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Home / Plant Anatomy & Taxonomy / Chemotaxonomy and Chemometric Palaeobotany

Plant Anatomy
Taxonomy, Systematics, Plant Classification
Cladistic Methods of Phylogenetic Analysis

! The Molecular Clock and/or/versus the Fossil Record
! Molecular Palaeobotany@
! Plant Fossil Preservation and Plant Taphonomy@
! Pyrite Preservation@
! Coalification@
Teaching Documents about Evolution@

Chemotaxonomy and Chemometric Palaeobotany

Y. Asar et al. (2022): Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution. In PDF, bioRxiv.
See also here.
! Note figure 1 (on PDF-page 9): A flowchart of simulation study. About molecular and morphological phylograms, morphological characters and sequence alignments.

! J. Barros et al. (2015): The cell biology of lignification in higher plants. Free access, Annals of Botany, 115: 1053–1074.

L. Bénichou et al. (2018): Consortium of European Taxonomic Facilities (CETAF) best practices in electronic publishing in taxonomy. European Journal of Taxonomy 475: 1–37. See also here.

Bernstein, Washington and New Orleans, March 21-27, 2003: (American Chemical Society, EurekAlert): Scientists find evidence for crucial root in the history of plant evolution.

M.E. Collinson (2011): Molecular Taphonomy of Plant Organic Skeletons. Abstract, In: Allison, P.A., Bottjer, D.J. (eds): Taphonomy. Aims & Scope Topics in Geobiology Book Series, 32: 223-247.

! J.A. Cunningham et al. (2016): The origin of animals: can molecular clocks and the fossil record be reconciled? Open access, Bioessays, 39. See also here (in PDF).
Note figure 1: Summary of major Ediacaran and early Cambrian fossil assemblages.
! Figure 2. The mismatch between the fossil and molecular clock records of early animal evolution.
"... Molecular clocks estimate that animals originated and began diversifying over 100 million years before the first definitive metazoan fossil evidence in the Cambrian. However, closer inspection reveals that clock estimates and the fossil record are less divergent than is often claimed.
[...] A considerable discrepancy remains, but much of this can be explained by the limited preservation potential of early metazoans and the difficulties associated with their identification in the fossil record.

J.A. D´Angelo et al. (2012): Compression map, functional groups and fossilization: A chemometric approach (Pennsylvanian neuropteroid foliage, Canada). Abstract, International Journal of Coal Geology.

J.A. D´Angelo et al. (2011): Chemometric analysis of functional groups in fossil remains of the Dicroidium flora (Cacheuta, Mendoza, Argentina): Implications for kerogen formation. In PDF.

! J.A. D´Angelo et al. (2010): Chemometric study of functional groups in Pennsylvanian gymnosperm plant organs (Sydney Coalfield, Canada): Implications for chemotaxonomy and assessment of kerogen formation. In PDF, Organic Geochemistry, 41: 1312-1325.

! M. Dohrmann and G. Wörheide (2017): Dating early animal evolution using phylogenomic data. Open access, Scientific reports, 7.
! Note Figure 4: Time-calibrated phylogeny of animals.

Royal Botanic Garden, Edinburgh. Molecular plant systematics.

Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey, UK: Research activities,
Molecular taphonomy, and
Molecular Palaeobotany.

European Asssociation of Organic Geochemistry

W.E. Friedman et al. (2004): The evolution of plant development. Free access, American Journal of Botany 91: 1726-1741.

William Friedman et al., Department of Ecology and Evolutionary Biology, University of Colorado, Boulder: Molecular and Organismal Research in Plant History, MORPH. MORPH, an NSF research coordination network, fosters cross-disciplinary interactions between organismic and molecular plant biologists studying the evolution of morphological diversity to promote a modern synthesis in plant evolutionary developmental biology. Go to: Publications.

! Linda E. Graham et al. (2000): The origin of plants: Body plan changes contributing to a major evolutionary radiation. Abstracts, Proceedings of the National Academy of Sciences, 97: 4535-4540.
! See also at here. (in PDF).

