Literature DB >> 30455217

Specimen-based analysis of morphology and the environment in ecologically dominant grasses: the power of the herbarium.

Christine A McAllister1, Michael R McKain2,3, Mao Li2, Bess Bookout4, Elizabeth A Kellogg5.   

Abstract

Herbaria contain a cumulative sample of the world's flora, assembled by thousands of people over centuries. To capitalize on this resource, we conducted a specimen-based analysis of a major clade in the grass tribe Andropogoneae, including the dominant species of the world's grasslands in the genera Andropogon, Schizachyrium, Hyparrhenia and several others. We imaged 186 of the 250 named species of the clade, georeferenced the specimens and extracted climatic variables for each. Using semi- and fully automated image analysis techniques, we extracted spikelet morphological characters and correlated these with environmental variables. We generated chloroplast genome sequences to correct for phylogenetic covariance and here present a new phylogeny for 81 of the species. We confirm and extend earlier studies to show that Andropogon and Schizachyrium are not monophyletic. In addition, we find all morphological and ecological characters are homoplasious but variable among clades. For example, sessile spikelet length is positively correlated with awn length when all accessions are considered, but when separated by clade, the relationship is positive for three sub-clades and negative for three others. Climate variables showed no correlation with morphological variation in the spikelet pair; only very weak effects of temperature and precipitation were detected on macrohair density.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
© 2018 The Author(s).

Entities:  

Keywords:  Andropogoneae; grassland dominants; herbarium; image analysis; plastome phylogeny

Mesh:

Year:  2018        PMID: 30455217      PMCID: PMC6282083          DOI: 10.1098/rstb.2017.0403

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  18 in total

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2.  MAFFT: iterative refinement and additional methods.

Authors:  Kazutaka Katoh; Daron M Standley
Journal:  Methods Mol Biol       Date:  2014

3.  High-throughput phenotyping.

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Review 4.  Grass inflorescence architecture and evolution: the origin of novel signaling centers.

Authors:  Clinton J Whipple
Journal:  New Phytol       Date:  2017-04-04       Impact factor: 10.151

5.  The Persistent Homology Mathematical Framework Provides Enhanced Genotype-to-Phenotype Associations for Plant Morphology.

Authors:  Mao Li; Margaret H Frank; Viktoriya Coneva; Washington Mio; Daniel H Chitwood; Christopher N Topp
Journal:  Plant Physiol       Date:  2018-06-05       Impact factor: 8.340

6.  Allopolyploidy, diversification, and the Miocene grassland expansion.

Authors:  Matt C Estep; Michael R McKain; Dilys Vela Diaz; Jinshun Zhong; John G Hodge; Trevor R Hodkinson; Daniel J Layton; Simon T Malcomber; Rémy Pasquet; Elizabeth A Kellogg
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-06       Impact factor: 11.205

7.  Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens.

Authors:  Saman Saeidi; Michael R McKain; Elizabeth A Kellogg
Journal:  J Vis Exp       Date:  2018-03-08       Impact factor: 1.355

8.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.

Authors:  Alexandros Stamatakis
Journal:  Bioinformatics       Date:  2014-01-21       Impact factor: 6.937

9.  A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales.

Authors:  Michael R McKain; Haibao Tang; Joel R McNeal; Saravanaraj Ayyampalayam; Jerrold I Davis; Claude W dePamphilis; Thomas J Givnish; J Chris Pires; Dennis Wm Stevenson; James H Leebens-Mack
Journal:  Genome Biol Evol       Date:  2016-04-21       Impact factor: 3.416

10.  Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes.

Authors:  Michael R McKain; Ryan H Hartsock; Molly M Wohl; Elizabeth A Kellogg
Journal:  Bioinformatics       Date:  2016-09-14       Impact factor: 6.937

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  4 in total

1.  Biological collections for understanding biodiversity in the Anthropocene.

Authors:  Emily K Meineke; T Jonathan Davies; Barnabas H Daru; Charles C Davis
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2018-11-19       Impact factor: 6.237

2.  Digitized collections elucidate invasion history and patterns of awn polymorphism in Microstegium vimineum.

Authors:  Craig F Barrett; Cynthia D Huebner; Zoe A Bender; Trezalka A Budinsky; Cameron W Corbett; Maribeth Latvis; Michael R McKain; M'Kayla Motley; Samuel V Skibicki; Hana L Thixton; Mathilda V Santee; Aubrey N Cumberledge
Journal:  Am J Bot       Date:  2022-05-27       Impact factor: 3.325

3.  Characterizing 3D inflorescence architecture in grapevine using X-ray imaging and advanced morphometrics: implications for understanding cluster density.

Authors:  Mao Li; Laura L Klein; Keith E Duncan; Ni Jiang; Daniel H Chitwood; Jason P Londo; Allison J Miller; Christopher N Topp
Journal:  J Exp Bot       Date:  2019-11-18       Impact factor: 6.992

4.  The Extended Specimen Network: A Strategy to Enhance US Biodiversity Collections, Promote Research and Education.

Authors:  James Lendemer; Barbara Thiers; Anna K Monfils; Jennifer Zaspel; Elizabeth R Ellwood; Andrew Bentley; Katherine LeVan; John Bates; David Jennings; Dori Contreras; Laura Lagomarsino; Paula Mabee; Linda S Ford; Robert Guralnick; Robert E Gropp; Marcy Revelez; Neil Cobb; Katja Seltmann; M Catherine Aime
Journal:  Bioscience       Date:  2019-11-22       Impact factor: 8.589

  4 in total

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