Phylogenomics and taxonomic implications of Old World Melastomataceae

Chen, Luo (2025): Phylogenomics and taxonomic implications of Old World Melastomataceae. Dissertation, LMU München: Fakultät für Biologie

Abstract

My PhD dissertation focuses on the phylogenetics of the Old World Melastomataceae, utilizing newly generated and publicly available Sanger and next-generation sequencing (NGS) data. Melastomataceae are one of the largest flowering plant families, comprising approximately 173 genera and 5,858 species, with 2,117 species across 89 genera in the Old World. When I began my PhD, our understanding of the phylogenetic relationships within Melastomataceae was largely based on sequences from a few DNA markers generated through Sanger sequencing, which is prone to random errors in phylogenetic inference and often insufficient for resolving the phylogeny of groups with complex evolutionary histories. To improve our understanding of the phylogenies in Old World Melastomataceae, I studied three tribes: Dissochaeteae, Melastomateae, and Sonerileae. Together, these tribes include 76 genera and 1,500 species in the Old World, accounting for 70.9% of species and 85.4% of genera within this region. By combining target enrichment and Sanger sequencing data, we found that the African endemic Medinilla mirabilis is sister to the tribe Dissochaeteae rather than grouping with other Medinilla species. This finding is supported by morphological and wood anatomical evidence. To reflect these results, we reinstated the genus Myrianthemum and included it within Dissochaeteae, expanding the previously Southeast Asian tribe to include Africa. Nearly 40% of the species in the tribe Sonerileae have fleshy fruits and belong to six genera: Medinilla, Pachycentria, Plethiandra, Heteroblemma, Catanthera, and Kendrickia. We reconstructed the phylogeny of the fleshy-fruited Sonerileae for the first time using 385 nuclear and 81 plastid loci, which were recovered from target enrichment and publicly available NGS data. Our results revealed that the fleshy-fruited Sonerileae are not monophyletic and belong to three distinct clades: Kendrickia is sister to the Afrotropical endemic clade; Heteroblemma and Catanthera form a clade closely related to some species of Phyllagathis and Driessenia; and Medinilla forms a clade with Pachycentria and Plethiandra nested within it. To achieve monophyly for Medinilla, we synonymized Pachycentria and Plethiandra under Medinilla, redefined the genus, and provided new names for the species previously belonging to Pachycentria and Plethiandra. Additionally, we identified and characterized 15 clades within the newly defined Medinilla, which can serve as a basis for future infrageneric classification. With all recognized Old World genera sampled, including three enigmatic taxa (Dissotis leonensis, D. splendens, and Dionychastrum schliebenii) that had never been sequenced before, we revisited the phylogeny of the Old World Melastomateae using 384 nuclear loci recovered from target enrichment data. Our results confirmed previous findings based on Sanger data, showing that the Old World Melastomateae are monophyletic, comprising two primary lineages: the Euheterotis and the Pseudoheterotis clades. Additionally, we found that the Malagasy clade is sister to the Asian clade, both nested within the African lineages. All Old World genera, except Osbeckia and Melastomastrum, were recovered as monophyletic. Dissotis leonensis and D. splendens formed distinct clades and were not closely related to Dissotis, which was supported by morphological, seed, and wood anatomical evidence. To reflect these findings, we established two new genera, Allodissotis and Paleodissotis, treated D. leonensis and D. splendens, and provided an updated key to the African Melastomateae. Finally, using a newly developed reference comprising 5,626 loci based on genomic and transcriptomic data, we integrated newly generated and publicly available NGS data from multiple sources to reconstruct a well-supported, near-comprehensive (41/46 genera) phylogeny for Sonerileae. The Neotropical lineages and the African endemic Benna are successively sister to the rest of the tribe, which consists of a clade comprising the Sri Lankan endemic Kendrickia and Afrotropical Sonerileae, and a primarily Asian clade. Phylogenetic relationships within both the Afrotropical and Asian clades were largely consistent with previous studies based on Sanger sequencing and genome resequencing data, respectively. Our analyses also provided evidence of rapid radiation within the Asian Sonerileae, likely driven by a whole genome duplication event that occurred before the divergence of the two major clades within the Asian lineage.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Keywords: systematics, taxonomy, phylogeny, phylogemomics, target enrichment, Melastomataceae, tropical botany, Africa
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
• Fakultäten: Fakultät für Biologie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 28. Februar 2025
• 1. Bericht­erstatter:in: Kadereit, Gudrun