Guido Grimm, Department of Palaeobotany, Swedish Museum of Natural History, Stockholm: Cladistic analyses of fossil and recent Cycadales based on morphological and molecular data. See also
here (abstract), and there (in German).

S. Guindon (2020): Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods. Open access, Frontiers in Genetics, 11.
"... molecular dating will undoubtedly keep playing a crucial role in biology in the future. Our understanding of important phenomena such as species diversification or dispersal, population migration and demography, or the molecular signature resulting from environmental changes, depends on our ability to date past evolutionary events. The wealth of available techniques to perform this task provides a powerful set of tools to make progress in this direction. ..."

Y. Hautevelle et al. (2006): Confined pyrolysis of extant land plants: A contribution to palaeochemotaxonomy. In PDF, Organic Geochemistry, 37: 1546-1561.

Yann Hauteville et al. (2005): Use of paleochemotaxonomy for tracing paleoflora and paleoclimatic changes during Jurassic. See also:
Determination of the molecular signature of fossil conifers by experimental palaeochemotaxonomy. Contribution to palaeofloristic and palaeoclimatic reconstructions. Powerpoint presentations.

Barbara W. Heavers, Jane Y. Meneray, Jane E. Obbink, and Harry J. Wolf: Molecular Evolution in Plants.

Heckman, D.S., et al. 2001: Molecular evidence for the early colonization of land by fungi and plants. Science 293: 1129-1133.

! R. Hegnauer (1967): Chemical characters in plant taxonomy: some possibilities and limitations. In PDF.

! K. Ilic et al. (2007): The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Free access, Plant Physiology, 143: 587-599. "... Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology.
[...] we created the Plant Structure Ontology (PSO), the first generic ontological representation of anatomy and morphology of a flowering plant ..."

A.H. Jahren and N.C. Arens (2009): Prediction of atmospheric δ13CO2 using plant cuticle isolated from fluvial sediment: tests across a gradient in salt content. PDF file, Palaios, 24, 394-401.
Now provided by the Internet Archive´s Wayback Machine.

A.H. Jahren, Johns Hopkins University: The carbon stable isotope composition of pollen. The d13C value of plant tissue is increasingly used to infer environmental and ecological conditions in modern and ancient environments. Review of Palaeobotany and Palynology, 2004, 132(3-4), 291-313. See also here.

Keith Karoly, Reed College Biology Department, Portland, OR: Contemporary Topics in Biology - Molecular Genetic Analysis of Plant Evolution. A range of online articles.
This expired link is available through the Internet Archive´s Wayback Machine.
Go to: Molecular clocks and plant evolution.

Andrew H. Knoll 1999: Enhanced: A New Molecular Window on Early Life. Science 285: 1025-1026.

! N.M. Koch and L.A. Parry (2020): Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses. Free access, Syst. Biol., 69: 1052–1067.
See also here and there.
"... Since the early years of phylogenetic systematics, different studies have dismissed the impact of fossils due to their incompleteness, championed their ability to overturn phylogenetic hypotheses or concluded that their behavior is indistinguishable from that of extant taxa. Based on taxon addition experiments on empirical data matrices, we show that the inclusion of paleontological data has a remarkable effect in phylogenetic inference. ..."

! I. Kögel-Knabner (2002): The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter. In PDF, Soil Biology and Biochemistry, 34: 139-162.
See also here.

! W.J. Kress and L. Penev (2011): Innovative electronic publication in plant systematics: PhytoKeys and the changes to the "Botanical Code" accepted at the XVIII International Botanical Congress in Melbourne. In PDF, PhytoKeys, 6: 1-4.

! G.Q. Liu et al. (2022): The Molecular Phylogeny of Land Plants: Progress and Future Prospects. Open access, Diversity, 14 (from the Special Issue Ecology, Evolution and Diversity of Plants).
Note figure 1: Summary of phylogenetic relationships among major clades of land plants.

