Pinus syvestris from the Iberian Peninsula was biometrically compared, using needle morphological and anatomical characteristics from 15, and cone morphological characteristics from nine natural populations. Samples of Scots pine represent subspecies nevadensis and varieties pyrenaica, catalaunica, and iberica. Analyses included 25 needle and 17 cone characteristics and numerical methods (principal component analysis, discrimination analysis, agglomeration on Euclidean/Mahalanobis’ distances). A strong differences were detected between P. sylvestris subsp. nevadensis when compared to varieties pyrenaica and iberica, and a closer relationship to var. catalaunica in needle characteristics. In cone characteristics, the differences were at a similar level. Alien individuals were found within every taxon and population. Samples from the southern part of Sistema Central had the highest level of alien individuals. The geographic pattern of differentiation resembles patterns previously revealed using molecular and isoenzymatic markers. We could not detect characteristics specific to either P. sylvestris subsp. nevadensis or varieties of P. sylvestris subsp. sylvestris. Supplemental data for this article is available online at https://doi.org/10.1080/11263504.2021.1922532 .
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