Historical biogeography and phylogeny of the pantropical Psychotrieae alliance (Rubiaceae), with particular emphasis on the Western Indian Ocean Region

Razafimandimbison, Sylvain G.; Kainulainen, Kent; Wikström, Niklas; Bremer, Birgitta

doi:10.3732/ajb.1700116

Cited by 25 publications

(47 citation statements)

References 75 publications

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“…Analyses based on combined plastid and nuclear ribosomal markers have largely produced results consistent with our results but have supported a Craterispermeae + Prismatomerideae clade ( Razafimandimbison et al, 2008 ), or the placement of Gaertnereae in a clade together with Schradereae, Prismatomerideae, Mitchelleae and Morindeae ( Razafimandimbison et al, 2017 ). It is interesting to note that the nuclear results and mitochondrial results agree and are both in conflict with the plastid signal.…”

Section: Discussionsupporting

confidence: 86%

“…The nuclear phylogeny presented here includes representatives of all nine currently recognized tribes of the Psychotrieae alliance ( Razafimandimbison et al, 2008 , 2017 ) and shows, in contrast to previous studies based on Sanger-data, strong support across almost all relationships (including all inter-tribal relationships). Our study further supports the rare case of an evolutionary change from one-seeded carpels to many-seeded carpels found in the Psychotrieae alliance ( Razafimandimbison et al, 2008 ), with Schradereae being the sole tribe with numerous ovules per locule.…”

Section: Discussioncontrasting

confidence: 81%

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Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

et al. 2022

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Subfamily Rubioideae is the largest of the main lineages in the coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes and other major clades within this group of plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from the organellar genomes and nuclear ribosomal DNA, we here use a large number of low-copy nuclear genes obtained via a target capture approach to infer phylogenetic relationships within Rubioideae. We included 101 Rubioideae species representing all but two (the monogeneric tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes, and all but one non-monogeneric tribe were represented by more than one genus. Using data from the 353 genes targeted with the universal Angiosperms353 probe set we investigated the impact of data type, analytical approach, and potential paralogs on phylogenetic reconstruction. We inferred a robust phylogenetic hypothesis of Rubioideae with the vast majority (or all) nodes being highly supported across all analyses and datasets and few incongruences between the inferred topologies. The results were similar to those of previous studies but novel relationships were also identified. We found that supercontigs [coding sequence (CDS) + non-coding sequence] clearly outperformed CDS data in levels of support and gene tree congruence. The full datasets (353 genes) outperformed the datasets with potentially paralogous genes removed (186 genes) in levels of support but increased gene tree incongruence slightly. The pattern of gene tree conflict at short internal branches were often consistent with high levels of incomplete lineage sorting (ILS) due to rapid speciation in the group. While concatenation- and coalescence-based trees mainly agreed, the observed phylogenetic discordance between the two approaches may be best explained by their differences in accounting for ILS. The use of target capture data greatly improved our confidence and understanding of the Rubioideae phylogeny, highlighted by the increased support for previously uncertain relationships and the increased possibility to explore sources of underlying phylogenetic discordance.

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Section: Discussionsupporting

confidence: 86%

Section: Discussioncontrasting

confidence: 81%

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

et al. 2022

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“…4, 5c). Disjunctions of this kind can be explained only by LDD, which has also been inferred in Amaracarpus (Rubiaceae; Razafimandimbison et al 2017).…”

Section: Discussionmentioning

confidence: 79%

Metapopulation Vicariance, Age of Island Taxa and Dispersal: A Case Study Using the Pacific Plant Genus Planchonella (Sapotaceae)

et al. 2019

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Oceanic islands originate from volcanism or tectonic activity without connections to continental landmasses, are colonized by organisms, and eventually vanish due to erosion and subsidence. Colonization of oceanic islands occurs through long-distance dispersals (LDDs) or metapopulation vicariance, the latter resulting in lineages being older than the islands they inhabit. If metapopulation vicariance is valid, island ages cannot be reliably used to provide maximum age constraints for molecular dating. We explore the relationships between the ages of members of a widespread plant genus (Planchonella, Sapotaceae) and their host islands across the Pacific to test various assumptions of dispersal and metapopulation vicariance. We sampled three nuclear DNA markers from 156 accessions representing some 100 Sapotaceae taxa, and analyzed these in BEAST with a relaxed clock to estimate divergence times and with a phylogeographic diffusion model to estimate range expansions over time. The phylogeny was calibrated with a secondary point (the root) and fossils from New Zealand. The dated phylogeny reveals that the ages of Planchonella species are, in most cases, consistent with the ages of the islands they inhabit. Planchonella is inferred to have originated in the Sahul Shelf region, to which it back-dispersed multiple times. Fiji has been an important source for range expansion in the Pacific for the past 23 myr. Our analyses reject metapopulation vicariance in all cases tested, including between oceanic islands, evolution of an endemic Fiji–Vanuatu flora, and westward rollback vicariance between Vanuatu and the Loyalty Islands. Repeated dispersal is the only mechanism able to explain the empirical data. The longest (8900 km) identified dispersal is between Palau in the Pacific and the Seychelles in the Indian Ocean, estimated at 2.2 Ma (0.4–4.8 Ma). The first split in a Hawaiian lineage (P. sandwicensis) matches the age of Necker Island (11.0 Ma), when its ancestor diverged into two species that are distinguished by purple and yellow fruits. Subsequent establishment across the Hawaiian archipelago supports, in part, progression rule colonization. In summary, we found no explanatory power in metapopulation vicariance and conclude that Planchonella has expanded its range across the Pacific by LDD. We contend that this will be seen in many other groups when analyzed in detail.

