Phylogeny of Coussareeae (Rubioideae, Rubiaceae)

Löfstrand, Stefan; Razafimandimbison, Sylvain G.; Rydin, Catarina

doi:10.1007/s00606-019-01572-8

Cited by 12 publications

(13 citation statements)

References 48 publications

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“…Samples were sent to Macrogen (Seoul, South Korea) for purification and sequencing. The sequences of the other primers (ETS, ndhF, rbcL y rps16) were obtained from Genbank (Löfstrand et al 2019, Table 1). Lat.…”

Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 99%

“…The petaloid character of the calyx has been used to recognize genera and species in Rubiaceae (Reiche 1902, Verdcourt 1958, Ricardi 1963), and the nature of calyx lobules has been used to recognize species of Cruckshanksia (Taylor 1996). Therefore, we performed ancestral reconstructions of the characters petaloid appendix (presence or absence: Ricardi 1963, Taylor 1996 and calyx lobes (equal or unequal: Taylor 1996, Löfstrand et al 2019, Table 1) on the combined Bayesian tree, using parsimony and maximum likelihood algorithms in Mesquite ver. 3.2 (Maddison and Maddison 2017).…”

Section: Divergence Times and Ancestral Character State Reconstructionmentioning

confidence: 99%

“…Following Ricardi (1963) Bremer and Eriksson (2009), using five plastid regions but sampling only one representative of Cruckshanksia, showed that within the Coussareeae, Oreopolus and Cruckshanksia form a well-supported clade. Löfstrand et al (2019) used six regions, including nuclear and plastid markers, to determine relationships within the tribe Coussareeae; their results showed that Oreopolus is sister to Cruckshanksia. However, resolution within Cruckshanksia was not clear and sampling was limited to a few species.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetics of Cruckshanksia and Oreopolus (Rubiaceae) based on nuclear and plastid DNA sequences

Jara‐Arancio,

Scognamillo,

Vidal

et al. 2024

Nordic Journal of Botany

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Cruckshanksia Hook. & Arn. and Oreopolus Schltdl. Rubiaceae (Rubioideae – Coussareeae), endemic genera of Chile and Andean Argentina, have historically been highly taxonomically unstable. Molecular analyses have confirmed Oreopolus as the sister group of Cruckshanksia; however, the relationships among its species are still not resolved because previous studies have not considered all species of the genus and the published topologies have many unsupported nodes. For this reason, we carried out a phylogenetic study with all the species currently recognized by recent revisions, using two nuclear DNA regions and five plastid regions, to elucidate the relationships between species. In addition, the evolutionary history of the group was estimated based on divergence times, and a character reconstruction was performed. The results corroborate that Oreopolus is the sister group of Cruckshanksia. Cruckshanksia is monophyletic and composed of two principal clades. Clade I is composed of Subclade I (C. pumila and C. verticillata) associated with C. montiana; Clade II is composed of Subclade II (C. palmae and C. macrantha) and Subclade III (C. lithiophila and C. hymenodon). With 81% probability the common ancestor of the genus Cruckshanksia had petaloid appendices associated with two independent lines of evolution. The probability that the common ancestor of the Oreopolus‒Cruckshanksia clade had equal calyx lobes is 50%.

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Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 99%

Section: Divergence Times and Ancestral Character State Reconstructionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phylogenetics of Cruckshanksia and Oreopolus (Rubiaceae) based on nuclear and plastid DNA sequences

Jara‐Arancio,

Scognamillo,

Vidal

et al. 2024

Nordic Journal of Botany

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“…According to Löfstrand et al (2019), Coussareeae forms a monophyletic group comprising two sister clades (Psychotrieae and Spermacoceae alliances). The tribe is well resolved into three suprageneric clades: Clade 1 – Cruckshanksia (Cruckshanksieae sensu Andersson and Rova 1999, including Cruckshanksia Hook.…”

