42 Works

Data from: Transgressive physiological and transcriptomic responses to light stress in allopolyploid Glycine dolichocarpa (Leguminosae)

Jeremy E. Coate, Adrian F. Powell, Tom G. Owens & Jeff J. Doyle
Allopolyploidy is often associated with increased photosynthetic capacity as well as enhanced stress tolerance. Excess light is a ubiquitous plant stress associated with photosynthetic light harvesting. We show that under chronic excess light, the capacity for non-photochemical quenching (NPQmax), a photoprotective mechanism, was higher in a recently formed natural allotetraploid (Glycine dolichocarpa, designated ‘T2’) than in its diploid progenitors (G. tomentella, ‘D3’; and G. syndetika, ‘D4’). This enhancement in NPQmax was due to an increase...

Data from: Host conservatism or host specialization? Patterns of fungal diversification are influenced by host plant specificity in Ophiognomonia (Gnomoniaceae, Diaporthales)

Donald M. Walker, Amy Y. Rossman, Lisa A. Castlebury & Lena Struwe
In this study evolutionary host plant patterns at ranks from order to species were analysed using spatial evolutionary and ecological vicariance analysis (SEEVA), based on a multigene phylogeny of 45 ascomycete fungal species. The objective was to understand speciation events and host associations in Ophiognomonia (Gnomoniaceae). Species of this genus are perithecial fungi that occur as endophytes, pathogens, and latent saprobes on plants in the families of Betulaceae, Fagaceae, Juglandaceae, Lauraceae, Malvaceae, Platanaceae, Rosaceae, Salicaceae,...

Data from: Response to persistent er stress in plants: a multiphasic process that transitions cells from prosurvival activities to cell death

Renu Srivastava, Zhaoxia Li, Giulia Russo, Jie Tang, Ran Bi, Usha Muppirala, Sivanandan Chudalayandi, Andrew Severin, Mingze He, Samuel I. Vaitkevicius, Carolyn J. Lawrence-Dill, Peng Liu, Ann E. Stapleton, Diane C. Bassham, Federica Brandizzi & Stephen H. Howell
The unfolded protein response (UPR) is a highly conserved response that protects plants from adverse environmental conditions. The UPR is elicited by endoplasmic reticulum (ER) stress, in which unfolded and misfolded proteins accumulate within the ER. Here, we induced the UPR in maize (Zea mays) seedlings to characterize the molecular events that occur over time during persistent ER stress. We found that a multiphasic program of gene expression was interwoven among other cellular events, including...

Data from: Expansion and diversification of the MSDIN family of cyclic peptide genes in the poisonous agarics Amanita phalloides and A. bisporigera

Jane A. Pulman, Kevin L. Childs, R. Michael Sgambelluri & Jonathan D. Walton
Background: The cyclic peptide toxins of Amanita mushrooms, such as α-amanitin and phalloidin, are encoded by the “MSDIN” gene family and ribosomally biosynthesized. Based on partial genome sequence and PCR analysis, some members of the MSDIN family were previously identified in Amanita bisporigera, and several other members are known from other species of Amanita. However, the complete complement in any one species, and hence the genetic capacity for these fungi to make cyclic peptides, remains...

Data from: Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote

Gerald Schönknecht, Wei-Hua Chen, Chad M. Ternes, Guillaume G. Barbier, Roshan P. Shrestha, Mario Stanke, Andrea Bräutigam, Brett J. Baker, Jillian F. Banfield, R. Michael Garavito, Kevin Carr, Curtis Wilkerson, Stefan A. Rensing, David Gagneul, Nicholas E. Dickenson, Christine Oesterhelt, Martin J. Lercher & Andreas P. M. Weber
Some microbial eukaryotes, such as the extremophilic red alga Galdieria sulphuraria, can live in hot, toxic metal-rich, acidic environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the 13.7 Mb genome of G. sulphuraria. This alga shows an enormous metabolic flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family...

Data from: Comparing the genetic architecture and potential response to selection of native and invasive populations of reed canary grass

Brittny Calsbeek, Manisha Patel, Sebastien Lavergne & Jane Molofsky
Evolutionary processes such as migration, genetic drift, and natural selection are thought to play a prominent role in species invasions into novel environments. However, few empirical studies have explored the mechanistic basis of invasion in an evolutionary framework. One promising tool for inferring evolutionarily important changes in introduced populations is the genetic variance-covariance matrix (G matrix). G matrix comparisons allow for the inference of changes in the genetic architecture of introduced populations relative to their...

