Age-related pharmacodynamics in a bumblebee-microsporidian system mirror similar patterns in vertebrates
Arran J. Folly, Philip C. Stevenson & Mark J. F. Brown
Dataset published via Dryad
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...
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https://doi.org/10.5061/dryad.rn1gf7k Cite
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...
https://doi.org/10.5061/dryad.9b9c1 Cite
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....
https://doi.org/10.5061/dryad.v75rj24 Cite
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
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...
https://doi.org/10.5061/dryad.jq5g627 Cite
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...
https://doi.org/10.5061/dryad.f4h2h Cite
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
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...
https://doi.org/10.5061/dryad.rh24n Cite
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...
https://doi.org/10.5061/dryad.bq091cg Cite
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
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...
https://doi.org/10.5061/dryad.7h3f6 Cite
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...
https://doi.org/10.5061/dryad.j8qv9 Cite
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...
https://doi.org/10.5061/dryad.x69p8czf6 Cite
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...
https://doi.org/10.5061/dryad.gf1vhhmk0 Cite
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...
https://doi.org/10.5061/dryad.3r2280gbv Cite
WEGE: A new metric for ranking locations for biodiversity conservation
Harith Farooq, Josué Andersson, Francesco Belluardo, Cristóvão Nanvonamuquitxo, Dominic Bennett, Justin Moat, Amadeu Soares, Søren Faurby & Alexandre Antonelli
Aim Effective policy making for biological conservation requires the identification and ranking of the most important areas for protection or management. One of the most frequently used systems for selecting priority areas is Key Biodiversity Areas (hereafter KBAs), developed by the International Union for Conservation of Nature (IUCN). However, KBAs cannot be used to rank areas, potentially limiting their use when limited funding is available. To tackle this shortcoming and facilitate spatial prioritization, here we...
https://doi.org/10.5061/dryad.jsxksn06s Cite
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...
https://doi.org/10.5061/dryad.xksn02vc8 Cite
Diversification of Crassula: Phylogenetic analysis and life-form traits
Marc Fradera-Soler, Meng Lu & Olwen M. Grace
These datasets are associated with the published paper - "Evidence linking life form to a major shift in diversification rate in Crassula" (DOI:10.1002/ajb2.1797) Crassula L. (Crassulaceae) is a characteristic element of the southern African flora, occurring in a wide range of habitats, and it exhibits a remarkable diversity of life forms. However, whether any particular life-form trait has shaped species diversification in Crassula has remained unexplored. Our study aimed to investigate diversification patterns within Crassula...
No usage information was reported.
https://doi.org/10.5061/dryad.qrfj6q5hg Cite
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...
https://doi.org/10.5061/dryad.69ph0 Cite
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...
https://doi.org/10.5061/dryad.1521 Cite
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: 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...
https://doi.org/10.5061/dryad.143r1 Cite
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...
https://doi.org/10.5061/dryad.s3h9r6j Cite
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...
https://doi.org/10.5061/dryad.353q5 Cite
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...
https://doi.org/10.5061/dryad.3df12 Cite
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...
https://doi.org/10.5061/dryad.r9c12 Cite
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...
https://doi.org/10.5061/dryad.6vb720f Cite
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...
https://doi.org/10.5061/dryad.gk138 Cite
State University of Feira de Santana