91 Works

Age-related pharmacodynamics in a bumblebee-microsporidian system mirror similar patterns in vertebrates

Arran J. Folly, Philip C. Stevenson & Mark J. F. Brown
Immune systems provide a key defence against diseases. However, they are not a panacea and so both vertebrates and invertebrates co-opt naturally occurring bioactive compounds to treat themselves against parasites and pathogens. In vertebrates this co-option is complex, with pharmacodynamics leading to differential effects of treatment at different life stages, which may reflect age-linked differences in the immune system. However, our understanding of pharmacodynamics in invertebrates is almost non-existent. Critically, this knowledge may elucidate broad...

Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)

Abigail J. Moore, Jurriaan M. De Vos, Lillian P. Hancock, Eric Goolsby, Erika J. Edwards, Jurriaan M De Vos, Abigail J Moore, Lillian P Hancock & Erika J Edwards
Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny...

Data from: Genetic diversity maintained among fragmented populations of a tree undergoing range contraction

James S. Borrell, Nian Wang, Richard A. Nichols & Richard J. A. Buggs
Dwarf birch (Betula nana) has a widespread boreal distribution but has declined significantly in Britain where populations are now highly fragmented. We analysed the genetic diversity of these fragmented populations using markers that differ in mutation rate: conventional microsatellites markers (PCR-SSRs), RADseq generated transition and transversion SNPs (RAD-SNPs), and microsatellite markers mined from RADseq reads (RAD-SSRs). We estimated the current population sizes by census and indirectly, from the linkage disequilibrium found in the genetic surveys....

Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient Neotropical mountains

Thais Vasconcelos, Suzana Alcantara, Caroline Andrino, Félix Forest, Marcelo Reginato, Marcelo Simon & José Pirani
Mountains are among the most biodiverse areas on the globe. In young mountain ranges, exceptional plant species-richness is often associated to recent and rapid radiations linked to the mountain uplift itself. In ancient mountains, however, orogeny vastly precedes the evolution of vascular plants, so species-richness has been explained by species accumulation during long periods of low extinction rates. Here we evaluate these assumptions by analyzing plant diversification dynamicsin thecampo rupestre, an ecosystem associated to pre-Cambrian...

Plant dispersal strategies of high tropical alpine communities across the Andes

Carolina Tovar, Inga Melcher, Buntarou Kusumoto, Francisco Cuesta, Antoine Cleef, Rosa Isela Meneses, Stephan Halloy, Luis Daniel Llambi, Stephan Beck, Priscilla Muriel, Ricardo Jaramillo, Jorge Jacome & Julieta Carilla
• Dispersal is a key ecological process that influences plant community assembly. Therefore, understanding whether dispersal strategies are associated with climate is of utmost importance, particularly in areas greatly exposed to climate change. We examined alpine plant communities located in the mountain summits of the tropical Andes across a 4000 km latitudinal gradient. We investigated species dispersal strategies and tested their association with climatic conditions and their evolutionary history. • We used dispersal-related traits (dispersal...

Data from: Ecological speciation in sympatric palms: 2. pre- and post-zygotic isolation

H. Hipperson, L.T. Dunning, W.J. Baker, R.K. Butlin, I. Hutton, A.S.T. Papadopulos, C.M. Smadja, T.C. Wilson, C. Devaux, Vincent Savolainen, R. K. Butlin, T. C. Wilson, W. J. Baker, A. S. T. Papadopulos & V. Savolainen
We evaluated reproductive isolation in two species of palms (Howea) that have evolved sympatrically on Lord Howe Island (LHI, Australia). We estimated the strength of some pre- and post-zygotic mechanisms in maintaining current species boundaries. We found that flowering time displacement between species is consistent across in and ex situ common gardens and is thus partly genetically determined. On LHI, pre-zygotic isolation due solely to flowering displacement was 97% for H. belmoreana and 80% for...

