Supermatrix analyses reveal the importance of outgroup, gene and taxon sampling in Onosma (Boraginaceae) phylogenetics
DOI:
https://doi.org/10.3989/ajbm.2630Keywords:
Cystostemon, Lithospermeae, Maharanga, Onosma, outgroup, phylogeny, taxon/gene samplingAbstract
Tribe Lithospermeae (Boraginaceae) consists of ca. 26 genera and 470 species, in which Onosma constitutes approximately one third of the species (~150). Although the tribe is strongly supported as monophyletic, both generic and species boundaries remain ambiguous. Among them, not only the phylogenetic position of Eastern Asian Onosma species, but also the taxonomic limits of the genus remain unclear. Whether Eastern Asian Onosma is monophyletic, or the genus should be widened to include Maharanga, and maybe Cystostemon, are still open questions. For these reasons, I performed 16 phylogenetic analyses with different taxon coverages, alignments, gene regions and outgroups, with up to 746 taxa of tribe Lithospermeae and with five DNA regions, using data from GenBank. The results, with the widest taxon coverage to date, show that while genus Onosma is not monophyletic in any of the analyses, the phylogenetic relationships among Onosma s.s., Eastern Asian Onosma, Maharanga and Cystostemon differ among analyses. However, the approximately unbiased (AU) test showed that the topology (((Eastern Asian Onosma+Maharanga) Cystostemon) Onosma s.s.) is overwhelmingly supported. Therefore, the current study highlights the importance of taxon, gene and outgroup sampling in Onosma phylogenetics.
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References
Álvarez I. & Wendel J.F. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434.
Aygoren Uluer D., Hawkins J.A. & Forest F. 2020a. Interfamilial relationships in order Fabales: new insights from the nuclear regions sqd 1 and 26S rDNA. Plant Systematics and Evolution 306: 1-14.
Aygoren Uluer D., Forest F. & Hawkins J.A. 2020b. Supermatrix analyses and molecular clock rooting of Fabales: Exploring the effects of outgroup choice and long branch attraction on topology. Botany 98: 231-247.
Barrett R.L., Clugston J.A., Cook L.G., Crisp M.D., Jobson P.C., Lepschi B.J., Renner M.A. & Weston P.H. 2021. Understanding Diversity and Systematics in Australian Fabaceae Tribe Mirbelieae. Diversity 13: 391.
Cecchi L. & Selvi F. 2009. Phylogenetic relationships of the monotypic genera Halacsya and Paramoltkia and the origins of serpentine adaptation in circum-mediterranean Lithospermeae (Boraginaceae): insights from ITS and matK DNA sequences. Taxon 58: 700-714.
Cecchi L., Coppi A. & Selvi F. 2011. Evolutionary dynamics of serpentine adaptation in Onosma (Boraginaceae) as revealed by ITS sequence data. Plant Systematics and Evolution 297: 185-199.
Cecchi L., Coppi A., Hilger H.H. & Selvi F. 2014. Non-monophyly of Buglossoides (Boraginaceae: Lithospermeae): Phylogenetic and morphological evidence for the expansion of Glandora and reappraisal of Aegonychon. Taxon 63: 1065-1078.
Chacón J., Luebert F. & Weigend M. 2017. Biogeographic events are not correlated with diaspore dispersal modes in Boraginaceae. Frontiers in Ecology and Evolution 5: 26.
Chacón J., Luebert F., Selvi F., Cecchi L. & Weigend M. 2019. Phylogeny and historical biogeography of Lithospermeae (Boraginaceae): Disentangling the possible causes of Miocene diversifications. Molecular Phylogenetics and Evolution 14: 106626.
Cohen J.I. & Davis J.I. 2009. Nomenclatural changes in Lithospermum (Boraginaceae) and related taxa following a reassessment of phylogenetic relationships. Brittonia 61: 101-111.
Cohen J.I. 2011. A phylogenetic analysis of morphological and molecular characters of Lithospermum L. (Boraginaceae) and related taxa: evolutionary relationships and character evolution. Cladistics 27: 559-580.
Cohen J.I. 2014. A phylogenetic analysis of morphological and molecular characters of Boraginaceae: evolutionary relationships, taxonomy, and patterns of character evolution. Cladistics 30: 139-169.
Coppi A., Cecchi L., Nocentini D. & Selvi F. 2015. Arnebia purpurea: a new member of formerly monotypic genus Huynhia (Boraginaceae-Lithospermeae). Phytotaxa 204: 123-136.
Darriba D., Taboada G.L., Doallo R. & Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772.
Guindon S. & Gascuel O. 2003 A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology 52: 696-704.