M.J. Lockheart et al. (2000): Chemotaxonomic classification of fossil leaves from the Miocene Clarkia lake deposit, Idaho, USA based on n-alkyl lipid distributions and principal component analyses. In PDF, Organic Geochemistry, 31: 1223-1246.

R.A. Marks et al. (2021): Representation and participation across 20 years of plant genome sequencing. Open access, Nature Plants, 7: 1571–1578.
"... We show that assembly quality has increased dramatically in recent years, that substantial taxonomic gaps exist ..."
Note figure 1: Changes in land plant genome assembly quality and availability over time. Assembly contiguity by submission date for 798 land plant species with publicly available genome assemblies.

C.R. Marshall (2019): Using the Fossil Record to Evaluate Timetree Timescales. Open access, Front Genet., 10.

Patrick T. Martone et al. (2009): Discovery of Lignin in Seaweed Reveals Convergent Evolution of Cell-Wall Architecture. Abstract, Current Biology, Volume 19, Issue 2, 169-175. See also here.

L. Marynowski et al. (2008): Systematic relationships of the Mesozoic wood genus Xenoxylon: an integrative biomolecular and palaeobotanical approach. PDF file, N. Jb. Geol. Paläont. Abh., 247: 177-189.
This expired link is now available through the Internet Archive´s Wayback Machine.

L. Marynowski et al. (2007): Biomolecules preserved in ca. 168 million year old fossil conifer wood. PDF file, Naturwissenschaften, 94: 228-236.

! S. Mathews (2009): Phylogenetic relationships among seed plants: persistent questions and the limits of molecular data. Free access, American Journal of Botany, 96: 228-236.

Laurence A. Moran, Dept. of Biochemistry, Faculty of Medicine, University of Toronto. See also here. Go to: What Is Evolution? See also here.

H. Morlon et al. (2011): Reconciling molecular phylogenies with the fossil record. In PDF, PNAS, 108: 16327-16332.

Pyrolysis and macromolecular geochemistry group, Fossil Fuels and Environmental Geochemistry, Newcastle Research Group (NRG), University of Newcastle, Newcastle upon Tyne.
Now provided by the Internet Archive´s Wayback Machine.

! Y. Nie et al. (2020): Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies. In PDF, Syst. Biol., 69: 1–16. See also here.
! Note figure 5: Time-tree of green plants.
! "... By taking into account various sources of uncertainty, we estimate that crown-group green plants originated in the Paleoproterozoic–Mesoproterozoic (1679.7–1025.6 Ma), crown-group Chlorophyta and Streptophyta originated in the Mesoproterozoic–Neoproterozoic (1480.0–902.9 Ma and 1571.8–940.9 Ma), and crown-group land plants originated in the Ediacaran to middle Ordovician (559.3– 459.9 Ma). ..."

Karl J. Niklas (1981): The Chemistry of Fossil Plants. Abstract, BioScience, 31: 820-825.

! K.E. Omland et al. (2008): Tree thinking for all biology: the problem with reading phylogenies as ladders of progress. In PDF, BioEssays, 30: 854–867.
See also here.

Organic Geochemistry. The official journal of the European Association of Organic Geochemists (by Elsevier).

Wolfgang Oschmann, Christian Dullo, Volker Mosbrugger & Fritz F. Steininger, "PALÄONTOLOGIE IM 21. JAHRHUNDERT". Go to: Molecular Palaeobiology (in German).

! Palaeontologia Electronica: Fossil Calibration Database (project developed by the Working Group "Synthesizing and Databasing Fossil Calibrations: Divergence Dating and Beyond").
The mission of the Fossil Calibration Database is to provide vetted fossil calibration points that can be used for divergence dating by molecular systematists. The curated collection of well-justified calibrations also promote best practices for justifying fossil calibrations and citing calibrations properly. Raising the Standard in Fossil Calibration! See also:
D.T. Ksepka et al. (2015): The Fossil Calibration Database, A New Resource for Divergence Dating. Abstract, Systematic Biology.

