53 Works

Data from: Evolution of angiosperm pollen. 6. the Celastrales, Oxalidales, and Malpighiales (COM) clade and Zygophyllales

Zhi-Bin Tao, Alexandra H. Wortley, Lu Lu, De-Zhu Li, Hong Wang & Stephen Blackmore
Analyzing pollen morphological data on a contemporary phylogenetic framework can enhance our understanding of the distribution, diversity, and evolution of palynological characters. In this paper, the sixth in a series detailing pollen morphological characters across angiosperms, we focus on the Celastrales, Oxalidales, and Malpighiales (COM) clade and Zygophyllales, together comprising ca. 20,000 species in 47 families within fabids. We first examined pollen grains from 21 species with light, scanning electron, and transmission electron microscopy, to...

Data from: Graphs in phylogenetic comparative analysis: Anscombe’s quartet revisited

Liam J. Revell, Klaus Schliep, Eugenio Valderrama & James E. Richardson
1. In 1973 the statistician Francis Anscombe used a clever set of bivariate datasets (now known as Anscombe’s quartet) to illustrate the importance of graphing data as a component of statistical analyses. In his example, each of the four datasets yielded identical regression coefficients and model fits, and yet when visualized revealed strikingly different patterns of covariation between x and y. 2. Phylogenetic comparative methods are statistical methods too, yet visualizing the data and phylogeny...

Data from: Bayesian estimation of the global biogeographical history of the Solanaceae

Julia Dupin, Nicholas J. Matzke, Tiina Särkinen, Sandra Knapp, Richard G. Olmstead, Lynn Bohs & Stacey D. Smith
Aim: The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long-distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood (ML) methods and newly developed biogeographical stochastic mapping (BSM) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present-day distribution. Location:...

Life history evolution, species differences and phenotypic plasticity in hemiparasitic eyebrights (Euphrasia)

Max Brown, Natacha Frachon, Edgar Wong & Alex Twyford
Premise of the study: Species delimitation in parasitic organisms is challenging as traits used in the identification of species are often plastic and vary depending on the host. Here, we use species from a recent radiation of generalist hemiparasitic Euphrasia to investigate trait variation and trait plasticity. We test whether Euphrasia species show reliable trait differences, investigate whether these differences correspond to life history trade-offs between growth and reproduction, and quantify plasticity in response to...

Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

Jialiang Li, Yujiao Zhang, Markus Ruhsam, Richard Ian Milne, Yi Wang, Dayu Wu, Shiyu Jia, Tongzhou Tao & Kangshan Mao
The eastern Asia (EA) – eastern North America (ENA) disjunction is a typical and well known biogeographic. Although its origin has been the topic of many studies, some new insights will arise when more complex evolutionary histories are revealed using phylogenomic methods. Here, we used targeted exon capture and sequenced >1,000 single copy nuclear, plus 73 chloroplast genes, to resolve interspecific relationships and the biogeographic history of an intercontinental disjunct genus Thuja. Two separate clades...

Fire and grazing determined grasslands of central Madagascar represent ancient assemblages

Cedrique Solofondranohatra, Maria Vorontsova, Gareth Hempson, Jan Hackel, Stuart Cable, Vololoniaina Jeannoda & Caroline Lehmann
The ecology of Madagascar’s grasslands is under-investigated and the dearth of ecological understanding of how disturbance by fire and grazing shapes these grasslands stems from a perception that disturbance shaped Malagasy grasslands only after human arrival. However, worldwide, fire and grazing shape tropical grasslands over ecological and evolutionary timescales, and it is curious Madagascar should be a global anomaly. We examined the functional and community ecology of Madagascar’s grasslands across 71 communities in the Central...

Campanula rotundifolia cytotype, distribution and first flowering dates

J. Wilson, A. Perry, Shepherd, M. Duran-Castillo, CE. Jeffree & S. Cavers
This dataset comprises information of location and cytotype of over 1300 samples of Campanula rotundifolia L. from the northern hemisphere (mostly from Britain and Ireland) and data from a common garden study in which British and Irish cytotypes were grown together and their flowering phenology and growth were assessed. Campanula rotundifolia L. is a widespread polyploid perennial herbaceous plant, with diploid, tetraploid, pentaploid and hexaploid cytotypes.