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“…The phylogenetic positions of the tribes Schizocoleeae and Craterispermeae as successive sisters of the rest of the Psychotrieae alliance are supported by Wikström & al. (2015) and Razafimandimbison & al. (2017) and further confirmed by the first two Rubiaceae phylogenomic studies (Rydin & al., 2017;Wikström & al., 2020) and this study.…”

Section: New Insights Into the Tribal Relationships Within The Psychomentioning

confidence: 96%

Molecular systematics of the tribe Prismatomerideae (Rubiaceae) and its taxonomic consequences, with notes on the importance of the inflorescence morphology for species‐group recognition in Rennellia

Razafimandimbison

Wong

Rydin

2020

TAXON

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Tropical Asia is one of the centers of species diversity of flowering plants, in particular the coffee family (Rubiaceae). Prismatomerideae (the Psychotrieae alliance, subfamily Rubioideae) are a mostly Southeast Asian tribe encompassing four genera of shrubs and small trees (monospecific Gentingia and Motleyia, Prismatomeris with 16 spp., Rennellia with 4-5 spp.). We conducted molecular phylogenetic analyses of this group based on the nuclear and plastid sequence data from six markers and using Bayesian inference. The main goal was to produce a robust phylogeny of the tribe, which was subsequently used to (1) reassess its monophyly and phylogenetic position within the Psychotrieae alliance; (2) rigorously test the monophyly of Prismatomeris and Rennellia;(3) assess the phylogenetic relationships between the genera; and (4) evaluate the phylogenetic value of the inflorescence type currently used for species recognition in Rennellia. Motleyia was not sequenced due to the lack of material, and therefore its affinity with the other genera was assessed based on morphology. The tribe was supported as monophyletic and resolved as sister to the (Gaertnereae (Mitchelleae-Morindeae)) clade. The monophyly of Prismatomeris sensu Johansson was strongly supported, but we argue for the merging of the monospecific genus Motleyia into Prismatomeris based on their strong morphological similarities coupled with the paraphyly of Prismatomeris with respect to Motleyia. Rennellia was strongly supported as paraphyletic with respect to Gentingia. We propose the transfer of the monospecific genus Gentingia to Rennellia, also consistent with their strong morphological resemblance. Prismatomerideae were resolved in two major sister lineages, the Prismatomeris and Rennellia clades, corresponding to our broadly delimited Prismatomeris and Rennellia. Three well-supported and morphologically distinct subclades were identified within Rennellia s.l., of which one was represented by Rennellia subsessilis, with sessile and reduced umbel-like inflorescences bearing two to four flowers. The other two subclades have compound spike-like (or sub-raceme-like) and raceme-like inflorescences, an important distinction in species-group recognition. We conclude that inflorescence type shows a strong phylogenetic signal and is, therefore, a reliable feature for recognizing groups of species in Rennellia. Additional taxonomic characters are, however, needed for teasing apart closely related species with the same inflorescence types. Subsequent to our taxonomic revision, the tribe Prismatomerideae comprises two genera: Prismatomeris and Rennellia. One and two new combinations, respectively, are presented, bringing the total number of species in the tribe to 25, of which 17 are in Prismatomeris and 8 in Rennellia. A new species key to Rennellia s.l. is presented.

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Historical biogeography and phylogeny of the pantropical Psychotrieae alliance (Rubiaceae), with particular emphasis on the Western Indian Ocean Region

Cited by 25 publications

References 75 publications

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

Metapopulation Vicariance, Age of Island Taxa and Dispersal: A Case Study Using the Pacific Plant Genus Planchonella (Sapotaceae)

Molecular systematics of the tribe Prismatomerideae (Rubiaceae) and its taxonomic consequences, with notes on the importance of the inflorescence morphology for species‐group recognition in Rennellia

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