Heath T.A., Hedtke S.M. & Hillis D.M. 2008. Taxon sampling and the accuracy of phylogenetic analyses. Journal of Systematics and Evolution 46: 239-257.
Jian S., Soltis P.S., Gitzendanner M.A., Moore M.J., Li R., Hendry T.A., Qiu Y.L., Dhingra A., Bell C.D. & Soltis D.E. 2008. Resolving an ancient, rapid radiation in Saxifragales. Systematic Biology 57: 38-57.
Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S., Duran C. & Thierer T. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28. 1647-1649.
Koyuncu O., Yaylacı Ö.K., Özgişi K., Sezer O. & Öztürk D. 2013. A new Onosma (Boraginaceae) species from central Anatolia, Turkey. Plant Systematics and Evolution 299: 1839-1847.
Letunic I. & Bork P. 2016. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research 44: W242-W245.
Mehrabian A.R., Sheidai M., Noormohammadi Z., Asrei Y. & Mozafarian V. 2011. Inter-simple sequence repeats (ISSR) and morphological diversity in Onosma L. (Boraginaceae) species in Iran. African Journal of Biotechnology 10: 10831-10838.
Miller M.A., Pfeiffer W. & Schwartz T. 2011. The CIPRES science gateway: a community resource for phylogenetic analyses. In: Proceedings of the Gateway Computing Environments Workshop (GCE). New Orleans, Louisiana.
Nasrollahi F., Kazempour-Osaloo S., Saadati N., Mozaffarian V. & Zare-Maivan H. 2019. Molecular phylogeny and divergence times of Onosma (Boraginaceae ss) based on nrDNA ITS and plastid rpl32-trnL (UAG) and trnH-psbA sequences. Nordic Journal of Botany 37: e02060.
Nilsson R.H., Ryberg M., Kristiansson E., Abarenkov K., Larsson K.H. & Kõljalg U. 2006. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PloS ONE 1: e59.
Qiu Y.L., Lee J., Whitlock B.A., Bernasconi-Quadroni F. & Dombrovska O. 2001. Was the ANITA rooting of the angiosperm phylogeny affected by long-branch attraction? Molecular Biology and Evolution 18: 1745-1753.
Rambaut A. & Drummond A.J. 2007. Tracer v1. 4. Website:https://beast.community/tracer [accessed: 23 Mar. 2022].
Ronquist F. & Huelsenbeck J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
Selvi F., Cecchi L., Hilger H.H. & Coppi A. 2017. A reappraisal of the genus Megacaryon (Boraginaceae, Lithospermeae) based on molecular, morphological, and karyological evidence. Systematics and Biodiversity 15: 552-563.
Shimodaira H. & Hasegawa M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16: 1114.
Smith A.B. 1994. Rooting molecular trees: problems and strategies. Biological Journal of the Linnean Society 51: 279-292.
Solís-Lemus C. & Ané C. 2016. Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. PLoS Genetics 12: e1005896.
Stamatakis A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313
Thomas D.C., Weigend M. & Hilger H.H. 2008. Phylogeny and systematics of Lithodora (Boraginaceae-Lithospermeae) and its affinities to the monotypic genera Mairetis, Halacsya and Paramoltkia based on ITS1 and trnLUAA-sequence data and morphology. Taxon 57: 79-97.
Trifinopoulos J., Nguyen L.T., von Haeseler A. & Minh B.Q. 2016. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research 44: W232-W235.
Weigend M., Gottschling M., Selvi F. & Hilger H.H. 2009. Marbleseeds are gromwells-Systematics and evolution of Lithospermum and allies (Boraginaceae tribe Lithospermeae) based on molecular and morphological data. Molecular Phylogenetics and Evolution 52: 755-768.
Wu H.Y., Chan K.T., But G.W.C. & Shaw P.C. 2021. Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification. Scientific Reports 11: 1-9.
Yang H.M., Zhang Y.X., Yang J.B. & Li D.Z. 2013. The monophyly of Chimonocalamus and conflicting gene trees in Arundinarieae (Poaceae: Bambusoideae) inferred from four plastid and two nuclear markers. Molecular Phylogenetics and Evolution 68: 340-356.
Zeng L., Zhang N., Zhang Q., Endress P.K., Huang J. & Ma H. 2017. Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets. New Phytologist 214: 1338-1354.
Zhu G.L., Harald R. & Rudolf K. 1995. Boraginaceae. In: Wu Z. Y. & Raven P. H. (eds), Flora of China 16: 329-427. Science Press, Beijing, & Missouri Botanical Garden Press, St. Louis.
Zwickl D.J. & Hillis D.M. 2002. Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51: 588-598.
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