Remember Me
Or use your Academic/Social account:


Or use your Academic/Social account:


You have just completed your registration at OpenAire.

Before you can login to the site, you will need to activate your account. An e-mail will be sent to you with the proper instructions.


Please note that this site is currently undergoing Beta testing.
Any new content you create is not guaranteed to be present to the final version of the site upon release.

Thank you for your patience,
OpenAire Dev Team.

Close This Message


Verify Password:
Verify E-mail:
*All Fields Are Required.
Please Verify You Are Human:
fbtwitterlinkedinvimeoflicker grey 14rssslideshare1
Julier, Adele C.M.; Jardine, Phillip E.; Coe, Angela L.; Gosling, William D.; Lomax, Barry H.; Fraser, Wesley T. (2016)
Publisher: Elsevier
Journal: Review of Palaeobotany and Palynology
Languages: English
Types: Article
Subjects: Ecology, Evolution, Behavior and Systematics, Palaeontology
The uniform morphology of different species of Poaceae (grass) pollen means that identification to below family level using light microscopy is extremely challenging. Poor taxonomic resolution reduces recoverable information from the grass pollen record, for example, species diversity and environmental preferences cannot be extracted. Recent research suggests Fourier Transform Infra-red Spectroscopy (FTIR) can be used to identify pollen grains based on their chemical composition. Here, we present a study of twelve species from eight subfamilies of Poaceae, selected from across the phylogeny but from a relatively constrained geographical area (tropical West Africa) to assess the feasibility of using this chemical method for identification within the Poaceae family. We assess several spectral processing methods and use K-nearest neighbour (k-nn) analyses, with a leave-one-out cross-validation, to generate identification success rates at different taxonomic levels. We demonstrate we can identify grass pollen grains to subfamily level with an 80% success rate. Our success in identifying Poaceae to subfamily level using FTIR provides an opportunity to generate high taxonomic resolution datasets in research areas such as palaeoecology, forensics, and melissopalynology quickly and at a relatively low cost.
  • The results below are discovered through our pilot algorithms. Let us know how we are doing!

