96 Works

Data associated with \"Floral pigmentation has responded rapidly to global change in ozone and temperature\"

Matthew Koski, Drew MacQueen & Tia-Lynn Ashman
Across kingdoms, organisms ameliorate UV stress by increasing UV-absorbing pigmentation. Rapid ozone degradation during the 20th century resulted in elevated UV incidence, yet pigmentation responses to this aspect of global change have yet to be demonstrated. In flowering plants, UV exposure favors larger areas of UV-absorbing pigmentation on petals, which protects pollen from UV-damage. Pigmentation also affects floral thermoregulation, suggesting climate warming may additionally impact pigmentation. We used 1238 herbarium specimens collected from 1941 to...

Litter decomposition and nutrient release from monospecific and mixed litters: comparisons of litter quality, fauna and decomposition sites effects

Kai Yang, Jiaojun Zhu, Weiwei Zhang, Qian Zhang, Deliang Lu, Yakun Zhang, Xiao Zheng, Shuang Xu & G. Geoff Wang
Litter decomposition and nutrient release are key processes for soil C and nutrient cycling. However, the relative importance of the effects of litter quality, fauna and decomposition sites on litter decomposition remains poorly understood. Moreover, the macronutrient and micronutrient (C, N, P, K, Ca, Mg, Mn, Cu and Zn) release in the decomposition process are even less well-known. In this study, we performed 5040 litterbag samplings of monospecific (Larix gmelinii, Acer mono, Quercus mongolica, and...

Floral spectral reflectance data for: Floral color properties of serpentine seep assemblages depend on community size and species richness

Kathryn LeCroy, Gerardo Arceo-Gómez, Matthew Koski, Nathan Morehouse & Tia-Lynn Ashman
Functional traits, particularly those that impact fitness, can shape the ecological and evolutionary relationships among coexisting species of the same trophic level. Thus, examining these traits and properties of their distributions (underdispersion, overdispersion) within communities can provide insights into key ecological interactions (e.g., competition, facilitation) involved in community assembly. For instance, the distribution of floral colors in a community may reflect pollinator-mediated interactions between sympatric plant species, and the phylogenetic distribution of color can inform...

Dental measurement and diet data for mammals

Samantha Hopkins, Samantha Price & Alec Chiono
Because teeth are the most easily preserved part of the vertebrate skeleton and are particularly morphologically variable in mammals, studies of fossil mammals rely heavily on dental morphology. Dental morphology is used both for systematics and phylogeny as well as for inferences about paleoecology, diet in particular. We analyze the influence of evolutionary history on our ability to reconstruct diet from dental morphology in the mammalian order Carnivora, and we find that much of our...

Data from: Corn stover removal responses on soil test P and K levels in Coastal Plain Ultisols

Jeffrey Novak, James Frederick, Donald Watts, Thomas Ducey & Douglas Karlen
This is digital research data corresponding to a published manuscript, Corn stover removal responses on soil test P and K levels in Coastal Plain Ultisols, in Sustainability. 2021. 13:4401. Corn (Zea mays L.) stover is used as a biofuel feedstock in the U.S. Selection of stover harvest rates for soils is problematic, however, because excessive stover removal may have consequences on plant available phosphorus (P) and potassium (K) concentrations. Our objective was to quantify stover...

Data from: Elevational divergence in pigmentation plasticity is associated with selection and pigment biochemistry

Matthew Koski
Phenotypic plasticity is predicted to evolve in environmentally variable habitats, or those experiencing a high frequency of strong selection. However, the evolution of plasticity may be constrained by costs or physiological constraints. In flowers, UV-absorbing pigmentation ameliorates UV damage to pollen, and is linked with elevated UV exposure. Whether plasticity contributes to this pattern remains unclear. Petals of Argentina anserina have larger UV-absorbing petal areas at high elevations where they experience higher and more variable...

Blueprint for phasing and assembling the genomes of heterozygous polyploids: Application to the octoploid genome of strawberry

Michael Hardigan, Mitchell Feldmann, Randi Famula, Michaela Vachev, Mary Madera, Philipp Zerbe, Kristin Mars, Paul Peluso, David Rank, Shujun Ou, Christopher Saski, Charlotte Acharya, Glenn Cole, Alan Yocca, Patrick Edger & Steven Knapp
The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated strawberry (Fragaria × ananassa) and its progenitors are outbred octoploids in which up to eight homologous and homoeologous alleles are preserved. This introduces significant risk of haplotype collapse, switching, and chimeric fusions during assembly. Using third generation HiFi sequences from PacBio, we assembled the genome of the...

