182 Works

Ambient temperature and female body condition are related to night incubation behavior in wood ducks (Aix sponsa)

Alexander Grimaudo, Sydney Hope, Sarah DuRant, Robert Kennamer, John Hallagan & William Hopkins
For many animals, parental care behavior is an important aspect of their life history that affects both parents and offspring. In birds, one of the most important parental care behaviors is incubation, which is costly to the parent but directly influences embryonic development and fitness of offspring. Some birds exhibit the intriguing behavior of partially incubating their eggs prior to clutch completion for only a portion of each day. This partial incubation is characterized by...

Longitudinal assessment of thermal and perceived air quality acceptability in relation to temperature, humidity, and CO2 exposure in Singapore

Toby Cheung, Stefano Schiavon, Elliott Gall, Ming Jin & William Nazaroff
Thermal acceptability (TA) and perceived air quality acceptability (PAQA) are typically analyzed in climate chambers or cross-sectional field studies. Individual factors, such as expectations and perceived environment history, may influence the acceptability response. Longitudinal studies with multi-day design are absent in the literature. Fifteen Singaporean subjects participated in a 7-day longitudinal experiment in which they carried a portable sensor that continuously recorded personal air temperature, relative humidity and carbon dioxide concentration at 1-min intervals. Instantaneous...

Bird Frugivore Abundance data from: Applied nucleation facilitates tropical forest recovery

Karen D. Holl, J. Leighton Reid, Rebecca J. Cole, Federico Oviedo‐Brenes, Juan A. Rosales & Rakan A. Zahawi
Applied nucleation, mostly based upon planting tree islands, has been proposed as a cost‐effective strategy to meet ambitious global forest and landscape restoration targets. We review results from a 15‐year study, replicated at 15 sites in southern Costa Rica, that compares applied nucleation to natural regeneration and mixed‐species tree plantations as strategies to restore tropical forest. We have collected data on planted tree survival and growth, woody vegetation recruitment and structure, seed rain, litterfall, epiphytes,...

Gene conversion facilitates the adaptive evolution of self-resistance in highly toxic newts

Kerry Gendreau, Joel McGlothlin, Angela Hornsby & Michael Hague
Reconstructing the histories of complex adaptations and identifying the evolutionary mechanisms underlying their origins are two of the primary goals of evolutionary biology. Taricha newts, which contain high concentrations of the deadly toxin tetrodotoxin (TTX) as an antipredator defense, have evolved resistance to self-intoxication, which is a complex adaptation requiring changes in six paralogs of the voltage-gated sodium channel (Nav) gene family, the physiological target of TTX. Here, we reconstruct the origins of TTX self-resistance...

Dancing bees evaluate central urban forage resources as superior to agricultural land

Ellouise Leadbeater, Ash Samuelson & Roger Schuerch
Recent evidence suggests that flower-rich areas within cities could play an important role in pollinator conservation, but direct comparison of floral resources within agricultural and urban areas has proved challenging to perform over large scales. Here we use the waggle dances of honeybees (Apis mellifera L.) to perform large-scale landscape surveys at heavily urban or agricultural sites for a key pollinator of wild and crop plants. We analyzed 2827 dances that were performed by 20...

Supplementary material: How should functional relationships be evaluated using phylogenetic comparative methods? A case study using metabolic rate and body temperature

Josef Uyeda, Nic Bone, Sean McHugh, Jonathan Rolland & Matthew Pennell
Phylogenetic comparative methods are often used to test functional relationships between traits. However, million-year macroevolutionary observational datasets cannot definitively prove causal links between traits --- correlation does not equal causation and experimental manipulation over such timescales is impossible. While this caveat is widely understood, it is far less appreciated that different phylogenetic approaches make different causal assumptions about the functional relationships of traits. In order to make meaningful inferences, it is critical that our statistical...