Section: Introductionmentioning

confidence: 99%

“…The pollen morphology of Coussareeae was mainly described by Melhem et al (1974), who analyzed one species of Coccocypselum and two species of Faramea ; by Jung-Mendaçolli and Melhem (1995), in a study characterizing heterostylous species of the tribe; and by Di Maio (1996), who conducted a taxonomic revision of Hindsia and palynologically described species belonging to this genus. Other studies include that of Piesschaert et al (2000), who described the genera Coccocypselum , Declieuxia , Faramea , and Hindsia , and that of Löfstrand et al (2019), who used palynological characters to investigate the phylogeny of Coussareeae.…”

Section: Introductionmentioning

confidence: 99%

Palynological diversity of some species of Coussareeae (Rubiaceae) from the Atlantic Forest, Brazil

et al. 2022

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Coussareeae is a neotropical tribe with a complex taxonomic history. Several authors considered it very close to the tribe Psychotrieae owing to similarities in their morphological characteristics, such as solitary ovules. The tribe Coussareeae constitutes the largest basal clade of the subfamily Rubioideae, and most of its genera are well represented in Brazil. The tribe is resolved into three suprageneric clades, including the Coccocypselum and Coussarea-Faramea clades, whose representatives are found in Brazil. This study aimed to ascertain whether pollen attributes corroborate the currently proposed phylogeny and systematics of the tribe. For this, pollen grains of 33 species belonging to the Coccocypselum and Coussarea-Faramea clades were analyzed. Specimens were obtained from herbaria, treated by the acetolysis method, measured, photographed, and described using light and scanning electron microscopy. Morphological analysis showed that pollen grains were medium (25-50 mm) or large (50-100 mm) in size; isopolar or apolar; 2-porate, 3-porate, or 3-colporate; and oblate spheroidal, suboblate, prolate spheroidal, or subprolate. Ornamentation varied among clade representatives. Multivariate analysis of quantitative data revealed that pollen diameter, apocolpium side, pore diameter, colpus length, and endoaperture width were the most significant characters. It can be seen from the results that the studied clades are formed by palynologically distinct genera in terms of polarity, aperture type, and ornamentation. Palynology confirms the proposed taxonomic classification.

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A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae

Ball,

Bedoya,

Taylor

et al. 2023

Appl Plant Sci

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PremiseRubiaceae is among the most species‐rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large‐scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single‐copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae‐specific probe set that allows for comparable phylogenetic inference across clades is lacking.MethodsHere, we use publicly accessible genomic resources to identify putatively single‐copy nuclear loci for target enrichment in two Rubiaceae groups: tribe Hillieae (Cinchonoideae) and tribal complex Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exonic regions corresponding to 1059 loci in our target clades and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set. To test the utility of our probe set for phylogenetic inference across Rubiaceae, we performed a coalescent‐aware phylogenetic analysis using a subset of 27 Rubiaceae taxa from 10 different tribes and three subfamilies, and one outgroup in Apocynaceae.ResultsWe recovered an average of 75% and 84% of targeted exons and loci, respectively, per Rubiaceae sample. Probes designed using genomic resources from a particular subfamily were most efficient at targeting sequences from taxa in that subfamily. The number of paralogs recovered during assembly varied for each clade. Phylogenetic inference of Rubiaceae with our target regions resolves relationships at various scales. Relationships are largely consistent with previous studies of relationships in the family with high support (≥0.98 local posterior probability) at nearly all nodes and evidence of gene tree discordance.DiscussionOur probe set, which we call Rubiaceae2270x, was effective for targeting loci in species across and even outside of Rubiaceae. This probe set will facilitate phylogenomic studies in Rubiaceae and advance systematics and macroevolutionary studies in the family.

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Phylogeny of Coussareeae (Rubioideae, Rubiaceae)

Abstract: Coussareeae are a Neotropical clade of morphologically heterogeneous plants in the subfamily Rubioideae of the coffee family (Rubiaceae). The tribe encompasses about 330 species assigned to ten genera: Bradea,

Cited by 12 publications

References 48 publications

Phylogenetics of Cruckshanksia and Oreopolus (Rubiaceae) based on nuclear and plastid DNA sequences

Phylogenetics of Cruckshanksia and Oreopolus (Rubiaceae) based on nuclear and plastid DNA sequences

Palynological diversity of some species of Coussareeae (Rubiaceae) from the Atlantic Forest, Brazil

A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae

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