110 Works

Data from: Interglacial microrefugia and diversification of a cactus species complex: phylogeography and palaeodistributional reconstructions for Pilosocereus aurisetus and allies

Isabel A. S. Bonatelli, Manolo F. Perez, A. Townsend Peterson, Nigel P. Taylor, Daniela C. Zappi, Marlon C. Machado, Ingrid Koch, Adriana H. C. Pires & Evandro M. Moraes
The role of Pleistocene climate changes in promoting evolutionary diversification in global biota is well documented, but the great majority of data regarding this subject come from North America and Europe, which were greatly affected by glaciation. The effects of Pleistocene changes on cold- and/or dry-adapted species in tropical areas where glaciers were not present remain sparsely investigated. Many such species are restricted to small areas surrounded by unfavourable habitats, which may represent potential interglacial...

Data from: Next-Gen phylogeography of rainforest trees: measuring landscape-level cpDNA variation from whole-genome sequencing.

Marlien Van Der Merwe, Hannah McPherson, Maurizio Rossetto & Juelian Siow
Standardized phylogeographic studies across co-distributed taxa can identify important refugia and biogeographic barriers, and potentially uncover how changes in adaptive constraints through space and time impact on the distribution of genetic diversity. The combination of Next Generation Sequencing and methodologies that enable uncomplicated analysis of the full chloroplast genome may provide an invaluable resource for such studies. Here we assess the potential of a shotgun-based method across twelve non-model rainforest trees sampled from two evolutionary...

Data from: ITS1 versus ITS2 as DNA metabarcodes for fungi

Rakel Blaalid, Surendra Kumar, R. Henrik Nilsson, Kessy Abarenkov, Paul M. Kirk & Håvard Kauserud
The nuclear ribosomal Internal Transcribed Spacer ITS region is widely used as a DNA metabarcoding marker to characterize the diversity and composition of fungal communities. In amplicon pyrosequencing studies of fungal diversity, one of the spacers ITS1 or ITS2 of the ITS region is normally used. In this methodological study we evaluate the usability of ITS1 vs. ITS2 as a DNA metabarcoding marker for fungi. We analyse three data sets: two comprising ITS1 and ITS2...

Data from: A comparative analysis of the mechanisms underlying speciation on Lord Howe Island

Alexander S. T. Papadopulos, Zuzana Price, Celine Devaux, Helen Hipperson, Carole M. Smadja, Ian Hutton, William J. Baker, Roger K. Butlin & Vincent Savolainen
On Lord Howe Island, speciation is thought to have taken place in situ in a diverse array of distantly related plant taxa (Metrosideros, Howea and Coprosma; Proc. Natl Acad. Sci. USA 108, 2011, 13188). We now investigate whether the speciation processes were driven by divergent natural selection in each genus by examining the extent of ecological and genetic divergence. We present new and extensive, ecological and genetic data for all three genera. Consistent with ecologically...

Data from: Palaeo-precipitation is a major determinant of palm species richness patterns across Madagascar: a tropical biodiversity hotspot

Mijoro Rakotoarinivo, Anne Blach-Overgaard, William J. Baker, John Dransfield, Justin Moat, Jens-Christian Svenning & J.-C. Svenning
The distribution of rainforest in many regions across the Earth was strongly affected by Pleistocene ice ages. However, the extent to which these dynamics are still important for modern-day biodiversity patterns within tropical biodiversity hotspots has not been assessed. We employ a comprehensive dataset of Madagascan palms (Arecaceae) and climate reconstructions from the last glacial maximum (LGM; 21 000 years ago) to assess the relative role of modern environment and LGM climate in explaining geographical...

Data from: The structure of Leguminosae-Detarioideae dominant rain forest in Korup National Park, Cameroon

Xander Van Der Burgt, David Newbery & Sylvanos Njibili
Background and aims – We studied a cluster of trees in the Leguminosae subfamily Detarioideae, to: (1) determine the size, structure, and tree species composition of this cluster; (2) map the size, shape, and structure of groups of individual Detarioideae tree species in the cluster; (3) hypothesize on the origin and maintenance of the cluster. Location – Lowland rain forest in south Korup National Park, in the Southwest Region of Cameroon. Material and methods –...