Data from: A new generic system for the pantropical Caesalpinia group (Leguminosae)

Edeline Gagnon, Anne Bruneau, Colin E. Hughes, Luciano Paganucci De Queiroz, Gwilym P. Lewis & Luciano De Queiroz
The Caesalpinia group is a large pantropical clade of ca. 205 species in subfamily Caesalpinioideae (Leguminosae) in which generic delimitation has been in a state of considerable flux. Here we present new phylogenetic analyses based on five plastid and one nuclear ribosomal marker, with dense taxon sampling including 172 (84%) of the species and representatives of all previously described genera in the Caesalpinia group. These analyses show that the current classification of the Caesalpinia group...

Data from: The phylogeny and biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a continental plant radiation

Marcel Cardillo, Peter H. Weston, Zoe K.M. Reynolds, Peter M. Olde, Austin R. Mast, Emily Lemmon, Alan Richard Lemmon, Lindell Bromham, Emily M. Lemmon, Alan R. Lemmon & Zoe K. M. Reynolds
The frequency of evolutionary biome shifts during diversification has important implications for our ability to explain geographic patterns of plant diversity. Recent studies present several examples of biome shifts, but whether frequencies of biome shifts closely reflect geographic proximity or environmental similarity of biomes remains poorly known. We explore this question by using phylogenomic methods to estimate the phylogeny of Hakea, a diverse Australian genus occupying a wide range of biomes. Model-based estimation of ancestral...

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: Phylogenetic systematics of subtribe Spiranthinae (Orchidaceae: Orchidoideae: Cranichideae) based on nuclear and plastid DNA sequences of a nearly complete generic sample

Gerardo A. Salazar, Joao A.N. Batista, Lidia I. Cabrera, Cassio Van Den Berg, W. Mark Whitten, Eric C. Smidt, Cristiano R. Buzatto, Rodrigo B. Singer, Gunter Gerlach, Rolando Jimenez-Machorro, Jose A. Radins, Irma S. Insaurralde, Leonardo R.S. Guimaraes, Fabio De Barros, Francisco Tobar, Jose L. Linares, Ernesto Mujica, Robert L. Dressler, Mario A. Blanco, Eric Hagsater & Mark W. Chase
Subtribe Spiranthinae is the most species-rich lineage of terrestrial Neotropical orchids, encompassing > 500 species and 40 genera. We conducted maximum parsimony and maximum likelihood phylogenetic analyses of DNA sequence data of plastid matK-trnK and trnL-trnF and nuclear ribosomal ITS sequences for 36 genera and 182 species of Spiranthinae plus appropriate outgroups. The results strongly support monophyly of Spiranthinae (minus Discyphus, Discyphinae and Galeottiella, Galeottiellinae) and five major lineages, namely monospecific Cotylolabium (sister to the...

Data from: The search for loci under selection: trends, biases and progress

Collin W Ahrens, Paul D Rymer, Adam Stow, Jason Bragg, Shannon Dillon, Kate D L Umbers, Rachael Y Dudaniec, Collin W. Ahrens, Paul D. Rymer, Kate D. L. Umbers & Rachael Y. Dudaniec
Detecting genetic variants under selection using FST outlier analysis (OA) and environmental association analyses (EAA) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field-based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends...

Data from: Evolutionary diversity in tropical tree communities peaks at intermediate precipitation

Danilo M. Neves, Kyle G. Dexter, Timothy R. Baker, Fernanda Coelho De Souza, Ary T. Oliveira-Filho, Luciano P. Queiroz, Haroldo C. Lima, Marcelo F. Simon, Gwilym P. Lewis, Ricardo A. Segovia, Luzmila Arroyo, Carlos Reynel, José L. Marcelo-Peña, Isau Huamantupa-Chuquimaco, Daniel Villarroel, G. Alexander Parada, Aniceto Daza, Reynaldo Linares-Palomino, Leandro V. Ferreira, Rafael P. Salomão, Geovane S. Siqueira, Marcelo T. Nascimento, Claudio N. Fraga & R. Toby Pennington
Global patterns of species and evolutionary diversity in plants are primarily determined by a temperature gradient, but precipitation gradients may be more important within the tropics, where plant species richness is positively associated with the amount of rainfall. The impact of precipitation on the distribution of evolutionary diversity, however, is largely unexplored. Here we detail how evolutionary diversity varies along precipitation gradients by bringing together a comprehensive database on the composition of angiosperm tree communities...

