Phylogenetic position of Oxygyne shinzatoi (Burmanniaceae) inferred from 18S rDNA sequences

Yokoyama, Jun; Koizumi, Yayoi; Yokota, Masatsugu; Tsukaya, Hirokazu

doi:10.1007/s10265-007-0136-6

Cited by 18 publications

(15 citation statements)

References 17 publications

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“…For this reason I do not agree with Hutchinson’s view to class the Thismieae as a separate family ...” (Jonker, 1938: 47). However, more recent molecular data have supported Hutchinson’s conclusion (e.g., Yokoyama et al, 2008; see below and Fig. 2).…”

Section: Introductionmentioning

confidence: 65%

“…In terms of phylogenetic placement within Dioscoreales, molecular analysis using 18S rDNA (Yokoyama et al, 2008) placed O. shinzatoi within the Thismia clade (Thismieae or Thismiaceae), most likely as sister to all other species of Thismiaceae (see Fig. 2, also Merckx & Smets, 2014).…”

Section: Taxonomic Treatmentmentioning

confidence: 99%

“…Oxygyne shinzatoi is perhaps the most well-studied of all species of Oxygyne ; it is the only species for which cytological (Tsukaya, Yokota & Okada, 2007) and molecular phylogenetic studies (Yokoyama et al, 2008) exist. It remained nomenclaturally invalidly published for many years since its first discovery in 1972, since two holotypes (contrary to the Code) were proposed by its discoverer Hatusima in the original publications where it was named Saionia shinzatoi (Hatusima, 1975; Hatusima, 1976).…”

Section: Taxonomic Treatmentmentioning

confidence: 99%

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Taxonomic monograph of Oxygyne (Thismiaceae), rare achlorophyllous mycoheterotrophs with strongly disjunct distribution

Cheek

Tsukaya

Rudall

et al. 2018

PeerJ

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Oxygyne Schltr. (Thismiaceae) is a rare and little-known genus of achlorophyllous mycoheterotrophic perennial herbs with one of the most remarkable distributions of all angiosperm plant genera globally, being disjunct between Japan and West–Central Africa. Each species is known only from a single location, and in most cases from a single specimen. This monographic study names, describes and maps two new species, Oxygyne duncanii Cheek from cloud forest in SW Region Cameroon and O. frankei Cheek from gallery forest in the Central African Republic, representing the first new Oxygyne species described from Africa in 112 years, and raising the number of described Oxygyne species from four to six. Oxygyne duncanii is remarkable for sharing more morphological characters with two of the three Japanese species (O. hyodoi C.Abe & Akasawa, O. shinzatoi (H. Ohashi) Tsukaya) than with the geographically much closer type species of the genus, O. triandra from Mt Cameroon. Based mainly on herbarium specimens and field observations made in Cameroon and Japan during a series of botanical surveys, we provide descriptions, synonymy, mapping and extinction risk assessments for each species of Oxygyne, together with keys to the genera of Thismiaceae and the species of Oxygyne. The subterranean structures of African Oxygyne are described for the first time, and found to be consistent with those of the Japanese species. We review and reject an earlier proposal that the Japanese species should be segregated from the African species as a separate genus, Saionia Hatus. The only character that separates the two disjunct species groups is now flower colour: blue or partly-blue in the Japanese species compared with orange-brown in the African species. Studies of the pollination biology and mycorrhizal partners of Oxygyne are still lacking. Two of the six species, O. triandra Schltr. and O. hyodoi, appear to be extinct, and the remaining four are assessed as Critically Endangered using the IUCN 2012 criteria. To avoid further extinction, an urgent requirement is for conservation management of the surviving species in the wild. Since few achlorophyllous mycoheterotrophs have been successfully cultivated from seed to maturity, ex situ conservation will not be viable for these species and protection in the wild is the only viable option. While natural habitat survives, further botanical surveys could yet reveal additional new species between Central Africa and Japan.