! J.F. Parham et al. (2012): Best Practices for Justifying Fossil Calibrations. In PDF, Syst Biol., 61: 346-359. See also here

! K.J. Peterson et al. (2007): Molecular palaeobiology. Free access, Palaeontology, 50: 775-809.

Imogen Poole and Pim F. van Bergen (2006): Physiognomic and chemical characters in wood as palaeoclimate proxies. PDF file, Plant Ecology, 182: 175-195.

Pim F. van Bergen and Imogen Poole (2002): Stable carbon isotopes of wood: a clue to palaeoclimate? PDF file, Palaeogeography, Palaeoclimatology, Palaeoecology, 182: 31-45.
This expired link is available through the Internet Archive´s Wayback Machine.

Imogen Poole, Pim F. van Bergen, Johan Kool, Stefan Schouten and David J. Cantrill: Molecular isotopic heterogeneity of fossil organic matter: implications for δ13Cbiomass and δ13Cpalaeoatmosphere proxies. PDF file, Organic Geochemistry 35(11-12) (2004) 1261-1274 (via Virtual Journal Geobiology, volume 3, Issue 9, September 2004, section 2B).

T.B. Quental, C.R. Marshall (2010): Diversity dynamics: molecular phylogenies need the fossil record. In PDF, Trends in Ecology & Evolution, 25: 434-441.
See also here.

S.S. Renner (2022): Plant Evolution and Systematics 1982–2022: Changing Questions and Methods as Seen by a Participant. In PDF, Progress in Botany.
See also here.
"... With DNA data came lab work, bioinformatics, and both the need and the possibility to collaborate, which brought systematists out of their niche, gave comparative biology a huge push, and resulted in a better integration of biodiversity studies within biology. ..."

Bruce Runnegar, Department of Earth and Space Sciences, (Center for Astrobiology, Institute of Geophysics and Planetary Physics), UCLA, Los Angeles, CA: UCLA ESS116 PALEONTOLOGY FALL 2002. Images and schemes. Go to: Molecular evolution and paleontology.

J. Rust (2007): Die Bedeutung von Fossilien für phylogenetische Rekonstruktionen. In PDF, go to PDF page 75. In: Species, Phylogeny and Evolution, Phylogenetisches Symposium Göttingen.
Snapshot provided by the Internet Archive´s Wayback Machine.

B. Saladin et al. (2017): Fossils matter: improved estimates of divergence times in Pinus reveal older diversification. BMC Evolutionary Biology.

H. Schneider (2007): Plant morphology as the cornerstone to the integration of fossil and extant taxa in phylogenetic systematics. In PDF, go to PDF page 65. In: Species, Phylogeny and Evolution, Phylogenetisches Symposium Göttingen.
Snapshot provided by the Internet Archive´s Wayback Machine.

Mary Higby Schweitzer, Department of Microbiology and Earth Sciences, Montana State University, Bozeman: Palaeontologia Electronica, Volume 5, Issue 2, (Coquina Press), 2003. Go to Reviews and Previews: THE FUTURE OF MOLECULAR PALEONTOLOGY (also available in PDF).

Michael G. Simpson: Plant Nomenclature. Powerpoint presentation.

B. Artur Stankiewicz et al. (1998): Chemical preservation of plants and insects in natural resins. PDF file, Proc. R. Soc. Lond. B, 265: 641-647. See also here.

B.A. Stankiewicz et al. (1998): Molecular taphonomy of arthropod and plant cuticles from the Carboniferous of North America: implications for the origin of kerogen. In PDF, Journal of the Geological Society, 155: 453-462.
See also here.