Data from: Artificial selection on anther exsertion in wild radish, Raphanus raphanistrum

Jeffrey K. Conner, Cynthia J. Mills, Vanessa A. Koelling & Keith Karoly
To study the genetic architecture of anther exsertion, a trait under stabilizing selection in wild radish, artificial selection on anther exsertion was applied for 11 generations. Two replicate lines each of increased and decreased exsertion plus two randomly-mated controls were included. Full pedigree information is available from generation five. To estimate correlated responses to selection, 571 plants from all lines and matrilines were grown in the greenhouse and a number of floral, growth, and phenology...

Data from: GloPL, a global data base on pollen limitation of plant reproduction

Joanne. M. Bennett, Janette. A. Steets, Jean. H. Burns, Walter Durka, Jana. C. Vamosi, Gerardo Arceo-Gómez, Martin Burd, Laura. A. Burkle, Allan. G Ellis, Leandro Freitas, Junmin Li, James. G. Rodger, Marina Wolowski, Jing Xia, Tia-Lynn Ashman & Tiffany. M. Knight
Plant reproduction relies on transfer of pollen from anthers to stigmas, and the majority of flowering plants depend on biotic or abiotic agents for this transfer. A key metric for characterizing if pollen receipt is insufficient for reproduction is pollen limitation, which is assessed by pollen supplementation experiments. In a pollen supplementation experiment, fruit or seed production by flowers exposed to natural pollination is compared to that following hand pollination either by pollen supplementation (i.e....

Data from: StomataCounter: a neural network for automatic stomata identification and counting

Karl C. Fetter, Sven Eberhardt, Rich S. Barclay, Scott Wing & Stephen R. Keller
Stomata regulate important physiological processes in plants and are often phenotyped by researchers in diverse fields of plant biology. Currently, there are no user friendly, fully-automated methods to perform the task of identifying and counting stomata, and stomata density is generally estimated by manually counting stomata. We introduce StomataCounter, an automated stomata counting system using a deep convolutional neural network to identify stomata in a variety of different microscopic images. We use a human-in-the-loop approach...

Data from: Edge effects and mating patterns in a bumblebee-pollinated plant

Dorothy Christopher, Randall J Mitchell, Dorset W Trapnell, Patrick A Smallwood, Wendy R Semski & Jeffrey D Karron
Researchers have long assumed that plant spatial location influences plant reproductive success and pollinator foraging behavior. For example, many flowering plant populations have small, linear, or irregular shapes that increase the proportion of plants on the edge, which may reduce mating opportunities through both male and female function. Additionally, plants that rely on pollinators may be particularly vulnerable to edge effects if those pollinators exhibit restricted foraging and pollen carryover is limited. To explore the...

Limited plasticity in thermally tolerant ectotherm populations: evidence for a trade-off

Jordanna Barley, Brian S. Cheng, Matthew Sasaki, Sarah Gignoux-Wolfsohn, Cynthia G. Hays, Alysha B. Putnam, Seema Sheth, Andrew Villeneuve, Morgan Kelly, Jordanna M. Barley & Andrew R. Villeneuve
Many species face extinction risks owing to climate change, and there is an urgent need to identify which species' populations will be most vulnerable. Plasticity in heat tolerance, which includes acclimation or hardening, occurs when prior exposure to a warmer temperature changes an organism's upper thermal limit. The capacity for thermal acclimation could provide protection against warming, but prior work has found few generalizable patterns to explain variation in this trait. Here, we report the...

Data from: Stasis and convergence characterize morphological evolution in eupolypod II ferns

Michael A. Sundue & Carl J. Rothfels
Background and Aims: Patterns of morphological evolution at levels above family rank remain underexplored in the ferns. The present study seeks to address this gap through analysis of 79 morphological characters for 81 taxa, including representatives of all ten families of eupolypod II ferns. Recent molecular phylogenetic studies demonstrate that the evolution of the large eupolypod II clade (which includes nearly one-third of extant fern species) features unexpected patterns. The traditional ‘athyrioid’ ferns are scattered...

