Skip to main content

Using near-infrared spectroscopy to discriminate closely related species: a case study of neotropical ferns

A Correction to this article was published on 20 April 2021

This article has been updated


Identifying plant species requires considerable knowledge and can be difficult without complete specimens. Fourier-transform near-infrared spectroscopy (FT-NIR) is an effective technique for discriminating plant species, especially angiosperms. However, its efficacy has never been tested on ferns. Here we tested the accuracy of FT-NIR at discriminating species of the genus Microgramma. We obtained 16 spectral readings per individual from the adaxial and abaxial surfaces of 100 specimens belonging to 13 species. The analyses included all 1557 spectral variables. We tested different datasets (adaxial + abaxial, adaxial, and abaxial) to compare the correct identification of species through the construction of discriminant models (Linear discriminant analysis and partial least squares discriminant analysis) and cross-validation techniques (leave-one-out, K-fold). All analyses recovered an overall high percentage (> 90%) of correct predictions of specimen identifications for all datasets, regardless of the model or cross-validation used. On average, there was > 95% accuracy when using partial least squares discriminant analysis and both cross-validations. Our results show the high predictive power of FT-NIR at correctly discriminating fern species when using leaves of dried herbarium specimens. The technique is sensitive enough to reflect species delimitation problems and possible hybridization, and it has the potential of helping better delimit and identify fern species.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Change history


Download references


This study was partly financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil (CAPES)—financing code 001, and Programa Nacional de Cooperação Acadêmica na Amazônia (PROCAD-AM/CAPES 21/2018, no 88887.200472/2018-00). RO Perdiz received a scholarship from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (process no. 142243/2015-9). The authors thank the following: B. Leal, L.L. Giacomin, M.A. Buitrago, and T. André for contributing to the manuscript; Mike Hopkins for all the support given to the first author while working at INPA; the herbaria that kindly gave us access to the specimens used in this research; and our colleagues from HSTM and INPA for the support and willingness to help.

Author information

Authors and Affiliations



Conceptualization: DNAP and TEA; methodology: DNAP, ROP, and TEA; formal analysis and investigation: DNAP, ROP, and TEA; writing—original draft preparation: DNAP and TEA; writing—review and editing: DNAP and TEA; funding acquisition: TEA; supervision: TEA.

Corresponding author

Correspondence to Darlem Nikerlly Amaral Paiva.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 114 KB)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Paiva, D.N.A., Perdiz, R.d. & Almeida, T.E. Using near-infrared spectroscopy to discriminate closely related species: a case study of neotropical ferns. J Plant Res 134, 509–520 (2021).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:


  • Barcoding
  • Discrimination of plant species
  • FT-NIR
  • Integrative taxonomy
  • Metabolomics
  • Microgramma