Longitudinal white-matter abnormalities in sports-related concussion: a diffusion MRI study of the NCAA-DoD CARE Consortium

Yu-Chien Wu, Jaroslaw Harezlak, Nahla Elsaid, Zikai Lin, Qiuting Wen, Sourajit Mustafi, Larry Riggen, Kevin Koch, Andrew Nencka, Timothy Meier, Andrew Mayer, Yang Wang, Christopher Giza, John DiFiori, Kevin Guskiewicz, Jason Mihalik, Stephen LaConte, Stefan Duma, Steven Broglio, Andrew Saykin, Michael McCrea & Thomas McAllister
Objective To study longitudinal recovery trajectories of white-matter after sports-related concussion (SRC), we performed diffusion tensor imaging (DTI) on collegiate athletes who sustained SRC. Methods Collegiate athletes (n=219, 82 concussed athletes, 68 contact-sport controls, and 69 non-contact-sport controls) were included from the Concussion Assessment, Research and Education (CARE) Consortium. The participants completed clinical assessments and DTI at four time points: 24-48-hours post-injury, asymptomatic state, seven days following return-to-play, and six-months post-injury. Tract-based spatial statistics were...

Sex linkage of the skeletal muscle sodium channel gene (SCN4A) explains apparent deviations from Hardy–Weinberg equilibrium of tetrodotoxin-resistance alleles in garter snakes (Thamnophis sirtalis)

Kerry Gendreau, Michael Hague, Chris Feldman, , & Joel McGlothlin
The arms race between tetrodotoxin-bearing Pacific newts (Taricha) and their garter snake predators (Thamnophis) in western North America has become a classic example of coevolution, shedding light on predator-prey dynamics, the molecular basis of adaptation, and patterns of convergent evolution. Newts are defended by tetrodotoxin (TTX), a neurotoxin that binds to voltage-gated sodium channels (Nav proteins), arresting electrical activity in nerves and muscles and paralyzing would-be predators. However, populations of the common garter snake (T....

Scaling between macro- to microscale climatic data reveals strong phylogenetic inertia in niche evolution in plethodontid salamanders

Vincent Farallo, Martha Muñoz, Josef Uyeda & Donald Miles
Macroclimatic niches are indirect and potentially inadequate predictors of the realized environmental conditions that many species experience. Consequently, analyses of niche evolution based on macroclimatic data alone may incompletely represent the evolutionary dynamics of species niches. Yet, understanding how an organisms’ climatic (Grinnellian) niche responds to changing macroclimatic conditions is of vital importance for predicting their potential response to global change. In this study, we integrate microclimatic and macroclimatic data across 26 species of plethodontid...

Data from: A bird-like skull in a Triassic diapsid reptile increases heterogeneity of the morphological and phylogenetic radiation of Diapsida

Adam C. Pritchard & Sterling J. Nesbitt
The Triassic Period saw the first appearance of numerous amniote lineages (e.g. Lepidosauria, Archosauria, Mammalia) that defined Mesozoic ecosystems following the end Permian Mass Extinction, as well as the first major morphological diversification of crown-group reptiles. Unfortunately, much of our understanding of this event comes from the record of large-bodied reptiles (total body length > 1 m). Here we present a new species of drepanosaurid (small-bodied, chameleon-like diapsids) from the Upper Triassic Chinle Formation of...

Data from: Contemporaneous radiations of fungi and plants linked to symbiosis

François Lutzoni, Michael D. Nowak, Michael E. Alfaro, Valérie Reeb, Jolanta Miadlikowska, Michael Krug, A. Elizabeth Arnold, Louise A. Lewis, David L. Swofford, David Hibbett, Khidir Hilu, Timothy Y. James, Dietmar Quandt & Susana Magallón
Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma),...

Data from: Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum

Michael A. Hardigan, Emily Crisovan, John P. Hamilton, Jeongwoon Kim, Parker Laimbeer, Courtney P. Leisner, Norma C. Manrique-Carpintero, Linsey Newton, Gina M. Pham, Brieanne Vaillancourt, Xueming Yang, Zixian Zeng, David S. Douches, Jiming Jiang, Richard E. Veilleux & C. Robin Buell
Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species, and...