D. Su et al. (2022): Large-scale phylogenomic analyses reveal the monophyly of bryophytes and neoproterozoic origin of land plants Open access, Molecular Biology and Evolution, 38: 3332–3344.
! Note figure 1: The concatenation species tree of land plants and their algal relatives.
! Figure 2: The coalescent species tree of land plants and their algal relatives.
"... We found that studies favoring a Neoproterozoic origin of land plants (980–682 Ma) are informed more by molecular data whereas those favoring a Phanerozoic origin (518–500 Ma) are informed more by fossil constraints. Our divergence time analyses highlighted the important contribution of the molecular data (time-dependent molecular change) when faced with contentious fossil evidence.
[..] A careful integration of fossil and molecular evidence will revolutionize our understanding of how land plants evolved.

Alfred E. Szmidt, Department of Plant Physiology, Umeå University, Sweden: Molecular evolution of plants. Phylogeny of Eurasian pines based on chloroplast DNA sequences.
Now provided by the Internet Archive´s Wayback Machine.

D. Tautz (2006), starting on PDF page 09: Morphologie versus DNA-Sequenzen in der Phylogenie-Rekonstruktion. PDF file, in German. Species, Phylogeny and Evolution 1. Themenheft Phylogenetisches Symposium Göttingen: Der Stellenwert der Morphologie in der heutigen Phylogenetische Systematik.
Provided by the Internet Archive´s Wayback Machine.

Kyle Trostle (2009), Franklin and Marshall College, Earth and Environment Department, Lancaster, PA: Diagenetic History of Fossil Wood from the Paleocene Chickaloon Formation, Matanuska Valley, Alaska. Snapshot taken by the Internet Archive´s Wayback Machine.

Pim F. van Bergen and Imogen Poole (2002): Stable carbon isotopes of wood: a clue to palaeoclimate? PDF file, Palaeogeography, Palaeoclimatology, Palaeoecology, 182: 31-45.
This expired link is available through the Internet Archive´s Wayback Machine.

Jing-Ke Weng and Clint Chapple (2010): The origin and evolution of lignin biosynthesis. New Phytologist, 187: 273-285.

Friedrich Widdel and Ralf Rabus (2001): Anaerobic biodegradation of saturated and aromatic hydrocarbons. PDF file, Current Opinion in Biotechnology, 12: 259-276.
Now provided by the Internet Archive´s Wayback Machine.

Wikipedia, the free encyclopedia:

C.J. Williams et al. (2010): Fossil wood in coal-forming environments of the late Paleocene-early Eocene Chickaloon Formation. PDF file, Palaeogeography, Palaeoclimatology, Palaeoecology, 295: 363-375.
Snapshot provided by the Internet Archive´s Wayback Machine.

Andrea D. Wolfe, Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus: The ISSR Resource Website.

Ewan Wolff, Montana State University Geoscience Education Web Development Team: Advances in Paleontology.
Still available through the Internet Archive´s Wayback Machine.

! H.S. Yoon et al. (2004): A molecular timeline for the origin of photosynthetic eukaryotes. PDF file, Mol. Biol. Evol., 21: 809-818. See also here.

M. Zech (2006): The Use of Biomarker and Stable Isotope Analyses in Palaeopedology. Reconstruction of Middle and Late Quaternary Environmental and Climate History, with Examples from Mt. Kilimanjaro, NE Siberia and NE Argentina. Dissertation, University of Bayreuth, Germany.
See also here.

ZINNIKER, D., J.M. MOLDOWAN, J. DAHL, F.J. FAGO, H. LI, L. J. HICKEY, G. W. ROTHWELL, AND D. W. TAYLOR: Techniques and advances in molecular paleobotany: Methods for evaluating hypotheses of plant evolution and phylogeny by molecular fossils. Abstract, 1998 Annual Meeting of the Botanical Society of America Baltimore. BR> This expired link is available through the Internet Archive´s Wayback Machine.

E.L. Zodrow et al. (2010): Phytochemistry of the fossilized-cuticle frond Macroneuropteris macrophylla (Pennsylvanian seed fern, Canada). Abstract, International Journal of Coal Geology, 84: 71-82.

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