The Rhododendron genome and chromosomal organization provide insight into shared whole-genome duplications across the heath family (Ericaceae)

Valerie L. Soza, Dale Lindsley, Adam Waalkes, Elizabeth Ramage, Rupali P. Patwardhan, Joshua N. Burton, Andrew Adey, Akash Kumar, Ruolan Qiu, Jay Shendure & Benjamin Hall
The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of >1,000 species. Here, we report the chromosome-scale de novo assembly and genome annotation of Rhododendron williamsianum as a basis for continued study of this large genus. We created multiple short fragment genomic libraries, which were assembled using ALLPATHS-LG. This was followed by contiguity preserving transposase sequencing (CPT-seq) and fragScaff scaffolding of a large fragment...

Soil microbial communities associated with giant sequoia: How does the world's largest tree affect some of the world's smallest organisms?

Stephen Hart, Chelsea J. Carey, Sydney I. Glassman, Thomas D. Bruns & Emma L. Aronson
Giant sequoia (Sequoiadendron giganteum) is an iconic conifer that lives in relic populations on the western slopes of the California Sierra Nevada. In these settings, it is unusual among the dominant trees in that it associates with arbuscular mycorrhizal fungi rather than ectomycorrhizal fungi. However, it is unclear whether differences in microbial associations extends more broadly to non-mycorrhizal components of the soil microbial community. To address this question, we characterized microbiomes associated with giant sequoia...

Data from: The edaphic environment mediates flowering-time differentiation between adjacent populations of Leptosiphon parviflorus

Emily L. Dittmar & Douglas W. Schemske
Flowering time is an important life history trait in plants that often affects fitness. The optimal time to flower may be influenced by trade-offs between flowering time and growth-related traits and is thus likely to differ among habitats. Because flowering-time differences between populations can also reduce gene flow, understanding the factors that contribute to variation in flowering time among closely adjacent populations that experience gene flow is of particular interest. Plant adaptation to different edaphic...

Data from: The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes

Dimitrios Floudas, Manfred Binder, Robert Riley, Kerrie Barry, Robert A. Blanchette, Bernard Henrissat, Angel T. Martínez, Robert Ortillar, Joseph W. Spatafora, Jagjit S. Yadav, Andrea Aerts, Isabelle Benoit, Alex Boyd, Alexis Carlson, Alex Copeland, Pedro M. Coutinho, Ronald P. De Vries, Patricia Ferreira, Keisha Findley, Brian Foster, Jill Gaskell, Dylan Glotzer, Paweł Górecki, Joseph Heitman, Cedar Hesse … & David S. Hibbett
Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non–lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as...

Data from: Three keys to the radiation of angiosperms into freezing environments

Amy E. Zanne, David C. Tank, William K. Cornwell, Jonathan M. Eastman, Stephen A. Smith, Richard G. FitzJohn, Daniel J. McGlinn, Brian C. O'Meara, Angela T. Moles, Peter B. Reich, Dana L. Royer, Douglas E. Soltis, Peter F. Stevens, Mark Westoby, Ian J. Wright, Lonnie Aarssen, Robert I. Bertin, Andre Calaminus, Rafaël Govaerts, Frank Hemmings, Michelle R. Leishman, Jacek Oleksyn, Pamela S. Soltis, Nathan G. Swenson, Laura Warman … & Alejandro Ordonez
Early flowering plants are thought to have been woody species restricted to warm habitats1, 2, 3. This lineage has since radiated into almost every climate, with manifold growth forms4. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf...

Data from: An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid.

Craig F Barrett & John V Freudenstein
In the spirit of recent calls for species delimitation studies to become more pluralistic, incorporating multiple sources of evidence, we adopted an integrative, phylogeographic approach to delimiting species and evolutionarily significant units (ESU) in the Corallorhiza striata species complex. This rare, North American, mycoheterotrophic orchid has been a taxonomic challenge with regard to species boundaries, displaying complex patterns of variation and reduced vegetative morphology. We employed plastid DNA, nuclear DNA, and morphometrics, treating the C....

Data from: Evidence for arrested succession in a liana‐infested Amazonian forest

Blaise Tymen, Maxime Réjou-Méchain, James W. Dalling, Sophie Fauset, Ted R. Feldausch, Natalia Norden, Oliver L. Phillips, Benjamin L. Turner, Jérôme Viers & Jérôme Chave
1. Empirical evidence and modelling both suggest that global changes may lead to an increased dominance of lianas, and thus to an increased prevalence of liana-infested forest formations in tropical forests. The implications for tropical forest structure and the carbon cycle remain poorly understood. 2. We studied the ecological processes underpinning the structure and dynamics of a liana-infested forest in French Guiana, using a combination of long-term surveys (tree, liana, seedling and litterfall), soil chemical...