Thermal niche traits of high alpine plant species and communities across the tropical Andes and their vulnerability to global warming

Francisco Cuesta & Carolina Tovar
Aim The Climate Variability Hypothesis (CVH) predicts that locations with reduced seasonal temperature variation select for species with narrower thermal ranges. Here we (1) test the CVH by assessing the effect of latitude and elevation on the thermal ranges of Andean vascular plant species and communities, and (2) assess tropical alpine plants vulnerability to warming based on their thermal traits. Location Tropical Andes Taxon Vascular plants Methods Temperature data for 505 vascular plant species from...

Data from: Using digital soil maps to infer edaphic affinities of plant species in Amazonia: problems and prospects

Gabriel Massaine Moulatlet, Gabriela Zuquim, Fernando Oliviera Gouvea Figueiredo, Samuli Lehtonen, Thaise Emilio, Kalle Ruokolainen & Hanna Tuomisto
Amazonia combines semi-continental size with difficult access, so both current ranges of species and their ability to cope with environmental change have to be inferred from sparse field data. Although efficient techniques for modeling species distributions on the basis of a small number of species occurrences exist, their success depends on the availability of relevant environmental data layers. Soil data are important in this context, because soil properties have been found to determine plant occurrence...

Data from: Disentangling visual and olfactory signals in mushroom-mimicking Dracula orchids using realistic three-dimensional printed flowers

Tobias Policha, Aleah Davis, Melinda Barnadas, Bryn T. M. Dentinger, Robert A. Raguso & Bitty A. Roy
Flowers use olfactory and visual signals to communicate with pollinators. Disentangling the relative contributions and potential synergies between signals remains a challenge. Understanding the perceptual biases exploited by floral mimicry illuminates the evolution of these signals. Here, we disentangle the olfactory and visual components of Dracula lafleurii, which mimics mushrooms in size, shape, color and scent, and is pollinated by mushroom-associated flies. To decouple signals, we used three-dimensional printing to produce realistic artificial flower molds...

Data from: Disease where you dine: plant species and floral traits associated with pathogen transmission in bumble bees

Lynn S. Adler, Kristen M. Michaud, Stephen P. Ellner, Scott H. McArt, Phillip C. Stevenson, Rebecca E. Irwin & Philip C. Stevenson
Hotspots of disease transmission can strongly influence pathogen spread. Bee pathogens may be transmitted via shared floral use, but the role of plant species and floral trait variation in shaping transmission dynamics is almost entirely unexplored. Given the importance of pathogens for the decline of several bee species, understanding whether and how plant species and floral traits affect transmission could give us important tools for predicting which plant species may be hotspots for disease spread....

Data from: Stable isotope signatures of underground seedlings reveal the organic matter gained by adult orchids from mycorrhizal fungi

Julienne Marie-Isabelle Schweiger, Martin I. Bidartondo, Gerhard Gebauer & Julienne M.-I. Schweiger
1.Orchids produce dust seeds dependent on the provision of organic carbon by mycorrhizal fungi for their early development stages. Hence, all chlorophyllous orchids experience a dramatic switch in trophic strategies from initial mycoheterotrophy to either autotrophy or partial mycoheterotrophy during ontogeny. Yet, the degree to which partially mycoheterotrophic orchids gain carbon from their mycorrhizal fungi is unclear based on existing approaches. 2.Here, we propose a novel approach to quantify the fungal-derived organic matter gain of...

Data from: Matching symbiotic associations of an endangered orchid to habitat to improve conservation outcomes

Noushka Reiter, Ann C. Lawrie, Celeste C. Linde, Ann C Lawrie & Celeste C Linde
Background and Aims: An understanding of mycorrhizal variation, orchid seed germination temperature and the effect of co-occurring plant species could be critical for optimising conservation translocation of endangered plants with specialised mycorrhizal associations. Methods: Focussing on the orchid Thelymitra epipactoides we isolated mycorrhizal fungi from ten plants within each of three sites; Shallow Sands Woodland (SSW), Damp Heathland (DH) and Coastal Heathland Scrub (CHS). Twenty-seven fungal isolates were tested for symbiotic germination under three temperature...

