Royal Botanic Garden Edinburgh
  • Edinburgh, Lothian, United Kingdom
Recent publications
Flower color variation is ubiquitous in many plant species, and several studies have been conducted to elucidate the underlying molecular mechanism. There are two flower color variants (yellowish-white and fuchsia) in the Rheum palmatum complex, however, few studies have investigated this phenomenon. Here, we used transcriptome sequencing of the two color variants to shed light on the molecular and biochemical basis for these color morphs. Comparison of the two transcriptomes identified 9641 differentially expressed unigenes (DEGs), including 6477 up-regulated and 3163 down-regulated genes. Functional analyses indicated that several DEGs were related to the anthocyanin biosynthesis pathway, and the expression profiles of these DEGs were coincident with the qRT-PCR validation results, indicating that expression levels of structural genes have a profound effect on the color variation in the R. palmatum complex. Our results suggested that the interaction of transcription factors (MYB, bHLH and WRKY) also regulated the anthocyanin biosynthesis in the R. palmatum complex. Estimation of selection pressures using the dN/dS ratio showed that 1106 pairs of orthologous genes have undergone positive selection. Of these positively selected genes, 21 were involved in the anthocyanin biosynthetic pathway, indicating that they may encode the proteins for structural alteration and affect flower color in the R. palmatum complex.
Background Ensuring the authenticity of raw materials is a key step prior to producing Chinese patent medicines. Pinelliaternata (Thunb.) Breit. is the botanical origin of Pinelliae Rhizoma (Banxia), a traditional Chinese medicine used to treat cough, insomnia, nausea, inflammation, epilepsy, and so on. Unfortunately, authentic Pinelliae Rhizoma is often adulterated by morphologically indistinguishable plant material due to the insufficient regulatory procedures of processed medicinal plant products. Thus, it is important to develop a molecular assay based on species-specific nucleotide signatures and primers to efficiently distinguish authentic Pinelliae Rhizoma from its adulterants. Methods and results The ITS2 region of 67 Pinelliae Rhizoma and its common adulterants were sequenced. Eight single nucleotide polymorphisms within a 28–43 bp stretch of ITS2 were used to develop six primer pairs to amplify these species-specific regions. We assayed 56 Pinelliae Rhizoma products sold on the Chinese market, including medicinal slices, powder and Chinese patent medicines, which revealed that about 66% of products were adulterated. The most common adulterants were Pinelliapedatisecta (found in 57% of the assayed products), Arisaemaerubescens (9%), Typhoniumgiganteum (2%) and Typhoniumflagelliforme (2%). Conclusions A severe adulteration condition was revealed in the traditional medicine market. The species-specific nucleotide assays developed in this study can be applied to reliably identify Pinelliae Rhizoma and its adulterants, aiding in the authentication and quality control of processed products on the herbal market.
Two short diatom rbcL barcodes, 331-bp and 263-bp in length, have frequently been used in diatom metabarcoding studies. They overlap in a common 263-bp region but differ in the presence or absence of a 68-bp tail at the 5′ end. Though the effectiveness of both has been demonstrated in separate biomonitoring and diversity studies, the impact of the 68-bp non-shared region has not been evaluated. Here we compare the two barcodes in terms of the values of a biotic index (IPS) and the ecological status classes derived from their application to an extensive metabarcoding dataset from United Kingdom rivers; this comprised 1703 samples and was produced using the 331-bp primers. In addition, we assess the effectiveness of each barcode for discrimination of genetic variants around and below the species level. The strong correlation found in IPS values between barcodes (Pearson's R = 0.98) indicates that the choice of the barcode does not have major implications for current WFD ecological assessments, although a very few sites (55: 3.23% of those analysed) were downgraded from an acceptable WFD class (“good”) to an unacceptable one (“moderate”). Analyses of the taxonomic resolution of the two barcodes indicate that for many ASVs, the use of either marker – 263-bp and 331-bp – gives unambiguous assignations at species level though with differences in bootstrap confidence values. Such differences are caused by the stochasticity involved in the naïve Bayesian classifier used and by the fact that genetic distance, regarding closely related species, is increased when using the 331-bp barcode. However, in three cases, species differentiation fails with the shorter marker, leading to underestimates of species diversity. Finally, two ASVs from Nitzschia species evidenced that the use of the shorter marker can sometimes lead to false positives when the extent and nature of infraspecific variation are poorly known.