Data from: Taller plants have lower rates of molecular evolution

Robert Lanfear, Simon Y. W. Ho, T. Jonathan Davies, Angela T. Moles, Lonnie Aarssen, Nathan G. Swenson, Laura Warman, Amy E. Zanne & Andrew P. Allen
Rates of molecular evolution have a central role in our understanding of many aspects of species’ biology. However, the causes of variation in rates of molecular evolution remain poorly understood, particularly in plants. Here we show that height accounts for about one-fifth of the among-lineage rate variation in the chloroplast and nuclear genomes of plants. This relationship holds across 138 families of flowering plants, and when accounting for variation in species richness, temperature, ultraviolet radiation,...

Beyond leaf habit: generalities in plant function across 97 tropical dry forest tree species

German Vargas G., Tim J. Brodribb, Juan M. Dupuy, Roy González‐M., Catherine M. Hulshof, David Medvigy, Tristan A. P. Allerton, Camila Pizano, Beatriz Salgado‐Negret, Naomi B. Schwartz, Skip J. Van Bloem, Bonnie G. Waring & Jennifer S. Powers
Leaf habit has been hypothesized to define a linkage between the slow-fast plant economic spectrum and the drought resistance-avoidance trade-off in tropical forests (‘slow-safe versus fast-risky’). However, variation in hydraulic traits as a function of leaf habit has rarely been explored for a large number of species. We sampled leaf and branch functional traits of 97 tropical dry forest tree species from four sites to investigate whether patterns of trait variation varied consistently in relation...

Data from: Phylogeography of speciation: allopatric divergence and secondary contact between outcrossing and selfing Clarkia

James B. Pettengill & David A. Moeller
The origins of hybrid zones between parapatric taxa have been of particular interest for understanding the evolution of reproductive isolation and the geographic context of species divergence. One challenge has been to distinguish between allopatric divergence (followed by secondary contact) versus primary intergradation (parapatric speciation) as alternative divergence histories. Here we use complementary phylogeographic and population genetic analyses to investigate the recent divergence of two subspecies of Clarkia xantiana and the formation of a hybrid...

Data from: Dynamic genomic architecture of mutualistic cooperation in a wild population of Mesorhizobium

Stephanie S. Porter, Joshua Faber-Hammond, Angeliqua P. Montoya, Maren L. Friesen & Cynthia Sackos
Research on mutualism seeks to explain how co-operation can be maintained when uncooperative mutants co-occur with cooperative kin. Gains and losses of the gene modules required for co-operation punctuate symbiont phylogenies and drive lifestyle transitions between cooperative symbionts and uncooperative free-living lineages over evolutionary time. Yet whether uncooperative symbionts commonly evolve from within cooperative symbiont populations or from within distantly related lineages with antagonistic or free-living lifestyles (i.e., third-party mutualism exploiters or parasites), remains controversial....

Data from: Plant functional traits and environmental conditions shape community assembly and ecosystem functioning during restoration

Chad R. Zirbel, Tyler Basset, Emily Grman, Lars A. Brudvig & Tyler Bassett
Recovering biological diversity and ecosystem functioning are primary objectives of ecological restoration, yet these outcomes are often unpredictable. Assessments based on functional traits may help with interpreting variability in both community composition and ecosystem functioning because of their mechanistic and generalizable nature. This promise remains poorly realized, however, because tests linking environmental conditions, functional traits, and ecosystem functioning in restoration are rare. Here, we provide such a test through what is to our knowledge the...

Data from: Correlated evolution of mating system and floral display traits in flowering plants and its implications for the distribution of mating system variation

Carol Goodwillie, Risa D. Sargent, Susan Kalisz, Richard H. Ree, David A. Moeller, Mario Vallejo-Marin, Christopher G. Eckert, Alice A. Winn, Elizabeth Elle, Monica A. Geber & Mark O. Johnston
Reduced allocation to structures for pollinator attraction is predicted in selfing species. We explored the association between outcrossing and floral display in a broad sample of angiosperms. We used the demonstrated relationship to test for bias against selfing species in the outcrossing rate distribution, the shape of which has relevance for the stability of mixed mating. Relationships between outcrossing rate, flower size, flower number and floral display, measured as the product of flower size and...

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