Data from: The contribution of maternal effects to selection response: an empirical test of competing models

Joel William McGlothlin & Laura F. Galloway
Maternal effects can dramatically influence the evolutionary process, in some cases facilitating and in others hindering adaptive evolution. Maternal effects have been incorporated into quantitative genetic models using two theoretical frameworks: the variance-components approach, which partitions variance into direct and maternal components, and the trait-based approach, which assumes that maternal effects are mediated by specific maternal traits. Here, we demonstrate parallels between these models and test their ability to predict evolutionary change. First, we show...

Data from: Changing measurements or changing movements? Sampling scale and movement model identifiability across generations of biologging technology

Leah R. Johnson, Philipp H. Boersch-Supan, Richard A. Phillips & Sadie J. Ryan
1. Animal movement patterns contribute to our understanding of variation in breeding success and survival of individuals, and the implications for population dynamics. 2. Over time, sensor technology for measuring movement patterns has improved. Although older technologies may be rendered obsolete, the existing data are still valuable, especially if new and old data can be compared to test whether a behavior has changed over time. 3. We used simulated data to assess the ability to...

Ancient and modern colonization of North America by hemlock woolly adelgid, Adelges tsugae (Hemiptera: Adelgidae), an invasive insect from East Asia

Nathan P. Havill, Shigehiko Shiyake, Ashley Lamb Galloway, Robert G. Foottit, Guoyue Yu, Annnie Paradis, Joseph Elkinton, Michael E. Montgomery, Masakazu Sano, Adalgisa Caccone & Annie Paradis
Hemlock woolly adelgid, Adelges tsugae, is an invasive pest of hemlock trees (Tsuga) in eastern North America. We used 14 microsatellites and mitochondrial COI sequences to assess its worldwide genetic structure and reconstruct its colonization history. The resulting information about its life cycle, biogeography and host specialization could help predict invasion by insect herbivores. We identified eight endemic lineages of hemlock adelgids in central China, western China, Ulleung Island (South Korea), western North America, and...

Managing, Collecting, and Sharing Data with OSF - VU Amsterdam

Tycho Hofstra, S. Sandt, Meron Vermaas, B.J.J. Hattink, Lena Karvovskaya, T.J.A.G. Münker, Brett Olivier, C Dijk, Jessica Hrudey, APC Van der Jagt, Lannie Ligthart, W Hugens, A Taimounti, Sam Heijnen, Koen Leuveld, Kacana Khadjavi, Mark Bruyneel, Elisa Rodenburg, H.J. Jorritsma, Haiyan Wang, Petra van Aken, Jolien Scholten, DA Unger, N.A. Dieleman, R.A. Onyango … & M. Hashemi Shabestari
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OSF Institutions

Eric Olson, Nicole Pfeiffer, Daniel Steger & Gretchen Gueguen
OSF Institutions enhances transparency and increases the visibility of research outputs, accelerating discovery and reuse. The Center for Open Science partners with institutions to provide infrastructure and tools to help researchers manage, collaborate and share their work, provide training and guide resources to enable researchers in transparent, open, and reproducible workflows, and collaborates with institutional staff to overcome challenges and showcase the open and reproducible outputs contributed by their research community. You can focus your...


Eric Olson, Daniel Steger & Gretchen Gueguen

Data from: Identifying differentially expressed genes under heat stress and developing molecular markers in orchardgrass (Dactylis glomerata L.) through transcriptome analysis

Lin K. Huang, Hai D. Yan, J. Wang, T. Frazier, X. X. Zhao, X. Q. Zhang, X. Huang, D. F. Yan, W. J. Zang, X. Ma, Y. Peng, Y. H. Yan, W. Liu & G. Yin
Orchardgrass (Dactylis glomerata L.) is a long-lived, cool-season forage grass that is commonly used for hay production. Despite its economic importance, orchardgrass genome remains relatively unexplored. In this study, we used Illumina RNA sequencing to identify gene-associated molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), as well as heat stress-induced differentially expressed genes (DEGs) in two orchardgrass genotypes, ‘Baoxing’ (heat resistant) and ‘01998’ (heat susceptible). Approximately 163 million high-quality trimmed reads...