White Sands desert lizard thermal data

Alex Gunderson, Eric Riddell, Michael Sears & Erica Bree Rosenblum
Traits often contribute to multiple functions, complicating our understanding of the selective pressures that influence trait evolution. In the Chihuahuan Desert, predation is thought to be the primary driver of cryptic light coloration in three White Sands lizard species relative to the darker coloration of populations on adjacent dark soils. However, coloration also influences radiation absorption and thus animal body temperatures. We combined comparative physiological experiments and biophysical models to test for thermal consequences of...

Data and code for analysis of effects of climate change on kangaskhan and summary of simulations from Warren et al. 2020

Dan Warren, Alex Dornburg, Katerina Zapfe & Teresa Iglesias
Species distribution models (SDMs) are frequently used to predict the effects of climate change on species of conservation concern. Biases inherent in the process of constructing SDMs and transferring them to new climate scenarios may result in undesirable conservation outcomes. We explore these issues and demonstrate new methods to estimate biases induced by the design of SDM studies. We present these methods in the context of estimating the effects of climate change on Australia’s only...

Black Scoter habitat use along the southeastern coast of the United States

Beth Ross, Hannah Plumpton & Emily Silverman
While the Atlantic Coast of the United States and Canada is a major wintering area for sea ducks, knowledge about their wintering habitat use is relatively limited. Black Scoters have a broad wintering distribution and are the only open water species of sea duck that is abundant along the southeastern coast of the United States. Our study identified variables that affected Black Scoter (Melanitta americana) distribution and abundance in the Atlantic Ocean along the southeastern...

Data from: A bridge between oceans: Overland migration of marine birds in a wind energy corridor

Juliet S. Lamb, David J. Newstead, Lianne M. Koczur, Bart M. Ballard, M. Clay Green, Patrick G.R. Jodice & Patrick G. R. Jodice
Located at the shortest overland route between the Gulf of Mexico and the Pacific Ocean, Mexico's Tehuantepec Isthmus is a globally important migratory corridor for many terrestrial bird species. The Pacific coast of the Isthmus also contains a significant wetland complex that supports large multi-species aggregations of non-breeding waterbirds during the boreal winter. In recent years, extensive wind energy development has occurred in the plains bordering these wetlands, directly along the migratory flyway. Using recent...

Data from: Characterization of microsatellite loci and repeat density in the gooseneck barnacle, Pollicipes elegans, using next generation sequencing

Louis V. Plough & Peter B. Marko
Pollicipes elegans is a commercially important and biogeographically significant rocky-shore gooseneck barnacle found along the eastern Pacific coasts of Peru, El Salvador, and Mexico. Little is known about its reproductive biology, and no genetic resources exist despite its growing importance as a fisheries species in the region. Next generation sequencing methods can provide rapid and cost-effective development of molecular markers such as microsatellites, which can be applied to studies of paternity, parentage, and population structure...

Data from: Wildlife differentially affect tree and liana regeneration in a tropical forest: an 18‐yr study of experimental terrestrial defaunation versus artificially abundant herbivores

Matthew S. Luskin, Kalan Ickes, Tze Leong Yao & Stuart J. Davies
1. Hunting and land use change modify herbivore abundances and cause cascading effects in natural ecosystems. The outcomes for vegetation depend on changes to specific plant-animal interactions, such as seed dispersal or predation, or physical disturbances. 2. We experimentally manipulated wildlife populations in a primary lowland forest in Malaysia over an 18-yr period (1996-2014) to understand how artificially high or low densities of terrestrial wildlife affects tree and liana regeneration. Our study site retains a...

Data from: Mapping resistance to Alternaria cucumerina in Cucumis melo

James Daley, Sandra E. Branham, Amnon Levi, Richard Hassell, William Patrick Wechter, Sandra Branham & Patrick Wechter
Infection with Alternaria cucumerina causes Alternaria leaf blight (ALB), a disease characterized by lesion formation on leaves, leading to substantial yield and quality losses in Cucumis melo (melon). While fungicides are effective against ALB, reduction in the frequency of application would be economically and environmentally beneficial. Resistant melon lines have been identified but the genetic basis of this resistance has not been determined. A saturated melon genetic map was constructed with markers developed through genotyping-by...