Forest plot inventory data from seasonally dry and moist Atlantic forest in Rio de Janeiro State, 2015-2017

R.T. Pennington, M. Nascimento, D. Villela, H Cavalcante De Lima, M. Iguatemy, P.J. Pena Rodrigues, F. Negreiros, A. Quinet, J.M. Braga, A. Costa & M. Souza
Data comprise plot location (latitude, longitude, elevation), taxonomic family and species names and measurements of trees (diameter, height, health). Presence of lianas (vines) and their measurements were also recorded. Funder: NERC - Brazil (CONFAP) Newton Fund: “Dry forest biomes in Brazil: biodiversity and ecosystem services” (NE/N000587/1)

A taxonomic revision of the African genus Desplatsia Bocq. (Malvaceae - Grewioideae)

Julia Wellsow & David J. Harris
The data set includes data of 800 herbarium specimens (and 295 duplicates) used for a taxonomic revision of Desplatsia Bocq. (Malvaceae s.l., subfamily Grewioideae, tribe Grewieae). Desplatsia is a genus of trees and shrubs found in tropical West and Central Africa and is characterised by subulately divided stipules, the absence of an androgynophore, stamens that are fused to a tube at the base, and large and distinctive fruits that are dispersed by elephants. In the...

Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

Edeline Gagnon
Premise of the study: Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants....

Data from: The origin of the legumes is a complex paleopolyploid phylogenomic tangle closely associated with the Cretaceous-Paleogene (K-Pg) mass extinction event

Erik Koenen, Dario Ojeda, Freek Bakker, Jan Wieringa, Catherine Kidner, Olivier Hardy, Toby Pennington, Patrick Herendeen, Anne Bruneau & Colin Hughes
The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine...

Data from: Combined observational and experimental data provide limited support for facilitation in lichens

Måns Svensson, Alexandro Caruso, Rebecca Yahr, Christopher Ellis, Göran Thor & Tord Snäll
It is increasingly recognized that facilitative interactions can shape communities. One of the mechanisms through which facilitation may operate is when one species facilitates the colonization of another through the exchange of shared symbionts. Lichens are symbiotic associations composed of a mycobiont (lichenised-fungus) and one or two photobionts (algae or cyanobacteria). Different lichen species may have overlapping specificity for photobionts, creating the possibility that facilitation drives lichen community assembly. To investigate whether facilitation occurs in...

Data from: RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia

Erin A. Tripp, Yi-Hsin Erica Tsai, Yongbin Zhuang & Kyle G. Dexter
Deserts, even those at tropical latitudes, often have strikingly low levels of plant diversity, particularly within genera. One remarkable exception to this pattern is the genus Petalidium (Acanthaceae), in which 37 of 40 named species occupy one of the driest environments on Earth, the Namib Desert of Namibia and neighboring Angola. To contribute to understanding this enigmatic diversity, we generated RADseq data for 47 accessions of Petalidium representing 22 species. We explored the impacts of...

Data from: Maintenance of species boundaries in a Neotropical radiation of Begonia

Alex D. Twyford, Catherine A. Kidner & Richard A. Ennos
A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number of endemic species is a by-product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by...

Resprouting grasses are associated with less frequent fire than seeders

Kimberley Simpson, Emma Jardine, Sally Archibald, Elizabeth Forrestel, Caroline Lehmann, Gavin Thomas & Colin Osborne
Plant populations persist under recurrent fire via resprouting from surviving tissues (resprouters) or seedling recruitment (seeders). Woody species are inherently slow-maturing, meaning that seeders are confined to infrequent fire regimes. However, for grasses, which mature faster, the relationships between persistence strategy and fire regime remains unknown. Globally, we analysed associations between fire regimes experienced by hundreds of grass species and their persistence strategy, within a phylogenetic context. We also tested whether persistence strategies are associated...

DiSSCo Prepare Milestone report MS5.3 \"Documentation of PIDs relevant for DiSSCo technical infrastructure\"

Sabine von Mering, Julia Reis, Falko Glöckler, Wouter Addink, Robert Cubey, Mathias Dillen, Anton Güntsch, Elspeth Haston, Sharif Islam & Mareike Petersen

Whence came these plants most foul? Phylogenomics and biogeography of Lowiaceae (Zingiberales)

Matti Niissalo, Elliot Gardner, Gillian Khew, Otakar Šída, Axel Poulsen & Jana Leong-Škornicková
Lowiaceae (order Zingiberales) is a small family of forest herbs in Southeast Asia. All species belong to the genus Orchidantha. They are known for possessing orchid-like flowers that are smelly, apparently mimicking dead animals, feces, or mushrooms. Little is known of the biogeographic patterns or character evolution of the family. We sampled the family extensively, including many recently discovered species, and reconstructed the phylogeny of the family using HybSeq with Lowiaceae-specific RNA baits. Our phylogenetic...

Persistent Identifiers at Royal Botanic Garden Edinburgh

Frances Madden & Lorna Mitchell
This case study provides an overview of the use of persistent identifiers (PIDs) at the Royal Botanic Garden Edinburgh (RBGE). RBGE delivers plant science, conservation and education programmes that are underpinned by the world-class RBGE Collections, comprising a Living Collection, a Herbarium collection and Library and Archive collections. Within the context of this case study, a persistent identifier is an identifier that is globally unique, actionable (it can be resolved to a resource or information...