A new genus, Doselia A.Orejuela & Särkinen, gen. nov. , is described in the tribe Solandreae (Solanaceae) consisting of four species of hemiepiphytic lianas endemic to the premontane forests of the Colombian and Ecuadorian Andes. The genus is distinguished based on the membranous leaves, usually sparsely pubescent with eglandular simple trichomes, pseudo-verticillate leaf arrangement, and elongated, pendulous, and few-flowered inflorescences with showy flowers and conical fruits. Three new combinations are made to transfer species to the new genus previously described as part of the polyphyletic genus Markea Rich. ( Doselia epifita (S.Knapp) A.Orejuela & Särkinen, comb. nov. , D. huilensis (A.Orejuela & J.M.Vélez) A.Orejuela & Särkinen, comb. nov. and D. lopezii (Hunz.) A.Orejuela & Särkinen, comb. nov. ). One new species is described from the western slopes of the eastern cordillera of the Colombian Andes, known only from three localities in the Boyacá, Santander, and Tolima departments ( Doselia galilensis A.Orejuela & Villanueva, sp. nov. ). The new species is unique in the genus in having glabrescent adult leaves, green-purplish calyces and long, greenish-white, infundibuliform corollas with delicate purplish veins and large lobes tinged with purple, and pubescent styles. Here we provide a revision of Doselia with a distribution map of all species, an identification key, photographs, preliminary conservation assessments, and line drawings of all four species.
Recent advances in molecular biomonitoring open new horizons for aquatic ecosystem assessment. Rapid and cost-effective methods based on organismal DNA or environmental DNA (eDNA) now offer the opportunity to produce inventories of indicator taxa that can subsequently be used to assess biodiversity and ecological quality. However, the integration of these new DNA-based methods into current monitoring practices is not straightforward, and will require coordinated actions in the coming years at national and international levels. To plan and stimulate such an integration, the European network DNAqua-Net (COST Action CA15219) brought together international experts from academia, as well as key environmental biomonitoring stakeholders from different European countries. Together, this transdisciplinary consortium developed a roadmap for implementing DNA-based methods with a focus on inland waters assessed by the EU Water Framework Directive (2000/60/EC). This was done through a series of online workshops held in April 2020, which included fifty participants, followed by extensive synthesis work. The roadmap is organised around six objectives: 1) to highlight the effectiveness and benefits of DNA-based methods, 2) develop an adaptive approach for the implementation of new methods, 3) provide guidelines and standards for best practice, 4) engage stakeholders and ensure effective knowledge transfer, 5) support the environmental biomonitoring sector to achieve the required changes, 6) steer the process and harmonise efforts at the European level. This paper provides an overview of the forum discussions and the common European views that have emerged from them, while reflecting the diversity of situations in different countries. It highlights important actions required for a successful implementation of DNA-based biomonitoring of aquatic ecosystems by 2030.
The Royal Botanic Garden Edinburgh (RBGE) has put the climate emergency and biodiversity crisis at the centre of its organisational strategy and is making changes to reduce the environmental impact of its activities and to adapt to the conditions created by changes in climate. This article looks at actions towards the Sustainable Development Goals (SDGs) within the physical boundaries of the four gardens of RBGE in Scotland. The article considers two areas. Firstly, the Horticultural sphere, including the reduction of the impacts on the environment made by horticultural practice to maintain the gardens, and adaptation of the landscapes to improve visitor access and the biodiversity benefits of plantings. Secondly, influencing behaviour and engaging visitors with respect to growing food and the enjoyment of being with plants for health and wellbeing. In both these areas, RBGE activities are contributing to targets within SDGs 11, 12, 13 and 15. These targets, the actions to realise them and subsequent outcomes are described below. Finally, a major project underway at the Garden which will significantly reduce the environmental impacts of the institution, the Edinburgh Biomes, is introduced.
is a Critically Endangered species utilized in Tibetan medicine. Due to the very limited numbers of wild individuals, the chemical and biological basis of its medicinal value has not been studied. The objective of this study was to explore the chemical constituents of Meconopsis bhutanica and to determine the antityrosinase activity and influence on human melanoma cell lines A375. The chemical constituents were mainly isolated through column chromatography and semipreparative high performance liquid chromatography, and the structures were elucidated by nuclear magnetic resonance spectra. The inhibition on tyrosinase was examined by microplate reader. High performance liquid chromatography, spectrofluorophotometer, and molecular docking were used to analyze the effects on the function and structure of tyrosinase. The influence on A375 cells were measured by the Cell Counting Kit. Finally, a total of eleven phenolic compounds were isolated and identified from Meconopsis bhu-tanica. All of these compounds were found in this plant for the first time. The results of antityrosinase activity assay showed that compound 9 exhibited tyrosinase inhibition obviously. Furthermore, compound 9 could decrease the oxidation products and fluorescence emission intensity of tyrosinase. However, compound 9 had no effect on the proliferation of human melanoma A375 cells at high concentrations. The present paper uncovered the chemical composition of Meconopsis bhutanica and assessed the tyrosinase inhibition activity, which will provide data for comparing bioactive chemical constituents between the wild and cultivated ones. This study paved the way for the conservation, cultivation, and application of Meconopsis bhutanica.
