Discordance in a South African <i>Memecylon</i> Clade (Melastomataceae): Evidence for Reticulate Evolution

Amarasinghe, Prabha; Pham, Phuc; Stone, Robert Douglas; Cellinese, Nico

doi:10.1086/715636

Cited by 5 publications

(4 citation statements)

References 56 publications

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“…In Euphorbiaceae (rosids: Malpighiales), a nuclear phylogeny was reported for the genus Euphorbia (Villaverde et al, 2018). Furthermore, the phylogeny of the Krameriaceae (rosids: Zygophyllales) genus Krameria (Ali et al, 2020) and the Melastomataceae (rosids: Myrtales) genus Memecylon (Amarasinghe et al, 2021) was analyzed using nuclear genes.…”

Section: Angiosperm Phylogenomics Using Nuclear Genesmentioning

confidence: 99%

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Zhang,

2024

JIPB

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Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,” hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next‐generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.

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Section: Angiosperm Phylogenomics Using Nuclear Genesmentioning

confidence: 99%

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Zhang,

2024

JIPB

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“…Indeed, for many template sequences in the Melastomataceae probe set, flanking intronic regions from samples of Memecylon and Tibouchina were assembled to the exon sequences. This seems to not be a problem when focusing on these two genera, as previous successful results were obtained (Amarasinghe et al, 2021a(Amarasinghe et al, , 2021b; however, the presence of these genera-specific intronic regions is problematic when focusing on other infrafamilial levels (such as tribes or other genera) or the family level. Indeed, as the template sequences are composed of both intronic and exonic regions, the limits between exons and introns are lost, blurring any downstream exon-intron delineation in the retrieved sequences.…”

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confidence: 91%

“…The probe set has been used with apparent success when focusing on the genera Memecylon and Tibouchina (Amarasinghe et al, 2021a , 2021b ; Jantzen et al, 2022 ); however, when trying to use the probe set on other Melastomataceae taxa, we faced several practical problems and conceptual questions at the time of bioinformatic assembly. First, in the probe set, the different template sequences of the same locus are supposed to have a relatively high similarity and align to each other, but for some loci, we found that some template sequences align better to the reverse complement of the other template sequences of the same locus.…”

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confidence: 99%

An updated and extended version of the Melastomataceae probe set for target capture

Dagallier,

Michelangeli

2024

Appl Plant Sci

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PremiseA probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae.MethodsIn order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version.ResultsThe final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery.DiscussionThis updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant‐targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available.

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“…This section (currently with 23 species) has an overall range encompassing East Africa (Kenya and Tanzania) westwards to Malawi (Mt. Mulanje), southwards to Mozambique and eastern South Africa and disjunctly in the dry forests of western and northern Madagascar (Stone, 2014;Stone et al, 2017aStone et al, , 2017bStone et al, , 2019Amarasinghe et al, 2021b). Members of Memecylon sect.…”

Section: Introductionmentioning

confidence: 99%

Revised treatment of Memecylon section Buxifolia (Melastomataceae) in Madagascar

Stone¹

2022

Candollea

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Memecylon sect. Buxifolia R.D. Stone (Melastomataceae, Olisbeoideae) is a group of forest shrubs and small understory trees distributed from tropical East Africa (Kenya and Tanzania) to eastern South Africa and with a disjunct occurrence in western and northern Madagascar. In a previous treatment, three endemic Malagasy species of this section were recognized: M. amplifolium R.D. Stone, M. buxifolium Blume (= M. perrieri Danguy), and M. multinode Jacq.-Fél. The present work describes and illustrates six new species from Madagascar belonging to this section: M. ambilobense R.D. Stone, M. angustatum R.D. Stone, M. leptophyllum R.D. Stone, M. minutifolium R.D. Stone, M. oblanceolatum R.D. Stone, and M. reductum R.D. Stone. With these revisions, the flora of Madagascar now holds nine species of Memecylon sect.Buxifolia, for which a formal taxonomic treatment is provided including a dichotomous key. The conservation status of each species is provisionally assessed in accordance with the IUCN Red List Categories and Criteria. Résumé

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Discordance in a South African Memecylon Clade (Melastomataceae): Evidence for Reticulate Evolution

Cited by 5 publications

References 56 publications

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

An updated and extended version of the Melastomataceae probe set for target capture

Revised treatment of Memecylon section Buxifolia (Melastomataceae) in Madagascar

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