Supermatrix analyses reveal insights into the importance of outgroup, gene and taxon sampling in Onosma (Lithospermeae) phylogenetics
Description
The dataset is related to Aygoren Uluer, 2023 (In press) Journal Name: Anales del Jardín Botánico de Madrid Title: Supermatrix analyses reveal insights into the importance of outgroup, gene and taxon sampling in Onosma (Lithospermeae) phylogenetics Abstract. Tribe Lithospermeae Dumort (Boraginaceae) consists of ca. 26 genera and 470 species, in which Onosma L. constitutes approximately one third of the species (∼150 species). While the tribe has been strongly supported as monophyletic, within the tribe both generic and species boundaries are ambiguous. Among them, to date, not only the phylogenetic position of Eastern Asian Onosma species, but also the taxonomic limits of the genus remains unclear. Whether Eastern Asian Onosma is monophyletic, or the genus should be widened including Maharanga DC. and maybe Cystostemon are still open questions. For these reasons, I performed 16 phylogenetic analyses with different taxon coverage, alignments, gene regions and outgroups, with up to 746 taxa of tribe Lithospermeae and with five DNA regions, downloaded from GenBank. The results of the present study, with the widest taxon coverage to date, have shown that while genus Onosma was not monophyletic in any of the analyses, the phylogenetic relationships among Onosma s.s., Eastern Asian Onosma, Maharanga and Cystostemon Balf.f. changes from one analysis to another. However, the results of approximately unbiased (AU) test showed that the (((Eastern Asian Onosma+Maharanga) Cystostemon) Onosma s.s.) topology is overwhelmingly supported. Therefore, the current study highlights the importance of taxon, gene and outgroup sampling in Onosma phylogenetics. Keywords. Boraginaceae, Onosma, outgroup, phylogeny, taxon/gene sampling. Appendix 1. Alignment of ITS (746 taxa) Appendix 2. Alignment of total evidence analysis with 350 taxa Appendix 3. ITS (323 taxa)- RAxML result Appendix 4. ITS (555 taxa)- RAxML result Appendix 5. ITS (746 taxa)- RAxML result Appendix 6. Plastid (339 taxa)- RAxML result Appendix 7. Total evidence (350 taxa)- RAxML result Appendix 8. Total evidence (345 taxa)- RAxML result Appendix 9. Total evidence with distant outgroup (347 taxa)- RAxML result Appendix 10. Total evidence with closely related outgroup (347 taxa)-RAxML result