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Section: Introductionmentioning

confidence: 65%

Section: Taxonomic Treatmentmentioning

confidence: 99%

Section: Taxonomic Treatmentmentioning

confidence: 99%

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Taxonomic monograph of Oxygyne (Thismiaceae), rare achlorophyllous mycoheterotrophs with strongly disjunct distribution

Cheek

Tsukaya

Rudall

et al. 2018

PeerJ

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“…However, given the extreme rarity of the study group and the scarcity of herbarium material our sampling is the most complete currently available. Recently Yokoyama et al. (2008) reported on the phylogenetic position of Oxygyne using an 18S rDNA sequence of O. shinzatoi .…”

Section: Methodsmentioning

confidence: 99%

“…Remarkably, Thismia is absent from Africa while the genus Afrothismia with 11 species is endemic to tropical Africa. Other Thismiaceae genera are Oxygyne , with one species from Cameroon and two from Japan, Haplothismia , with one species endemic to the Western Ghats (India), and the recently discovered Tiputinia , with a single species from Ecuador (Sasidharan and Sujanapal, 2000; Woodward et al., 2007; Yokoyama et al., 2008). A remarkably common feature of most Thismiaceae is their extreme scarcity (Franke, 2004).…”

Section: Introductionmentioning

confidence: 99%

Bias and conflict in phylogenetic inference of myco‐heterotrophic plants: a case study in Thismiaceae

Merckx

Bakker²,

Huysmans

et al. 2009

Cladistics

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Due to morphological reduction and absence of amplifiable plastid genes, the identification of photosynthetic relatives of heterotrophic plants is problematic. Although nuclear and mitochondrial gene sequences may offer a welcome alternative source of phylogenetic markers, the presence of rate heterogeneity in these genes may introduce bias ⁄ systematic error in phylogenetic analyses. We examine the phylogenetic position of Thismiaceae based on nuclear 18S rDNA and mitochondrial atpA DNA sequence data, as well as using parsimony, likelihood and Bayesian inference methods. Significant differences in evolutionary rates of these genes between closely related taxa lead to conflicting results: while parsimony analyses of 18S rDNA and combined data strongly support the monophyly of Thismiaceae, Bayesian inference, with and without a relaxed molecular clock, as well as the Swofford-OlsenWaddell-Hillis (SOWH) test confidently reject this hypothesis. We show that rate heterogeneity in our data leads to long-branch attraction artifacts in parsimony analysis. However, using model-based inference methods the question of whether Thismiaceae are monophyletic remains elusive. On the one hand maximum likelihood nonparametric bootstrapping and parametric hypothesis tests fail to support a paraphyletic Thismiaceae, on the other hand Bayesian inference methods (both without and with a relaxed clock) significantly reject a monophyletic Thismiaceae. These results show that an adequate sampling, the use of rate homogeneous data, and the application of different inference methods are important factors for developing phylogenetic hypotheses of mycoheterotrophic plants.

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Plastid phylogenomics and molecular evolution of Thismiaceae (Dioscoreales)

Garrett

Viruel

Klimpert

et al. 2023

American J of Botany

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Premise Species in Thismiaceae can no longer photosynthesize and instead obtain carbon from soil fungi. Here we infer Thismiaceae phylogeny using plastid genome data and characterize the molecular evolution of this genome. Methods We assembled five Thismiaceae plastid genomes from genome skimming data, adding to previously published data for phylogenomic inference. We investigated plastid‐genome structural changes, considering locally colinear blocks (LCBs). We also characterized possible shifts in selection pressure in retained genes by considering changes in the ratio of nonsynonymous to synonymous changes (ω). Results Thismiaceae experienced two major pulses of gene loss around the early diversification of the family, with subsequent scattered gene losses across descendent lineages. In addition to massive size reduction, Thismiaceae plastid genomes experienced occasional inversions, and there were likely two independent losses of the plastid inverted repeat (IR) region. Retained plastid genes remain under generally strong purifying selection (ω << 1), with significant and sporadic weakening or strengthening in several instances. The bifunctional trnE‐UUC gene of Thismia huangii may retain a secondary role in heme biosynthesis, despite a probable loss of functionality in protein translation. Several cis‐spliced group IIA introns have been retained, despite the loss of the plastid intron maturase, matK. Conclusions We infer that most gene losses in Thismiaceae occurred early and rapidly, following the initial loss of photosynthesis in its stem lineage. As a species‐rich, fully mycoheterotrophic lineage, Thismiaceae provide a model system for uncovering the unique and divergent ways in which plastid genomes evolve in heterotrophic plants.

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Phylogenetic position of Oxygyne shinzatoi (Burmanniaceae) inferred from 18S rDNA sequences

Cited by 18 publications

References 17 publications

Taxonomic monograph of Oxygyne (Thismiaceae), rare achlorophyllous mycoheterotrophs with strongly disjunct distribution

Taxonomic monograph of Oxygyne (Thismiaceae), rare achlorophyllous mycoheterotrophs with strongly disjunct distribution

Bias and conflict in phylogenetic inference of myco‐heterotrophic plants: a case study in Thismiaceae

Plastid phylogenomics and molecular evolution of Thismiaceae (Dioscoreales)

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