Genetic diversity and structure of the endangered lady's slipper orchid <i>Cypripedium japonicum</i> Thunb. (Orchidaceae) in Japan

Yamashita, Yumi; Satoh, Natsuki; Kurosawa, Takahide; Kaneko, Shingo

doi:10.1002/1438-390x.12134

Cited by 4 publications

(1 citation statement)

References 33 publications

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“…A well-resolved and robust phylogeny is fundamental for addressing further questions regarding their divergence time, diversification rate shifts, ancestral spatial distribution patterns, and hybridization events. Furthermore, it will provide a solid foundation for the efficient management of their conservation, especially as their continuous human-driven 9 population decline is predicted to exacerbate due to climate change (Nicolè et al, 2005;Izawa et al, 2007;Minasiewicz et al, 2018;Kolanowska and Jakubska-Busse, 2020;H Liu et al, 2021b;Chandra et al, 2023;Yamashita et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid GenusCypripediumL

Lagou,

Kadereit,

Morales-Briones

2024

Preprint

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Cypripediumis the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies based on Sanger sequencing data, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny ofCypripediumand explore its evolutionary history using target capture data for the first time. We used the orchid-specific bait set "Orchidaceae963" to reconstruct the phylogeny ofCypripediumbased on 614 nuclear loci, covering 11 out of 13 sections. Subsequently, we investigated tree discordance, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies, and diversification rate shifts, and identified gene duplication and hybridization events. All sections were recovered as monophyletic, contrary to the subsections within sect.Cypripedium. Although the two subclades within this section did not correspond to its two subsections, they matched the geographic distribution of their species. Additionally, we discovered high levels of discordance in the short backbone branches of the genus and within sect.Cypripedium, which can be attributed to gene duplication and hybridization events, a potential whole genome duplication, and incomplete lineage sorting caused by rapid radiation. Our biogeographic analysis suggested a Neotropical origin of the genus during the Early Miocene (~20 Ma). The rapid radiations at the backbone likely occurred in Southeast Asia around the Middle Miocene Climatic Transition (~15-13 Ma), followed by several independent dispersals back to the New World. Moreover, the Pliocene-Quaternary glacial cycles may have contributed to further speciation and reticulate evolution, giving rise to a hybrid swarm within sect.Cypripedium. Our study provided novel insights into the evolutionary history ofCypripediumbased on high-throughput molecular data, shedding light on the dynamics of its distribution and diversity patterns from its origin to the present.

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Section: Introductionmentioning

confidence: 99%

Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid GenusCypripediumL

Lagou,

Kadereit,

Morales-Briones

2024

Preprint

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Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in the slipper orchid genus Cypripedium

Lagou,

Kadereit,

Morales-Briones

2024

Annals of Botany

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Background and Aims Cypripedium is the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny of Cypripedium and explore its evolutionary history using target capture data for the first time. Methods We used the orchid-specific bait set Orchidaceae963 in combination with transcriptomic data to reconstruct the phylogeny of Cypripedium based on 913 nuclear loci, covering all 13 sections. Subsequently, we investigated discordance among nuclear and chloroplast trees, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies, and diversification rate shifts, and identified potential gene (genome) duplication and hybridization events. Key Results All sections were recovered as monophyletic, contrary to the two subsections within sect. Cypripedium. The two subclades within this section did not correspond to its subsections but matched the geographic distribution of their species. Additionally, we discovered high levels of discordance in the short backbone branches of the genus and within sect. Cypripedium, which can be attributed to hybridization events detected based on phylogenetic network analyses, and incomplete lineage sorting caused by rapid radiation. Our biogeographic analysis suggested a Neotropical origin of the genus during the Oligocene (~30 Ma), with a lineage of potentially hybrid origin spreading to the Old World in the Early Miocene (~22 Ma). The rapid radiation at the backbone likely occurred in Southeast Asia around the Middle Miocene Climatic Transition (~15–13 Ma), followed by several independent dispersals back to the New World. Moreover, the Pliocene-Quaternary glacial cycles may have contributed to further speciation and reticulate evolution within Cypripedium. Conclusions Our study provided novel insights into the evolutionary history of Cypripedium based on high-throughput molecular data, shedding light on the dynamics of its distribution and diversity patterns from its origin to the present.

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Continuous Degradation of Forest Structure and Composition Causes a Shift in Phorophytes and Population Genetics in Aphyllous Vanilla Species

Botomanga,

Andriamihaja,

Besse

et al. 2024

Tropical Conservation Science

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Background and Research Aims The natural habitats of aphyllous vanillas in Madagascar have been extensively degraded by human activities. The implications of this degradation are complex given their intricate interactions with other organisms. This study highlights possible approaches to the conservation of aphyllous vanillas after examining the impact of forest degradation on phorophyte diversity, reproductive modes, and genetic diversity. Methods We conducted comparative studies of conserved and degraded forests in two contrasting bioclimatic zones. We characterized the changes in horizontal and vertical forest structures and assessed the ecological importance of the tree species. We identified the preferred phorophytes of two aphyllous Vanilla species, Vanilla madagascariensis and Vanilla decaryana, and investigated their population genetics. Results and Conclusions Our findings confirmed a declining trend in tree diversity, number of trees, and cover rate in degraded forests. Canopy openness is associated with an increase in the number of phorophytes and the asexual reproductive mode of Vanilla species. Dominant tree species were more likely to become phorophytes, and there was a positive correlation between phorophyte diameter and number of hosted vanilla individuals. Significant deviations from the Hardy-Weinberg equilibrium were observed in each population, particularly in the dry forest and degraded sites, compared with the conserved sites. Additionally, slight differentiation was observed between vanilla populations in conserved and degraded forests, with an alarming effective population size (Ne) that did not exceed 13 individuals. Conservation Implications We recommend the introduction of new genotypes to promote genetic enrichment, the ban on logging potential phorophytes, and the inclusion of some degraded forests comprising Vanilla species in conservation.

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Genetic diversity and structure of the endangered lady's slipper orchid Cypripedium japonicum Thunb. (Orchidaceae) in Japan

Cited by 4 publications

References 33 publications

Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid GenusCypripediumL

Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid GenusCypripediumL

Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in the slipper orchid genus Cypripedium

Continuous Degradation of Forest Structure and Composition Causes a Shift in Phorophytes and Population Genetics in Aphyllous Vanilla Species

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