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To estimate diversification rates we used the phylogeny with the complete taxon sampling according to the classification of reference [ 132].
The a priori classification of reference museum specimens (those identified by [ 25]), was compared to results of clustering by linear discriminant analyses (LDA) in R 3.0.1 [ 53].
Linear Discriminant Analyses (LDA) almost completely matched manual morphotype identifications based on geometric morphometric analyses of unidentified specimens and showed high correspondence with a priori classification of reference museum samples.
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Inconsistencies in the classification of references as relevant or non-relevant were resolved by consensus.
General classifications of reference materials and their use in the calibration process are clarified.
The 16S rRNA encoding genes for the type and reference strains of the species P. acidipropionici, P. jensenii and P. thoenii were also sequenced to remove ambiguous positions present in the current database reports, such to improve the classification scheme of reference.
cTaxonomic classification of the reference microorganism identified by fragment recruitment.
Initial classification of the reference data identified trends with a net change in concentration greater than 10%%.
The classification of allergy references also required development of a similar approach, because a classification based on the organism source of the allergen would not conform to the established classification in use in the allergy community.
Finally, we would like to point out how the current data is by necessity preliminary, as the accuracy of the classification of the references is dependent on the stage of the curation process.
Hence, in this paper, we use the former three subspecies classification for ease of reference to earlier publications.
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