    • Andersen, T.S., Bertelsen, F., 1972. Scanning electron microscope studies of pollen of cereals and other grasses. Grana 12, 79-86.
    • Blokker, P., Boelen, P., Broekman, R., Rozema, J., 2006. The occurrence of p-coumaric acid and ferulic acid in fossil plant materials and their use as UV-proxy. Plant Ecol. 182, 197-207. http://dx.doi.org/10.1007/s11258-005-9026-y.
    • Boom, A., 2004. A Geochemical Study of Lacustrine Sediments: Towards Palaeo-climatic Reconstructions of High Andean Biomes in Colombia (PhD Thesis). University of Amsterdam, The Netherlands http://hdl.handle.net/11245/1.225858.
    • Brown, C.D., Vega-Montoto, L., Wentzell, P.D., 2000. Derivative preprocessing and optimal corrections for baseline drift in multivariate calibration. Appl. Spectrosc. 54, 1055-1068. http://dx.doi.org/10.1366/0003702001950571.
    • Bush, M.B., 2002. On the interpretation of fossil Poaceae pollen in the lowland humid neotropics. Palaeogeogr. Palaeoclimatol. Palaeoecol. 177, 5-17. http://dx.doi.org/10. 1016/S0031-0182(01)00348-0.
    • Datta, K., Chaturvedi, M., 2004. Pollen morphology of Basmati cultivars (Oryza sativa race Indica) - exine surface ultrastructure. Grana 43, 89-93. http://dx.doi.org/10.1080/ 00173130310017391.
    • de Leeuw, J.W., Versteegh, G.J.M., van Bergen, P.F., 2006. Biomacromolecules of algae and plants and their fossil analogues. Plant Ecol. 182, 209-233. http://dx.doi.org/10.1007/ s11258-005-9027-x.
    • Dell'Anna, R., Lazzeri, P., Frisanco, M., Monti, F., Campeggi, F.M., Gottardini, E., Bersani, M., 2009. Pollen discrimination and classification by Fourier transform infrared (FT-IR) microspectroscopy and machine learning. Anal. Bioanal. Chem. 394, 1443-1452. http://dx.doi.org/10.1007/s00216-009-2794-9.
    • Duarte, I.F., Barros, A., Almeida, C., Spraul, M., Gil, A.M., 2004. Multivariate analysis of NMR and FTIR data as a potential tool for the quality control of beer. J. Agric. Food Chem. 52, 1031-1038. http://dx.doi.org/10.1021/jf030659z.
    • Faegri, K., Iversen, J., Krzywinski, K., Kaland, P.E., 1989. Textbook of Pollen Analysis. 4th ed. Wiley, Chichester.
    • Fraser, W.T., 2008. Evaluation of Spore Wall Chemistry as a Novel Biochemical Proxy for UV-B Radiation (PhD Thesis). The Open University, UK http://ethos.bl.uk/ OrderDetails.do?uin=uk.bl.ethos.494651.
    • Fraser, W.T., Sephton, M.A., Watson, J.S., Self, S., Lomax, B.H., James, D.I., Wellman, C.H., Callaghan, T.V., Beerling, D.J., 2011. UV-B absorbing pigments in spores: biochemical responses to shade in a high-latitude birch forest and implications for sporopolleninbased proxies of past environmental change. Polar Res. 30, 8312. http://dx.doi.org/10. 3402/polar.v30i0.8312.
    • Fraser, W.T., Scott, A.C., Forbes, A.E.S., Glasspool, I.J., Plotnick, R.E., Kenig, F., Lomax, B.H., 2012. Evolutionary stasis of sporopollenin biochemistry revealed by unaltered Pennsylvanian spores. New Phytol. 196, 397-401. http://dx.doi.org/10.1111/j.1469-8137. 2012.04301.x.
    • Fraser, W.T., Lomax, B.H., Jardine, P.E., Gosling, W.D., Sephton, M.A., 2014a. Pollen and spores as a passive monitor of ultraviolet radiation. Paleoecology 2, 12. http://dx. doi.org/10.3389/fevo.2014.00012.
    • Fraser, W.T., Watson, J.S., Sephton, M.A., Lomax, B.H., Harrington, G., Gosling, W.D., Self, S., 2014b. Changes in spore chemistry and appearance with increasing maturity. Rev. Palaeobot. Palynol. 201, 41-46. http://dx.doi.org/10.1016/j.revpalbo.2013.11.001.
    • Germeraad, J.H., Hopping, C.A., Muller, J., 1968. Palynology of Tertiary sediments from tropical areas. Palinol. Tert. Sediments Trop. Areas 6, 189-348. http://dx.doi.org/10. 1016/0034-6667(68)90051-1.
    • Grass Phylogeny Working Group II, 2012. New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. New Phytol. 193, 304-312. http://dx.doi. org/10.1111/j.1469-8137.2011.03972.x.
    • Herrero, B., Valencia-Barrera, R.M., San Martin, R., Pando, V., 2002. Characterization of honeys by melissopalynology and statistical analysis. Can. J. Plant Sci. 82, 75-82. http://dx.doi.org/10.4141/P00-187.