Data from: Upward elevation and northwest range shifts for alpine Meconopsis species in the Himalaya-Hengduan Mountains region

Xie He, Kevin Burgess, Xuefei Yang, Antje Ahrends, Lian-Ming Gao & De-Zhu Li
Climate change may impact the distribution of species by shifting their ranges to higher elevations or higher latitudes. The impacts on alpine plant species may be particularly profound due to a potential lack of availability of future suitable habitat. To identify how alpine species have responded to climate change during the past century as well as to predict how they may react to possible global climate change scenarios in the future, we investigate the climatic...

Data from: Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Yang Liu, Matthew G. Johnson, Cymon J. Cox, Rafael Medina, Nicolas Devos, Alain Vanderpoorten, Lars Hedenäs, Neil E. Bell, James R. Shevock, Blanka Aguero, Dietmar Quandt, Norman J. Wickett, A. Jonathan Shaw & Bernard Goffinet
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30...

Data from: Origin of angiosperms and the puzzle of the Jurassic gap

Hong-Tao Li, Ting-Shuang Yi, Lian-Ming Gao, Peng-Fei Ma, Ting Zhang, Jun-Bo Yang, Matthew A. Gitzendanner, Peter W. Fritsch, Jie Cai, Yang Luo, Hong Wang, Michelle Van Der Bank, Shu-Dong Zhang, Qing-Feng Wang, Jian Wang, Zhi-Rong Zhang, Chao-Nan Fu, Jing Yang, Peter M. Hollingsworth, Mark W. Chase, Douglas E. Soltis, Pamela S. Soltis & De-Zhu Li
Angiosperms are by far the most species-rich clade of land plants, but their origin and early evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny based on 80 genes from 2,881 plastid genomes representing 85% of extant families and all orders. With a well-resolved plastid tree and 62 fossil calibrations, we dated the origin of the crown angiosperms to the Upper Triassic, with major angiosperm radiations occurring in the Jurassic and Lower Cretaceous. This estimated...

Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

Carl J. Rothfels, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Anders Larsson, Dylan O. Burge, Markus Ruhsam, Michael Deyholos, Douglas E. Soltis, , Shane W. Shaw, Lisa Pokorny, Tao Chen, Claude DePamphilis, Lisa DeGironimo, Li Chen, Xiaofeng Wei, Xiao Sun, Petra Korall, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer, C. Neal Stewart, Gane K-S. Wong … & Claude De Pamphilis
Premise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. Methods: Here we take a curated phylogenomics approach to infer the...

Data from: Insights into the genetic relationships and breeding patterns of the African tea germplasm based on nSSR markers and cpDNA sequences

Moses C. Wambulwa, Muditha K. Meegahakumbura, Samson Kamunya, Alice Muchugi, Michael Moller, Jie Liu, Jian-Chu Xu, Sailesh Ranjitkar, De-Zhu Li & Lian-Ming Gao
Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used...

Data from: Low genetic diversity in small leading edge populations of a European paleoendemic Ramonda serbica (Gesneriaceae) in Bulgaria

Galya Petrova, Stefan Petrov & Michael Möller
Ramonda serbica Panč. (Gesneriaceae) is an endangered endemic species of the Balkan Peninsula. It has been the subject of several studies in the past, but has not yet been investigated in terms of its genetic variation. Here, an Inter Simple Sequence Repeat (ISSR) analysis was performed to determine the genetic diversity of five populations sampled from the geographically eastern fringe of its range in northwestern Bulgaria. We found low levels of genetic diversity and significant...

Data from: Applying plant DNA barcodes to identify species of Parnassia (Parnassiaceae)

Jun-Bo Yang, Yi-Ping Wang, Michael Möller, Lian-Ming Gao & Ding Wu
DNA barcoding is a technique to identity species by using standardized DNA sequences. In the present study, a total of 105 samples, representing 30 Parnassia species were collected to test the effectiveness of four proposed DNA barcodes (rbcL, matK, trnH-psbA and ITS) for species identification. Our results demonstrated that all four candidate DNA markers have a maximum level of primer universality and sequencing success. As single DNA marker, ITS region provided the highest species resolution...

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  • Royal Botanic Garden Edinburgh
  • University of Edinburgh
  • Chinese Academy of Sciences
  • Naturalis Biodiversity Center
  • Botanischer Garten und Botanisches Museum Berlin
  • Duke University
  • Royal Botanic Gardens
  • University of Alberta
  • University of California, Berkeley
  • Meise Botanic Garden