Extinction dynamics under extreme conservation threat: the flora of St Helena

Quentin Cronk & Phil Lambdon
The flora of the island of St Helena provides an amplified system for the study of extinction by reason of the island’s high endemism, small size, vulnerable biota, length of time of severe disturbance (since 1502) and severity of threats. Endemic plants have been eliminated from 96.5% of St Helena by habitat loss. There are eight recorded extinctions in the vascular flora since 1771 giving an extinction rate of 581 extinctions per million species per...

Phylogeny, biogeography, and morphological evolution among and within the Neotropical and Asian clades of Schefflera (Araliaceae)

Gregory Plunkett, Porter Lowry, Pedro Fiaschi, David Frodin & Antoine Nicolas
Schefflera is the largest and most complex genus of Araliaceae, with ~600 described species (and many additional species awaiting formal description), but recent studies indicate that it is polyphyletic, forming five geographically centered clades spread across the major lineages of the family. Significant progress has been made in revising the three smallest clades, but the two largest groups, centered in Asia and the Neotropics, remain poorly understood. To advance our knowledge of these groups, a...

Data from: Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

James A. Nicholls, R. Toby Pennington, Erik J. Koenen, Colin E. Hughes, Jack Hearn, Lynsey Bunnefeld, Kyle G. Dexter, Graham N. Stone, Catherine A. Kidner & Erik J. M. Koenen
Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown...

Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

Matthew G. Johnson, Lisa Pokorny, Steven Dodsworth, Laura R. Botigue, Robyn S. Cowan, Alison Devault, Wolf L. Eiserhardt, Niroshini Epitawalage, Félix Forest, Jan T. Kim, James Leebens-Mack, Ilia J. Leitch, Olivier Maurin, Doug Soltis, Pamela S. Soltis, Gane Ka-Shu Wong, William J. Baker & Norman Wickett
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used...

Data from: Flower preferences and pollen transport networks for cavity nesting solitary bees: implications for the design of agri-environment schemes

Catherine E.A. Gresty, Elizabeth Clare, Dion S. Devey, Robyn S. Cowan, Laszlo Csiba, Panagiota Malakasi, Owen T. Lewis, Katherine J. Willis & Catherine E. A. Gresty
Floral foraging resources are valuable for pollinator conservation on farmland, and their provision is encouraged by agri-environment schemes in many countries. Across Europe, wildflower seed mixtures are widely sown on farmland to encourage pollinators, but the extent to which key pollinator groups such as solitary bees exploit and benefit from these resources is unclear. We used high-throughput sequencing of 164 pollen samples extracted from the brood cells of 6 common cavity nesting solitary bee species...

Data from: Comparative analysis of Begonia plastid genomes and their utility for species-level phylogenetics

Catherine Kidner, Nicola Harrison, Richard Harrison, Richard J. Harrison & Catherine A. Kidner
Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia.

Data from: Environment and host as large-scale controls of ectomycorrhizal fungi

Sietse Van Der Linde, Laura M. Suz, C. David L. Orme, Filipa Cox, Henning Andreae, Endla Asi, Bonnie Atkinson, Sue Benham, Christopher Carroll, Nathalie Cools, Bruno De Vos, Hans-Peter Dietrich, Johannes Eichhorn, Joachim Germann, Tine Grebenc, Hyun S. Gweon, Karin Hansen, Frank Jacob, Ferdinand Kristöfel, Pawel Lech, Miklos Manninger, Jan Martin, Henning Meesenburg, Päivi Merilä, Manuel Nicolas … & Martin I. Bidartondo
Explaining the large-scale diversity of soil organisms that drive biogeochemical processes—and their responses to environmental change—is critical. However, identifying consistent drivers of belowground diversity and abundance for some soil organisms at large spatial scales remains problematic. Here we investigate a major guild, the ectomycorrhizal fungi, across European forests at a spatial scale and resolution that is—to our knowledge—unprecedented, to explore key biotic and abiotic predictors of ectomycorrhizal diversity and to identify dominant responses and thresholds...

Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

, Anne Bruneau, Nasim Azani, Marielle Babineau, Edeline Gagnon, Carole Sinou, Royce Steeves, Erin Zimmerman, C. Donovan Bailey, Lynsey Kovar, Madhugiri Nageswara-Rao, Hannah Banks, RuthP. Clark, Manuel De La Estrella, Peter Gasson, GeoffreyC. Kite, BenteB. Klitgaard, GwilymP. Lewis, Danilo Neves, Gerhard Prenner, María De Lourdes Rico-Arce, ArianeR. Barbosa, Maria Cristina López-Roberts, Luciano Paganucci De Queiroz, PétalaG. Ribeiro … & Tingshuang Yi
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most...

Data from: Frugivory-related traits promote speciation of tropical palms

Renske E. Onstein, William J. Baker, Thomas L. P. Couvreur, Søren Faurby, Jens-Christian Svenning & W. Daniel Kissling
Animal-mediated seed dispersal by frugivorous birds and mammals is central to the ecology and functioning of ecosystems, but whether and how frugivory-related traits have affected plant speciation remains little explored. Fruit size is directly linked to plant dispersal capacity and therefore influences gene flow and genetic divergence of plant populations. Using a global species-level phylogeny with comprehensive data on fruit sizes and plant species distributions, we test whether fruit size has affected speciation rates of...

Data from: The relevance of gene flow in metapopulation dynamics of an oceanic island endemic, Olea europaea subsp guanchica

Carlos García-Verdugo, Alan D Forrest, Michael F Fay & Pablo Vargas
Theoretical and empirical studies suggest that geographical isolation and extinction-recolonization dynamics are two factors causing strong genetic structure in metapopulations. Here, we investigated the effect of population age structure and isolation by distance in the patterns of genetic diversity in a tree species (Olea europaea subsp. guanchica) sporadically affected by volcanic events across the Canarian archipelago. Genetic variation was assessed at six nuclear microsatellites (nDNA) and six chloroplast fragments (cpDNA) in nine subpopulations sampled on...

Data from: Stable epigenetic effects impact adaptation in allopolyploid orchids (Dactylorhiza: Orchidaceae)

Ovidiu Paun, Richard M. Bateman, Michael F. Fay, Mikael Hedrén, Laure Civeyrel & Mark W. Chase
Epigenetic information includes heritable signals that modulate gene expression but are not encoded in the primary nucleotide sequence. We have studied natural epigenetic variation in three allotetraploid sibling orchid species that differ radically in geography/ecology. The epigenetic variation released by genome doubling has been restructured in species-specific patterns that reflect their recent evolutionary history, and have an impact on their ecology and evolution, hundreds of generations after their formation. Epigenome scans pinpointed epiloci under divergent...

Data from: Where did all the trees come from? A novel multispecies approach reveals the impacts of biogeographical history and functional diversity on rain forest assembly

Maurizio Rossetto, Hannah McPherson, Juelian Siow, Robert Kooyman, Marlien Van Der Merwe & Peter D. Wilson
Aim: We take advantage of next generation sequencing-based technology to assess how landscape-level dynamics, biogeographical history and functional factors shape the distribution of genetic diversity in rain forest trees. To achieve this, we explore chloroplast genomic diversity and divergence patterns across multiple, co-distributed species from three major centres of rain forest diversity. Location: Subtropical rain forests in south-eastern Australia: Nightcap–Border Ranges, Dorrigo and Washpool. Methods: We assembled chloroplast genomic data from whole-genome shotgun libraries for...