Data from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation

James B. Pease, David C. Haak, Matthew W. Hahn & Leonie C. Moyle
Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately...

Data from: Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information

Oscar Cortés, A. M. Martinez, J. Cañon, N. Sevane, L. T. Gama, C. Ginja, V. Landi, P. Zaragoza, N. Carolino, A. Vicente, P. Sponenberg & J. V. Delgado
Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different...

Data from: Genetic footprints of Iberian cattle in America 500 years after the arrival of Columbus

Amparo M. Martínez, Luis T. Gama, Javier Cañón, Catarina Ginja, Juan V. Delgado, Susana Dunner, Vincenzo Landi, Inmaculada Martín-Burriel, M. Cecilia T. Penedo, Clementina Rodellar, Jose Luis Vega-Pla, Atzel Acosta, Luz Ángela Álvarez, Esperanza Camacho, Óscar Cortés, José Ribamar Marques, Óscar Roberto Martínez, Rubén Darío Martínez, Lilia Melucci, Guillermo Martínez-Velázquez, Jose Ernesto Muñoz, Alicia Postiglioni, Jorge Quiroz, Philip Sponenberg, Odalys Uffo … & Ruben D. Martínez
BACKGROUND: American Creole cattle presumably descend from animals imported from the Iberian Peninsula during the period of colonization and settlement, through different migration routes, and may have also suffered the influence of cattle directly imported from Africa. The introduction of European cattle, which began in the 18th century, and later of Zebu from India, has threatened the survival of Creole populations, some of which have nearly disappeared or were admixed with exotic breeds. Assessment of...

Data from: Response of bluebunch wheatgrass to invasion: differences in competitive ability among invader-experienced and naïve populations

Alexis L. Gibson, Cara R. Nelson, Daniel Z. Atwater & Alexis Gibson
1. Invasive species may alter selective pressures on native plant populations, and there is some evidence that competition with invasive plants may lead to differences in competitive ability between populations that have experienced invasion and those that have not. Previous results have varied among species but also among populations of the same species. 2. We conducted a greenhouse experiment to determine whether there was variation in traits, or in ability to tolerate or suppress an...

Data from: Variable drivers of primary versus secondary nesting: density-dependence and drought effects on greater sage-grouse

Erik J. Blomberg, Daniel Gibson, Michael T. Atamian & James S. Sedinger
Organisms seek to maximize fitness by balancing reproductive allocations against mortality risk, given selection pressures inherent to the environment. However, environmental conditions are often dynamic and unpredictable, which complicates the ability to achieve such a balance, and may require reproductive adjustments depending on prevailing conditions. We evaluated the effects of density-dependent, density-independent (drought), and individual (age, body condition) factors on nesting decisions of female greater sage-grouse in the American Great Basin. We obtained relocations and...

Data from: Are thyroid hormones mediators of incubation temperature-induced phenotypes in birds?

Sarah E. DuRant, Amanda W. Carter, Robert J. Denver, Gary R. Hepp & William A. Hopkins
Incubation temperature influences a suite of traits in avian offspring. However, the mechanisms underlying expression of these phenotypes are unknown. Given the importance of thyroid hormones in orchestrating developmental processes, we hypothesized that they may act as an upstream mechanism mediating the effects of temperature on hatchling phenotypic traits such as reduced growth and thermoregulation. We found that plasma T3, but not T4 concentrations, differed among newly-hatched wood ducks (Aix sponsa) from different embryonic incubation...

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