Publications by authors named "Phillip C Klahs"

4 Publications

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3D shape analysis of grass silica short cell phytoliths: a new method for fossil classification and analysis of shape evolution.

New Phytol 2020 10 1;228(1):376-392. Epub 2020 Jul 1.

University of Washington Biology Department, Life Sciences Building, Seattle, WA, 98105, USA.

Fossil grass silica short cell phytoliths (GSSCP) have been used to reconstruct the biogeography of Poaceae, untangle crop domestication history and detect past vegetation shifts. These inferences depend on accurately identifying the clade to which the fossils belong. Patterns of GSSCP shape and size variation across the family have not been established and current classification methods are subjective or based on a 2D view that ignores important 3D shape variation. Focusing on Poaceae subfamilies Anomochlooideae, Pharoideae, Pueliodieae, Bambusoideae and Oryzoideae, we observed in situ GSSCP to establish their orientation and imaged isolated GSSCP using confocal microscopy to produce 3D models. 3D geometric morphometrics was used to analyze GSSCP shape and size. Classification models were applied to GSSCP from Eocene sediments from Nebraska, USA, and Anatolia, Turkey. There were significant shape differences between nearly all recognized GSSCP morphotypes and between clades with shared morphotypes. Most of the Eocene GSSCP were classified as woody bamboos with some distinctive Nebraska GSSCP classified as herbaceous bamboos. 3D morphometrics hold great promise for GSSCP classification. It accounts for the complete GSSCP shape, automates size measurements and accommodates the complete range of morphotypes within a single analytical framework.
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http://dx.doi.org/10.1111/nph.16677DOI Listing
October 2020

Leaf shape and size track habitat transitions across forest-grassland boundaries in the grass family (Poaceae).

Evolution 2019 05 26;73(5):927-946. Epub 2019 Mar 26.

Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011.

Grass leaf shape is a strong indicator of their habitat with linear leaves predominating in open areas and ovate leaves distinguishing forest-associated grasses. This pattern among extant species suggests that ancestral shifts between forest and open habitats may have coincided with changes in leaf shape or size. We tested relationships between habitat, climate, photosynthetic pathway, and leaf shape and size in a phylogenetic framework to evaluate drivers of leaf shape and size variation over the evolutionary history of the family. We also estimated the ancestral habitat of Poaceae and tested whether forest margins served as transitional zones for shifts between forests and grasslands. We found that grass leaf shape is converging toward different shape optima in the forest understory, forest margins, and open habitats. Leaf size also varies with habitat. Grasses have smaller leaves in open and drier areas, and in areas with high solar irradiance. Direct transitions between linear and ovate leaves are rare as are direct shifts between forest and open habitats. The most likely ancestral habitat of the family was the forest understory and forest margins along with an intermediate leaf shape served as important transitional habitat and morphology, respectively, for subsequent shifts across forest-grassland biome boundaries.
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http://dx.doi.org/10.1111/evo.13722DOI Listing
May 2019

A refined method for digitally modeling small and complex plant structures in 3D: An example from the grasses (Poaceae).

Appl Plant Sci 2018 Aug 27;6(8):e01177. Epub 2018 Aug 27.

Department of Ecology, Evolution, and Organismal Biology Iowa State University 2200 Osborn Drive Ames Iowa 50011 USA.

Premise Of The Study: A refined procedure is described for modeling small, intricate plant structures using computer-aided design software. The procedure facilitates the study of wind pollination in the family Poaceae and provides virtual biological illustrations for public outreach.

Methods And Results: Spikelets were fixed in gFAA, dehydrated using ethanol and xylene, embedded in paraffin wax, and then sectioned with a rotary microtome. Images of serial sections were used as a reference for modeling the shape of bracts with splines in a computer-aided design program. Virtual models produced by this method have many potential uses; examples include geometric morphometric analyses and simulations of computational fluid dynamics.

Conclusions: This protocol is a synthesis of modern biological illustration and engineering technology. Virtual models facilitate quantitative experiments that may address questions about reproductive biology, conditions shaping the form of anatomical support, or the morphological evolution of structures of biomechanical interest.
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http://dx.doi.org/10.1002/aps3.1177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6110240PMC
August 2018

Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace.

Front Plant Sci 2018 25;9:553. Epub 2018 Apr 25.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.

Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.
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http://dx.doi.org/10.3389/fpls.2018.00553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996898PMC
April 2018
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