for ancestral areas, dispersal and extinction rate


  • There are a few radiations of Himalayan Carex
  • association with the Indomalayan and palearctic spps, but many origins

Jimenez-Mejias, Pedro, New York Botanic Garden -- Geographical and ecological drivers of diversification in Mediterranean Carex

Study group

  • Carex panormitana
  • C. reuteriana


  1. Differentiation due to allopatric speciation, resulting from range restriction during Pleisotcene glaciations
  2. Niche conservatism


  • DNA data
  • AFLPs
  • ENM based on extant spp and fossils


  1. Divergence from sister group during Pleistocene
  2. divergence between spp ca. 1 mya
  3. Niche overlap, but differentiation between the subspecies of C. reuteriana (reuteriana and mauritanica) is somewhat greater
  4. checking model predictions against fossil distributions, recovers approximately the same distribution

Pender, Jocelyn, University of Ottawa (Canada) -- Community assembly in North American sedges


  • So many Carex
  • Availability of sequence and trait data
  • Why are there so many North American Carex? Niche segregation? morphological differentiation? other?
  • Q: does rapid exploration of morphospace and ecological space lead to high sp richness?


  • Restricted to 480 spp of FNA region
  • Sequence data: matK, rps16, ITS, ETS; inferred phylogeny
  • Morphological data from FNA: culm height, leaf blade width, perigynium length, perigynium width, achene length
  • GBIF data wtih WORLDCLIM
  • NWPL for wetlands
  • Habitat data, light: scored by Andrew and Julian
  • analysis:
  1. Brownian motion to estimate rate of evolution
  2. sister clade analysis for looking at non-nested sisters


  1. Strongest correlations (r2 = 0.24) between reproductive characters and diversity
  2. Habitat differentiation also associates with diversity

Reznicek, Tony, University of Michigan (USA) -- Sedges of Mexico

Notes currently under review

Spalink, Daniel, University of Utah (USA) -- Phylogenetic patterns of community assembly in North American sedges

Notes currently under review

Bruederle, Leo, University of Colorado - Denver (USA) -- ddRAD Seq data on Carex scirpoidea

Notes currently under review

Maguilla, Enrique, Pablo de Olavide University (Spain) -- RADseq phylogenetics in Carex: Glareosae and Schoenoxiphium

Notes currently under review

Villaverde, Tamara, Real Jardín Botanico de Madrid (Spain) -- A preliminary HybSeq phylogeny of the genus Carex, and markers for the Cyperaceae

Notes currently under review

Kim, Sangtae, Sungshin Women’s University (S. Korea) -- Floral evo-devo studies in Carex

Notes currently under review

Lee, Bora, Sungshin Women’s University (S. Korea) -- Dynamic evolution of chloroplast IR borders in Cyperaceae

Notes currently under review

Larridon, Isabel, RBG Kew (England) -- Cyperaceae studies at Kew

Costularia s.l. (Schoeneae)

  • Macrophylogeny: There are appear to be 4 independently evolved lineages, in two different Schoeneae clades together forming four genera instead of one
  • Taxonomy of the African / Malagasy spp

==Scleria (Sclerieae)

  1. New spp of Scleria subg. Hypoporum
  2. Mol phyl of Scleria subg Hypoporum
  3. Revision worldwide
  4. Revision of W African Scleria


  1. Character evolution -- importance of small embryos
  2. Collaboration with Ghent

Science strategy: sedges

  1. PAFTOL is taking HybSeq approach to generate a new angiosperm tree; Cyperaceae is a part of this (120 samples, one sample per genus, plus major infrageneric lineages)
  2. TIPAs
  3. Is climate change differentially affecting C3 and C4 plant lineages in Africa? A case study in Cyperaceae (100 samples of species belonging to all c4 lineages plus their key C3 relatives will be sequenced using the Kew HybSeq kit)
  4. Anatomical enablers and evolution of C4 in sedges: Kew slide collection + living collections at UGENT
  5. Future collaborations: which bait kit for Cyperaceae?
  6. "SedgeBase" trait database?

Waterway, Marcia, McGill University (Canada) -- Effects of adding genes and adding taxa on topology and support across the Carex tree


250 taxa, 9 gene regions, representatives from 92 sections. gene sampling:

  • nrDNA, ETS + ITS: 1444 bp
  • plastid coding: matK + rbcL: 2194 bp
  • plastid non-coding: rpl16, rps16, trnEYD, trnK, trnL-trnF: 5874 bp

nearly complete sampling: less than 1% empty cells (mostly trnK)

Nature of the data

Informative characters: most informative characters from cpDNA for most of the tree, but ETS + ITS beats cpDNA in Vignea Various permutations of datasets analyzed


Q1: is there a Caricoid clade?

  • single-gene trees: matK, strong; trnk, trnL-trnF, weak
  • combination trees:
    • ETS + ITS + plastid coding, ETS + ITS + plastid non-coding, 3-gene, 5-gene, 9-gene: all strong
    • plastid DNA only: weak

Q2: what are the relationships among the major clades

  • All trees except matK single-gene tree support Siderostictae as the sister to the restriction
  • Caricoid sister to Vignea + core carex: plastid alone is weak, and both coalescent analyses
  • Vignea + Caricoid: none
  • Caricoid + core Carex: strongly supported by ITS / ETS, no matter what else is with it

Sectional relationships

  • Spirostachyae + Echonochlaenae + Rostrales + Strigosae + Rhynchocycstis + Triquetrae + C. frigida: supported by almost all character sets and analyses
  • Careyanae + Griseae + Granulares strongly supported, but nearly always sister to Collinseae + C. luzulina group
  • Rhomboidales + Mitratae + Cryptostachyae + part of Aulocystis: supported by 9-gene tree and plastid tree, but 3 gene and 5-gene trees break it up. On this matter, morphology agrees better with the 9-gene and plastid trees
  • What about Vigneastra: the nature of early divergence in Core Carex.
Personal tools