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Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae)
Swedish Museum of Natural History, Department of Botany.
2024 (English)In: Ecology and Evolution, E-ISSN 2045-7758, article id 14:e10868Article in journal (Refereed) Published
Abstract [en]

Genome skimming (shallow whole-genome sequencing) offers time-and cost-efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter-plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnSGGA – rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade.

Place, publisher, year, edition, pages
2024. article id 14:e10868
Keywords [en]
inversions, mitochondrial DNA, mitochondrial DNA insertion, nuclear ribosomal DNA, phylogenetic discordance, plastid DNA
National Category
Biological Sciences
Research subject
Diversity of life
Identifiers
URN: urn:nbn:se:nrm:diva-5587DOI: 10.1002/ece3.10868OAI: oai:DiVA.org:nrm-5587DiVA, id: diva2:1859869
Available from: 2024-05-22 Created: 2024-05-22 Last updated: 2024-05-28Bibliographically approved

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