    • Holst, I., Moreno, J.E., Piperno, D.R., 2007. Identification of teosinte, maize, and Tripsacum in Mesoamerica by using pollen, starch grains, and phytoliths. Proc. Natl. Acad. Sci. 104, 17608-17613. http://dx.doi.org/10.1073/pnas.0708736104.
    • Horrocks, M., Coulson, S.A., Walsh, K.A.J., 1998. Forensic palynology: variation in the pollen content of soil surface samples. J. Forensic Sci. 43, 320-323. http://dx.doi.org/10. 1520/JFS16139J.
    • Jardine, P.E., Fraser, W.T., Lomax, B.H., Gosling, W.D., 2015. The impact of oxidation on spore and pollen chemistry. J. Micropalaeontol. 34, 139-149. http://dx.doi.org/10. 1144/jmpaleo2014-022.
    • Jiang, Y., Lahlali, R., Karunakaran, C., Kumar, S., Davis, A.R., Bueckert, R.A., 2015. Seed set, pollen morphology and pollen surface composition response to heat stress in field pea. Plant Cell Environ. 38, 2387-2397. http://dx.doi.org/10.1111/pce.12589.
    • Joly, C., Barillé, L., Barreau, M., Mancheron, A., Visset, L., 2007. Grain and annulus diameter as criteria for distinguishing pollen grains of cereals from wild grasses. Rev. Palaeobot. Palynol. 146, 221-233. http://dx.doi.org/10.1016/j.revpalbo.2007.04.003.
    • Lahlali, R., Jiang, Y., Kumar, S., Karunakaran, C., Liu, X., Borondics, F., Hallin, E., Bueckert, R., 2014. ATR-FTIR spectroscopy reveals involvement of lipids and proteins of intact pea pollen grains to heat stress tolerance. Front. Plant Sci. 5, 747. http://dx.doi.org/10. 3389/fpls.2014.00747.
    • Liland, K.H., Mevik, B.-H., 2015. Baseline: Baseline Correction of Spectra. R Package Version 1.2-1. https://CRAN.R-project.org/package=baseline.
    • Lomax, B.H., Fraser, W.T., Sephton, M.A., Callaghan, T.V., Self, S., Harfoot, M., Pyle, J.A., Wellman, C.H., Beerling, D.J., 2008. Plant spore walls as a record of long-term changes in ultraviolet-B radiation. Nat. Geosci. 1, 592-596. http://dx.doi.org/10.1038/ ngeo278.
    • Looy, C.V., Twitchett, R.J., Dilcher, D.L., Van Konijnenburg-Van Cittert, J.H.A., Visscher, H., 2001. Life in the end-Permian dead zone. Proc. Natl. Acad. Sci. U. S. A. 98, 7879-7883. http://dx.doi.org/10.1073/pnas.131218098.
    • Lupia, R., Lidgard, S., Crane, P.R., 1999. Comparing palynological abundance and diversity: implications for biotic replacement during the Cretaceous angiosperm radiation. Paleobiology 25, 305-340. http://dx.doi.org/10.1017/S009483730002131X.
    • Magri, D., 2011. Past UV-B flux from fossil pollen: prospects for climate, environment and evolution. New Phytol. 192, 310-312. http://dx.doi.org/10.1111/j.1469-8137.2011. 03864.x.
    • Mander, L., Punyasena, S.W., 2014. On the taxonomic resolution of pollen and spore records of Earth's vegetation. Int. J. Plant Sci. 175, 931-945. http://dx.doi.org/10.1086/ 677680.
    • Mander, L., Li, M., Mio, W., Fowlkes, C.C., Punyasena, S.W., 2013. Classification of grass pollen through the quantitative analysis of surface ornamentation and texture. Proc. R. Soc. B Biol. Sci. 280, 20131905. http://dx.doi.org/10.1098/rspb.2013.1905.
    • Martin, P., 2005. Importance of melissopalynology for beekeeping and trade. Bee World 86, 75-76. http://dx.doi.org/10.1080/0005772X.2005.11417317.
    • Mildenhall, D.C., Wiltshire, P.E.J., Bryant, V.M., 2006. Forensic palynology: why do it and how it works. Forensic Sci. Int. 163, 163-172. http://dx.doi.org/10.1016/j.forsciint. 2006.07.012.
    • Miller, C.S., Gosling, W.D., 2014. Quaternary forest associations in lowland tropical West Africa. Quat. Sci. Rev. 84, 7-25. http://dx.doi.org/10.1016/j.quascirev.2013.10.027.
    • Mohlenhoff, B., Romeo, M., Diem, M., Wood, B.R., 2005. Mie-type scattering and non-beerLambert absorption behavior of human cells in infrared microspectroscopy. Biophys. J. 88, 3635-3640. http://dx.doi.org/10.1529/biophysj.104.057950.
    • Pappas, C.S., Tarantilis, P.A., Harizanis, P.C., Polissiou, M.G., 2003. New method for pollen identification by FT-IR spectroscopy. Appl. Spectrosc. 57, 23-27. http://dx.doi.org/ 10.1366/000370203321165160.
    • Pummer, B.G., Bauer, H., Bernardi, J., Chazallon, B., Facq, S., Lendl, B., Whitmore, K., Grothe, H., 2013. Chemistry and morphology of dried-up pollen suspension residues. J. Raman Spectrosc. 44, 1654-1658. http://dx.doi.org/10.1002/jrs.4395.
