iForest - Biogeosciences and Forestry


Chloroplast DNA barcoding genes matK and psbA-trnH are not suitable for species identification and phylogenetic analyses in closely related pines

Sanna Olsson (1)   , Guia Giovannelli (2), Anne Roig (2), Ilaria Spanu (3), Giovanni Giuseppe Vendramin (3), Bruno Fady (2)

iForest - Biogeosciences and Forestry, Volume 15, Issue 2, Pages 141-147 (2022)
doi: https://doi.org/10.3832/ifor3913-015
Published: Apr 25, 2022 - Copyright © 2022 SISEF

Research Articles

The largest and most economically important conifer genus Pinus is widespread in the northern hemisphere. Comprehensive phylogenies relying on complete chloroplast gene sequences are now available for the entire genus. However, phylogenetic relationships remain unresolved for certain lineages. One such example, which is also inconsistent in terms of biogeography, is within the subsection Pinus and includes five taxa: Pinus densiflora, P. nigra, P. resinosa, P. sylvestris and P. mugo / uncinata species complex. In this study, we use this clade as an example to explain weak support in phylogenetic studies of closely related pine species and show that some of the most popular genetic markers, namely the chloroplast DNA barcoding sequences matK, psbA- trnH and rbcL, are not recommended for species identification purposes in European pines. In addition, we show that matK and psbA-trnH contain contradicting phylogenetic signals in some of the most economically important pine species.


Gene Tree, Taxonomy, Pinus, GenBank

Authors’ address

Sanna Olsson 0000-0002-1199-4499
Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, E-28040 Madrid (Spain)
Guia Giovannelli 0000-0003-4776-3219
Anne Roig
Bruno Fady 0000-0003-2379-7617
INRAE, UR629, Ecologie des Forêts Méditerranéennes - URFM, Domaine Saint Paul, F-84914 Avignon (France)
Ilaria Spanu 0000-0002-5682-133X
Giovanni Giuseppe Vendramin 0000-0001-9921-7872
Institute of Biosciences and Bioresources, National Research Council, Division of Florence, I-50019 Sesto Fiorentino, FI (Italy)

Corresponding author

Sanna Olsson


Olsson S, Giovannelli G, Roig A, Spanu I, Vendramin GG, Fady B (2022). Chloroplast DNA barcoding genes matK and psbA-trnH are not suitable for species identification and phylogenetic analyses in closely related pines. iForest 15: 141-147. - doi: 10.3832/ifor3913-015

Academic Editor

Alberto Santini

Paper history

Received: Jun 25, 2021
Accepted: Feb 15, 2022

First online: Apr 25, 2022
Publication Date: Apr 30, 2022
Publication Time: 2.30 months

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