Data from: Reducing wildlife damage with cost-effective management programmes

Cheryl R. Krull, Margaret C. Stanley, Bruce R. Burns, David Choquenot, Thomas E. Etherington & Thomas R. Etherington
Limiting the impact of wildlife damage in a cost effective manner requires an understanding of how control inputs change the occurrence of damage through their effect on animal density. Despite this, there are few studies linking wildlife management (control), with changes in animal abundance and prevailing levels of wildlife damage. We use the impact and management of wild pigs as a case study to demonstrate this linkage. Ground disturbance by wild pigs has become a...

Data from: Plant toxin levels in nectar vary spatially across native and introduced populations

Paul A. Egan, Phillip C. Stevenson, Erin Jo Tiedeken, Geraldine A. Wright, Fabio Boylan & Jane C. Stout
Secondary compounds in nectar can function as toxic chemical defences against floral antagonists, but may also mediate plant-pollinator interactions. Despite their ecological importance, few studies have investigated patterns of spatial variation in toxic nectar compounds in plant species, and none outside their native range. Grayanotoxin I (GTX I) occurs in nectar of invasive Rhododendron ponticum where it is toxic to honeybees and some solitary bee species. We examined (i) geographic variation in the composition of...

Data from: An allometry between seed kernel and seed coat shows greater investment in physical defense in small seeds

La-Mei Wu, Si-Chong Chen & Bo Wang
PREMISE OF THE STUDY: Numerous studies have treated the mass of a whole seed as an integrated unit, although the two components, seed kernel and seed coat, play different roles and suffer from different evolutionary selection pressures. In this study, we provided the first global-scale quantification of the relative biomass investments in seed coats and seed kernels. We tested the following hypotheses: there is a negative allometry between seed kernel mass and seed coat mass,...

Data from: Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

Gregory Bonito, Hannah Reynolds, Brendan P. Hodkinson, Jessica Nelson, Gerald Tuskan, , Christopher W. Schadt, Rytas Vilgalys & Michael S. Robeson
Microbial communities in plant roots provide critical links between above and belowground processes in terrestrial ecosystems. Variation in root communities has been attributed to plant host effects and microbial host preferences, as well as to factors pertaining to soil conditions, microbial biogeography and the presence of viable microbial propagules. To address hypotheses regarding the influence of plant host and soil biogeography on root fungal and bacterial communities we designed a trap-plant bioassay experiment. Replicate Populus,...

Data from: Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae)

Elizabeth W. McCarthy, Jacob B. Landis, Amelda Kurti, Amber J. Lawhorn, Mark W. Chase, Sandra Knapp, Steven C. Le Comber, Andrew R. Leitch & Amy Litt
Background: Polyploidy has played a major role in angiosperm evolution. Previous studies have examined polyploid phenotypes in comparison to their extant progenitors, but not in context of predicted progenitor phenotypes at allopolyploid origin. In addition, differences in the trends of polyploid versus diploid evolution have not been investigated. We use ancestral character-state reconstructions to estimate progenitor phenotype at allopolyploid origin to determine patterns of polyploid evolution leading to morphology of the extant species. We also...

Data from: Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae)

Christian Lexer, Rafael O. Wüest, Sofia Mangili, Myriam Heuertz, Kai N. Stolting, Peter B. Pearman, Felix Forest, Nicolas Salamin, Niklaus E. Zimmermann & Eligio Bossolini
Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species-rich radiations inhabiting the world’s biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analyzed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species-rich and ecologically important plant family of the Cape...

Data from: Phylogeny and classification of the East Asian Amitostigma alliance (Orchidaceae: Orchideae) based on six DNA markers

Ying Tang, Tomohisa Yukawa, Richard M. Bateman, Hong Jiang & Hua Peng
Background: Tribe Orchideae dominates the orchid flora of the temperate Northern Hemisphere but its representatives in East Asia had been subject to less intensive phylogenetic study than those in Eurasia and North America. Although this situation was improved recently by the molecular phylogenetic study of Jin et al., comparatively few species were analyzed from the species-rich and taxonomically controversial East Asian Amitostigma alliance. Here, we present a framework nrITS tree of 235 accessions of Orchideae...

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