    • RStudio Team, 2012. RStudio: Intergrated development for R. RStudio, Inc., Boston, MA. http://www.rstudio.com.
    • Rubinstein, C.V., Gerrienne, P., de la Puente, G.S., Astini, R.A., Steemans, P., 2010. Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana). New Phytol. 188, 365-369. http://dx.doi.org/10.1111/j.1469-8137.2010.03433.x.
    • Salih, A., Jones, A.S., Bass, D., Cox, G., 1997. Confocal imaging of exine as a tool for grass pollen analysis. Grana 36, 215-224. http://dx.doi.org/10.1080/00173139709362610.
    • Schüler, L., Behling, H., 2010. Poaceae pollen grain size as a tool to distinguish past grasslands in South America: a new methodological approach. Veg. Hist. Archaeobotany 20, 83-96. http://dx.doi.org/10.1007/s00334-010-0265-z.
    • Sivaguru, M., Mander, L., Fried, G., Punyasena, S.W., 2012. Capturing the surface texture and shape of pollen: a comparison of microscopy techniques. PLoS One 7, e39129. http://dx.doi.org/10.1371/journal.pone.0039129.
    • Steemans, P., Lepot, K., Marshall, C.P., Le Hérissé, A., Javaux, E.J., 2010. FTIR characterisation of the chemical composition of Silurian miospores (cryptospores and trilete spores) from Gotland, Sweden. Rev. Palaeobot. Palynol. 162, 577-590. http://dx.doi. org/10.1016/j.revpalbo.2010.07.006.
    • Stevens, A., Ramirez-Lopez, L., 2013. An Introduction to the Prospectr Package: R Package Vignette R Package Version 0.1.3. https://CRAN.R-project.org/package=prospectr.
    • Strömberg, C.A.E., 2011. Evolution of grasses and grassland ecosystems. Annu. Rev. Earth Planet. Sci. 39, 517-544. http://dx.doi.org/10.1146/annurev-earth040809-152402.
    • The Plant List, 2013. Version 1.1. Published on the Internet. http://www.theplantlist.org/ (accessed 14 February 2015).
    • Tschudy, R.H., Pillmore, C.L., Orth, C.J., Gilmore, J.S., Knight, J.D., 1984. Disruption of the terrestrial plant ecosystem at the Cretaceous-Tertiary boundary, Western Interior. Science 225, 1030-1032. http://dx.doi.org/10.1126/science.225.4666.1030.
    • Venables, W.N., Ripley, B.D., 2002. Modern Applied Statistics with S, Statistics and Computing. Springer New York, New York, NY https://CRAN.R-project.org/package=class.
    • Waikhom, S., Louis, B., Roy, P., Singh, W., Bharwaj, P., Talukdar, N., 2014. Scanning electron microscopy of pollen structure throws light on resolving Bambusa- Dendrocalamus complex: bamboo flowering evidence. Plant Syst. Evol. 300, 1261-1268. http://dx. doi.org/10.1007/s00606-013-0959-7.
    • Watson, J.S., Sephton, M.A., Sephton, S.V., Self, S., Fraser, W.T., Lomax, B.H., Gilmour, I., Wellman, C.H., Beerling, D.J., 2007. Rapid determination of spore chemistry using thermochemolysis gas chromatography-mass spectrometry and micro-Fourier transform infrared spectroscopy. Photochem. Photobiol. Sci. 6, 689-694. http://dx. doi.org/10.1039/B617794H.
    • Watson, J.S., Fraser, W.T., Sephton, M.A., 2012. Formation of a polyalkyl macromolecule from the hydrolysable component within sporopollenin during heating/pyrolysis experiments with Lycopodium spores. J. Anal. Appl. Pyrolysis 95, 138-144. http://dx.doi. org/10.1016/j.jaap.2012.01.019.
    • Zimmermann, B., 2010. Characterization of pollen by vibrational spectroscopy. Appl. Spectrosc. 64, 1364-1373. http://dx.doi.org/10.1366/000370210793561664.
    • Zimmermann, B., 2016. Analysis of allergenic pollen by FTIR microspectroscopy. Anal. Chem. 88, 803-811. http://dx.doi.org/10.1021/acs.analchem.5b03208.
    • Zimmermann, B., Kohler, A., 2013. Optimizing Savitzky-Golay parameters for improving spectral resolution and quantification in infrared spectroscopy. Appl. Spectrosc. 67, 892-902. http://dx.doi.org/10.1366/12-06723.
    • Zimmermann, B., Kohler, A., 2014. Infrared spectroscopy of pollen identifies plant species and genus as well as environmental conditions. PLoS One 9, e95417. http://dx.doi. org/10.1371/journal.pone.0095417.
    • Zimmermann, B., Tkalčec, Z., Mešić, A., Kohler, A., 2015. Characterizing aeroallergens by infrared spectroscopy of fungal spores and pollen. PLoS One 10, e0124240. http:// dx.doi.org/10.1371/journal.pone.0124240.
  • No similar publications.