Woody encroachment is ubiquitous in grassy ecosystems worldwide, but its global impacts on the diversity of herbaceous plants that characterise and define these ecosystems remain unquantified. The pervasiveness of encroachment is relatively easily observed via remote sensing, but its impacts on plant diversity and richness below the canopy can only be observed via field-based studies. Via a meta-analysis of 42 field studies across tropical to temperate grassy ecosystems, we quantified how encroachment altered herbaceous species richness, and the richness of forbs, C3 graminoids and C4 graminoids. Across studies, the natural logarithm of the response ratio (lnRR) of herbaceous species richness ranged from -3.33 to 0.34 with 87% of encroached ecosystems negatively impacted. Assessment of the extent of encroachment, duration of encroachment, mean annual rainfall, latitude, and continent demonstrated that only extent of encroachment had relevance in the data (univariate model including a random effect of study explained 45.4% of variance). The global weighted mean lnRR of species richness decreased from -0.245 at <33% of woody cover increase, to -0.562 at 33%-66%, and to -0.962 at >66%. Continued encroachment results in substantial loss of herbaceous diversity at medium and high extents, with a loss of richness that is not replaced. Although all functional groups are significantly negatively impacted by encroachment, forb richness is relatively more sensitive than graminoid richness, and C4 graminoid richness relatively more than C3 graminoid richness. Although no geographic or climatic correlates had relevance in the data, encroachment as an emergent product of global change coalesces to decrease ground layer light availability, lead to loss of fire and grazers, and alter hydrology and soils. Encroachment is accelerating and grassy ecosystems require urgent attention to determine critical woody cover thresholds that facilitate diverse and resilient grassy ecosystems.
In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse group of aquatic microalgae that includes important bioindicator species and many such lineages. One example is Nitzschia palea, a widespread species complex with several morphologically defined taxonomic varieties, some of which are critical pollution indicators. Morphological differences among the varieties are subtle and phylogenetic studies based on a few genes fail to resolve their evolutionary relationships. We conducted morphometric and transcriptome analyses of 10 Nitzschia palea strains to resolve the relationships among strains and taxonomic varieties. Nitzschia palea was resolved into three clades, one of which corresponds to a group of strains with narrow linear‐lanceolate valves. The other morphological group recovered in the shape outline analysis was not monophyletic and consisted of two clades. Gene‐tree concordance analyses and phylogenetic network estimations revealed patterns of incomplete lineage sorting and gene flow between intraspecific lineages. We detected reticulated evolutionary patterns among lineages with different morphologies, resulting in a putative recent hybrid. Our study shows that phylogenomic analyses of unlinked nuclear loci, complemented with morphometrics, can resolve complex evolutionary histories of recently diverged species complexes.
Premise: Hedychium J.Koenig (Zingiberaceae) is endemic to the Indo-Malayan Realm and is known for its colorful and fragrant flowers. Historically, two different pollination syndromes characterize Hedychium: diurnal or bird pollination and nocturnal or moth pollination. In this study we aim to understand the evolution of nocturnal and diurnal flowers, and to test its putative association with lineage diversification in Hedychium. Methods: A molecular tree of Hedychium was used as a scaffold upon which we estimated ancestral character-states, phylogenetic signals, and correlations for certain categorical and continuous floral traits. Further, we employed phylomorphospace and trait-dependent diversification rate estimation analyses to understand phenotypic evolution and associated lineage diversification in Hedychium. Results: Although floral color and size lacked any association with specific pollinators, white or pale flowers were most common in the early branching clades, when compared to bright-colored flowers which were more widely represented in the most derived clade IV. Five categorical and two continuous characters were identified to have informative evolutionary patterns which also emphasized that ecology may have played a critical role in the diversification of Hedychium. Conclusions: From our phylogenetic analyses and ecological observations, we conclude that specializations in pollinator interactions are rare in the hyperdiverse clade IV, thus challenging the role of both moth-specialization and bird-specialization as central factors in the diversification of Hedychium. However, our results also suggest that clade III (predominantly island clade) may show specializations, and future studies should investigate ecological and pollinator interactions, along with inclusion of new traits such as floral fragrance and anthesis time. This article is protected by copyright. All rights reserved.
