Abstract
Since the first description of the genus in 1754, the taxonomy of Ananas underwent many fundamental changes and it is still the subject of a vivid debate. We present a phylogeny comprising all seven known Ananas taxa, Pseudananas sagenarius as well as closely related members of Bromelioideae (Aechmea subg. Chevaliera) based on three nuclear markers (agt1, ETS, phyC), five plastid markers (atpB–rbcL, trnL–trnF, matK, two segments of ycf1) and AFLP data. This study reveals a close relationship between Ananas, P. sagenarius, Aechmea tayoensis and Disteganthus basilateralis, and proposes novel relationship of the Ananas clade and Aechmea fernandae. Taxonomic implications of our analysis in particular the recognition of species versus varieties in Ananas are discussed. Furthermore, we could show that the evolution of two traits (scape bracts and the apical coma of the inflorescence) might be interlinked.
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Acknowledgements
We thank Ingo Michalak (University of Leipzig) for his support with the Shimodaira-Hasegawa test. The study was financially supported by the research funding programme “LOEWE—Landesoffensive zur Entwicklung wissenschaftlich-ökologischer Exzellenz” of Hesse’s Ministry of higher education as well as the “Freunde und Förderer” of Goethe-University Frankfurt and Paul Ungerer-Stiftung. We also acknowledge financial support of the German Research Foundation (DFG ZI 557/6-2 and 7-1, SCHU 2426/1-1).
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Online Resource 1.
List of species names included in this study, specimen information, and GenBank accession numbers for all sequences.
Online Resource 2.
Alignment of studied markers (agt1, atpB–rbcL, ETS, matK, phyC, trnL–trnF, ycf1 pos. 1114-2102 and 4550-5532) and AFLP data.
Online Resource 3.
Primer combinations used for selective AFLP amplifications in initial screening and in final analyses.
Online Resource 4.
Results of the Shimodaira-Hasegawa test as implemented in RAxML. Pairwise comparison of single-ML trees inferred by atpB–rbcL, trnL–trnF, matK, ycf1 pos. 1114-2102 and 4550-5532, agt1, ETS, phyC, and AFLP data to test for topological incongruences.
Online Resource 5.
Maximum credibility trees of post-burnin Bayesian analyses, each ran for 30 million generations, based on a. AFLP, b. nuclear (agt1, ETS, phyC) or c. plastid (atpB–rbcL, trnL–trnF, matK, ycf1 pos. 1114-2102 and 4550-5532) data.
Online Resource 6.
Transition model selection for stochastic character mapping and state frequencies per node for Fig. 2. a. The corrected Akaike information criterion (AICc) was used for model selection. b. Table showing the inferred state frequencies calculated across 1000 stochastically mapped character histories (using ER model) for each node in Fig. 2 for two morphological traits: Apical coma (conspicuous, inconspicuous, missing) and Scape bracts (foliaceous, not foliaceous/often imbricate, lacking).
Online Resource 7.
Overview of the published chromosome numbers in the genus Ananas and Pseudananas.
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Information on Electronic Supplementary Material
Online Resource 1. List of species names included in this study, specimen information, and GenBank accession numbers for all sequences.
Online Resource 2. Alignment of studied markers (agt1, atpB–rbcL, ETS, matK, phyC, trnL–trnF, ycf1 pos. 1114-2102 and 4550-5532) and AFLP data.
Online Resource 3. Primer combinations used for selective AFLP amplifications in initial screening and in final analyses.
Online Resource 4. Results of the Shimodaira-Hasegawa test as implemented in RAxML. Pairwise comparison of single-ML trees inferred by atpB–rbcL, trnL–trnF, matK, ycf1 pos. 1114-2102 and 4550-5532, agt1, ETS, phyC, and AFLP data to test for topological incongruences.
Online Resource 5. Maximum credibility trees of post-burnin Bayesian analyses, each ran for 30 million generations, based on a. AFLP, b. nuclear (agt1, ETS, phyC) or c. plastid (atpB–rbcL, trnL–trnF, matK, ycf1 pos. 1114-2102 and 4550-5532) data.
Online Resource 6. Transition model selection for stochastic character mapping and state frequencies per node for Fig. 2. a. The corrected Akaike information criterion (AICc) was used for model selection. b. Table showing the inferred state frequencies calculated across 1000 stochastically mapped character histories (using ER model) for each node in Fig. 2 for two morphological traits: Apical coma (conspicuous, inconspicuous, missing) and Scape bracts (foliaceous, not foliaceous/often imbricate, lacking).
Online Resource 7. Overview of the published chromosome numbers in the genus Ananas and Pseudananas.
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Matuszak-Renger, S., Paule, J., Heller, S. et al. Phylogenetic relationships among Ananas and related taxa (Bromelioideae, Bromeliaceae) based on nuclear, plastid and AFLP data. Plant Syst Evol 304, 841–851 (2018). https://doi.org/10.1007/s00606-018-1514-3
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DOI: https://doi.org/10.1007/s00606-018-1514-3