Data from: The influence of size on body shape diversification across Indo-Pacific shore fishes

Sarah T. Friedman, Christopher M. Martinez, Samantha Ann Price & Peter C. Wainwright
Understanding the causes of body shape variability across the tree of life is one of the central issues surrounding the origins of biodiversity. One potential mechanism driving observed patterns of shape disparity is a strongly conserved relationship between size and shape. Conserved allometry has been shown to account for as much as 80% of shape variation in some vertebrate groups. Here, we quantify the amount of body shape disparity attributable to changes in body size...

Data from: Biomechanical factors influencing successful self-righting in the pleurodire turtle, Emydura subglobosa

Alexander M Rubin, Richard W Blob & Christopher J Mayerl
Self-righting performance is a key ability for most terrestrial animals, and has been used as a metric of fitness, exhaustion, and thermal limits in a variety of taxa. However, there is little understanding of the underlying mechanisms that drive variation in self-righting performance. To evaluate the mechanical factors that contribute to success versus failure when animals attempt to self-right, we compared force production and kinematic behavior in the rigid-bodied, pleurodire turtle Emydura subglobosa between successful...

Data from: Hindlimb muscle function in turtles: is novel skeletal design correlated with novel muscle function?

Christopher J. Mayerl, Jenna E. Pruett, Morgan N. Summerlin, Angela R. V. Rivera & Richard W. Blob
Variations in musculoskeletal lever systems have formed an important foundation for predictions about the diversity of muscle function and organismal performance. Changes in the structure of lever systems may be coupled with changes in muscle use and give rise to novel muscle functions. The two extant turtle lineages, cryptodires and pleurodires, exhibit differences in hindlimb structure. Cryptodires possess the ancestral musculoskeletal morphology, with most hip muscles originating on the pelvic girdle, which is not fused...

Data from: Biomass resilience of Neotropical secondary forests

Lourens Poorter, Frans Bongers, T. Mitchell Aide, Angélica M. Almeyda Zambrano, Patricia Balvanera, Justin M. Becknell, Vanessa Boukili, Pedro H. S. Brancalion, Eben N. Broadbent, Robin L. Chazdon, Dylan Craven, Jarcilene S. De Almeida-Cortez, George A. L. Cabral, Ben H. J. De Jong, Julie S. Denslow, Daisy H. Dent, Saara J. DeWalt, Juan M. Dupuy, Sandra M. Durán, Mario M. Espírito-Santo, María C. Fandino, Ricardo G. César, Jefferson S. Hall, José Luis Hernandez-Stefanoni, Catarina C. Jakovac … & Danaë M. A. Rozendaal
Land-use change occurs nowhere more rapidly than in the tropics, where the imbalance between deforestation and forest regrowth has large consequences for the global carbon cycle1. However, considerable uncertainty remains about the rate of biomass recovery in secondary forests, and how these rates are influenced by climate, landscape, and prior land use2, 3, 4. Here we analyse aboveground biomass recovery during secondary succession in 45 forest sites and about 1,500 forest plots covering the major...

Transcript- and annotation-guided genome assembly of the European starling

Katarina Stuart, Richard Edwards, Yuanyuan Cheng, Wes Warren, Dave Burt, William Sherwin, Natalie Hofmeister, Scott Werner, Gregory Ball, Melissa Bateson, Matthew Brandley, Katherine Buchanan, Phillip Cassey, David Clayton, Tim De Meyer, Simone Meddle & Lee Rollins
The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second North American genome (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterisation. S. vulgaris vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length...

Data from: Ancestral polyploidy in seed plants and angiosperms

Yuannian Jiao, Norman J. Wickett, Ayyampalayam Saravanaraj, André S. Chanderbali, Lena Landherr, Paula E. Ralph, Lynn P. Tomsho, Yi Hu, Haiying Liang, Pamela S. Sotis, Douglas E. Soltis, Sandra W. Clifton, Scott E. Schlarbaum, Stephan C. Schuster, Hong Ma, Jim Leebens-Mack & Claude W. DePamphilis
Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms1, 2, 3, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications4, 5, 6, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive...

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  • Clemson University
  • University of California, Davis
  • University of Virginia
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  • United States Department of Agriculture
  • University of Massachusetts Amherst
  • Columbia University
  • University of California, Berkeley
  • Agricultural Research Service
  • Chinese Academy of Sciences