Genome size variation within plant taxa is due to presence/absence variation, which may affect low-copy sequences or genomic repeats of various frequency classes. However, identifying the sequences underpinning genome size variation is challenging because genome assemblies commonly contain collapsed representations of repetitive sequences and because genome skimming studies by design miss low-copy number sequences. Here, we take a novel approach based on k-mers, short sub-sequences of equal length k, generated from whole-genome sequencing data of diploid eyebrights (Euphrasia), a group of plants that have considerable genome size variation within a ploidy level. We compare k-mer inventories within and between closely related species, and quantify the contribution of different copy number classes to genome size differences. We further match high-copy number k-mers to specific repeat types as retrieved from the RepeatExplorer2 pipeline. We find genome size differences of up to 230Mbp, equivalent to more than 20% genome size variation. The largest contributions to these differences come from rDNA sequences, a 145-nt genomic satellite and a repeat associated with an Angela transposable element. We also find size differences in the low-copy number class (copy number ≤ 10×) of up to 27 Mbp, possibly indicating differences in gene space between our samples. We demonstrate that it is possible to pinpoint the sequences causing genome size variation within species without the use of a reference genome. Such sequences can serve as targets for future cytogenetic studies. We also show that studies of genome size variation should go beyond repeats if they aim to characterise the full range of genomic variants. To allow future work with other taxonomic groups, we share our k-mer analysis pipeline, which is straightforward to run, relying largely on standard GNU command line tools.
Within the very uniform series Laurifoliae, Passiflora acuminata (treated as a synonym of P. laurifolia in the Flora of China), P. tolimana, P. gleasonii and P. metae appear particularly similar. A review of their descriptions and the associated specimens confirms their lack of morphological differentiation and leads us to formally resurrect P. acuminata and place the three other taxa under its synonymy. This taxonomic move is also supported by a revision of 72 additional geolocalized specimens (for a grand total of 78) and an analysis of their distribution and habitats. In fact, the bioclimatic space corresponding to the specimens previously assigned to P. acuminata encompasses that of all specimens previously assigned to the three other taxa under study. The species range covers a wide region, comprising the lower Amazon and the north of its basin, mostly below 200 m, and, to the west, in the upper Amazon, the Orinoco basin, and along the Andean foothills and valleys, from Venezuela to Peru, at elevations between 100 and 2200 m. In the lowlands, the species appears associated with white sand savannas and water courses. A more complete description is proposed for the species, including its unusual fusiform and slightly ribbed fruit. Another rare trait in the series Laurifoliae is that the outer corona filaments tend to be longer than the corolla.
We tested the congruence in dispersal patterns of the two main symbionts of the lichen Cladonia stellaris using genotyping-by-sequencing data. Based on 122 samples from eastern Canada, we recovered more than 21000 loci from the photobiont of C. stellaris. We described the population structure and estimate genetic diversity of the photobiont and identified the factors that contribute to explain genetic variation in both lichen partners. We also determined the identity of the dominant photobiont associated to C. stellaris using two molecular markers. Our results showed that C. stellaris is associated with Asterochloris glomerata, A. irregularis, and A. pseudoirregularis. Congruence in the genetic structure of photobiont and mycobiont were confirmed, suggesting co-dispersal of thallus fragments of C. stellaris. Genetic diversity of each symbiont was the factor that explained most of the genetic variation of the other symbiont, whereas geographical location and bioclimatic region seemed to have small or null explanatory power.
Aim: Climate change is expected to impact mountain biodiversity by shifting species ranges and the biomes they shape. The extent and regional variation in these impacts are still poorly understood, particularly in the highly biodiverse Andes. Regional syntheses of climate change impacts on vegetation are pivotal to identify and guide research priorities. Here we review current data, knowledge and uncertainties in past, present and future climate change impacts on vegetation in the Andes.