Data from: Seed size and the evolution of leaf defences

Thomas S. Kraft, S. Joseph Wright, Ian Turner, Peter W. Lucas, Christopher E. Oufiero, , I-Fang Sun & Nathaniel J. Dominy
1. Leaf defences vary widely among tree species, affecting rates of herbivory, survival and reproduction. 2. Two contrasting hypotheses account for variation in leaf defences among species. The first predicts that a slow life history, which is characteristic of larger seeded species adapted to resource-limited environments, is associated with well-defended leaves. The second, apparency theory, predicts that elevated leaf defences are necessitated for species that are more detectable to herbivores. 3. Here we use comparative...

Data from: Analysis of phylogenomic tree space resolves relationships among marsupial families

David A. Duchêne, Jason G. Bragg, Sebastian Duchêne, Linda E. Neaves, Sally Potter, Craig Moritz, Rebecca N. Johnson, Simon Y. W. Ho & Mark D. B. Eldridge
A fundamental challenge in resolving evolutionary relationships across the Tree of Life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group. Using simulations and a new phylogenomic data set comprising nucleotide sequences of 1550 loci from 18 of the 22 extant marsupial families, we demonstrate the power of a...

Orchis nuclear microsatellite data

Leif Bersweden
Premise of the study The genetic structure of hybrid zones provides an insight into the potential for gene flow to occur between plant taxa. Four closely related European orchid species (Orchis anthropophora, O. militaris, O. purpurea and O. simia) hybridize when they co-occur. We aimed to characterize patterns of hybridization in O. militaris – O. purpurea, O. purpurea – O. simia and O. anthropophora – O. simia hybrid zones using molecular and morphological data. Methods...

Shade alters grass growth and architecture by reducing root biomass

Cedrique Solofondranohatra, Maria Vorontsova, Rebecca Dewhirst, Claire Belcher, Stuart Cable, Vololoniaina Jeannoda & Caroline Lehmann
Variable tree cover characterizes tropical grassy biomes. Light availability in the ground layer becomes increasingly limited as tree cover increases while open canopy environments are associated with a flammable grassy ground layer. Grass species dominating the ground layer of these ecosystems have adopted strategies to persist and proliferate with frequent fire. However, there is limited understanding of how grass growth and flammability traits respond to changes in light availability. We experimentally grew 14 grass species...

Ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner: Additional data (images, phylogenetic alignments and trees)

Nikolai Adamski, James Simmonds, Jemima Brinton, Anna Backhaus, Yi Chen, Mark Smedley, Sadiye Hayta, Tobin Florio, Pamela Crane, Peter Scott, Alice Pieri, Olyvia Hall, J. Elaine Barclay, Myles Clayton, John Doonan, Candida Nibau & Cristobal Uauy
Flower development is an important determinant of grain yield in crops. In wheat, natural variation for the size of spikelet and floral organs is particularly evident in Triticum polonicum, a tetraploid subspecies of wheat with long glumes, lemmas, and grains. Using map-based cloning, we identified VRT2, a MADS-box transcription factor belonging to the SVP family, as the gene underlying the P1 locus. The causal P1 mutation is a sequence substitution in intron-1 that results in...

DNA barcode analyses improve accuracy in fungal species distribution models

Javier Fernández-López, M. Teresa Telleria, Margarita Dueñas, Tom May & María P. Martín
Species distribution models based on environmental predictors are useful to explain a species geographic range. For many groups of organisms, including fungi, the increase of occurrence data sets has generalized their use. However, fungal species are not always easy to distinguish, and taxonomy of many groups is not completely settled. This study explores the effect of taxonomic uncertainty in databases used for modeling fungal distributions. We analyze distribution models for three morphospecies from the corticioid...

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 & 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...

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  • Royal Botanic Gardens
  • University of Melbourne
  • University of Oxford
  • Australian National University
  • Aarhus University
  • State University of Feira de Santana
  • University of Sheffield
  • University of Edinburgh
  • Imperial College London
  • Cornell University