Understanding the genetic diversity of wild populations is fundamental to conserving species in-situ and ex-situ. To aid conservation plans and to inform ex-situ conservation, we examined the genetic diversity of the cycad Cycas calcicola (Cycadaceae). Samples were collected from wild populations in the Litchfield National Park and Katherine regions in the Northern Territory, Australia. Additional samples were obtained from botanic garden plants that were originally collected in the Katherine region, Daly River and Spirit Hills in the Northern Territory, Australia. Using RADseq we recovered 2271 informative genome-wide SNPs, revealing low to moderate levels of gene diversity (uHe = 0.037 to 0.135), very low levels of gene flow, and significant levels of inbreeding (mean FIS = 0.491). Population structure and multivariate analysis showed that populations fall into two genetic groups (Katherine vs Litchfield + Daly River + Spirit Hills). Genetic differentiation was twice as high between populations of the Katherine and Litchfield regions (FST ~ 0.1) compared to within these two regions (FST ~ 0.05). Increasing population fragmentation together with high levels of inbreeding and very little gene flow are concerning for the future adaptability of this species. The results indicated that the ex-situ collections (1) had significantly lower genetic diversity than the wild populations, and (2) only partly capture the genetic diversity present, particularly because the Litchfield National Park populations are not represented. We recommend that ex-situ collections be expanded to incorporate the genetic diversity found in Litchfield National Park and to increase the number of representatives from Daly River/Spirit Hills, and that in-situ populations from the Katherine and Greater Litchfield regions be conserved as separate management units.
The attribution of biodiversity trends to the action of individual drivers is a first step in developing strategies to conserve, enhance and restore that diversity. One approach to that identification is to link information on species trends with information on ecological preferences that relate to the drivers. Long-term and short-term occupancy trends for 326 bryophyte species (1972–2015 and 2005–2015, respectively) and 437 lichen species (1971–2015 and 2005–2015, respectively) for Scotland were linked with appropriate indicators to assess the action of specific drivers. Bryophyte species of heathlands and woodlands showed positive trends, whilst lichen species from these habitats showed negative trends. Bryophytes and lichens of drier habitats and locations tended to have more positive trends whilst those of wetter habitats tended to be negative. Similarly, evidence suggested that bryophytes and lichens of open areas had more negative trends than those of shadier habitats and that species from both groups of higher fertility habitats had more positive trends than those of less fertile ones. Bryophyte species from warmer areas tended to increase in range. Opposite trends for bryophytes and lichens in heathlands and woodlands suggest competition for space or opposite reactions to other drivers, but it is clear that they should not be lumped into a single functional grouping. There were clear trends for suggesting that increased temperatures (bryophytes only), cumulative nitrogen pollution and reduced land use intensity were shifting assemblages. The overall predominance of negative trends for lichens suggests that many species have lost habitat through decreasing light availability and increased dryness, and potentially through competition with bryophytes. Given the international importance of Scotland for both these groups, these trends for lichens are of concern.
To determine the role of environmental and host genetic factors in shaping fungal endophyte communities we used culturing and metabarcoding techniques to quantify fungal taxa within healthy Scots pine (Pinus sylvestris) needles in a 7-y old provenance-progeny trial replicated at three sites. Both methods revealed a community of ascomycete and basidiomycete taxa dominated by the needle pathogen Lophodermium seditiosum. Differences in fungal endophyte taxon composition and diversity indices were highly significant among trial sites. Within two sites, fungal endophyte communities varied significantly among provenances. Furthermore, the communities differed significantly among maternal families within provenances in 11/15 and 7/15 comparisons involving culture and metabarcoding data respectively. We conclude that both environmental and host genetic variation shape the fungal endophyte community of P. sylvestris needles.
In response to the worldwide coronavirus outbreak, which effectively shut down fieldwork, laboratory and herbarium‐based studies, an evaluation was made of the effectiveness and limitations of undertaking a virtual taxonomic study using only online herbarium specimen resources related to the genus Madhuca (Sapotaceae) for the Flora of Singapore. The study demonstrated the immense value of digital images to basic taxonomic research but also found that diagnostic micro‐morphological characters, often critical in defining species boundaries, cannot be seen in many digital images, even at high resolution. Several recommendations are made on how to maximise the utility of online herbarium specimen images to help facilitate future taxonomic research, though it is clear that physical access to herbarium specimens remains essential.
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104 members
Philip Thomas
  • International Conifer Conservation Programme
Sabina Knees
  • Department of Science
Michael Moeller
  • Department of Science
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20A Inverleith Row, EH35LR, Edinburgh, Lothian, United Kingdom
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Regius Keeper
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www.rbge.org.uk
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