38 Works

Data from: Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions

Jonathan Chang, Daniel L. Rabosky & Michael E. Alfaro
Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread...

Data from: Specifying high-altitude electrons using low-altitude LEO systems: the SHELLS model

Seth Claudepierre
The dataset includes a tarball of all of the data shown in the figures in the manuscript, along with the neural network coefficients as described in the Appendix of the manuscript.

Assessing seasonal demographic covariation to understand environmental-change impacts on a hibernating mammal

Maria Paniw, Dylan Childs, Kenneth Armitage, Daniel Blumstein, Julien Martin, Madan Oli & Arpat Ozgul
Natural populations are exposed to seasonal variation in environmental factors that simultaneously affect several demographic rates (survival, development, reproduction). The resulting covariation in these rates determines population dynamics, but accounting for its numerous biotic and abiotic drivers is a significant challenge. Here, we use a factor-analytic approach to capture partially unobserved drivers of seasonal population dynamics. We use 40 years of individual-based demography from yellow-bellied marmots (Marmota flaviventer) to fit and project population models that...

Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations

Alayna Mead, Juan Peñaloza Ramirez, Megan Bartlett, Jessica Wright, Lawren Sack & Victoria Sork
Drought is a major stress for plants, creating a strong selection pressure for traits that enable plant growth and survival in dry environments. Many drought responses are conserved species-wide responses while others vary among populations distributed across heterogeneous environments. We tested how six populations of the widely-distributed California valley oak (Quercus lobata) sampled from contrasting climates would differ in their response to soil drying relative to well-watered controls in a common environment by measuring ecophysiological...

Data from: Complex patterns of sex-biased demography in canines

Tanya N. Phung, Robert K. Wayne, Melissa A. Wilson & Kirk E. Lohmueller
The demographic history of dogs is complex, involving multiple bottlenecks, admixture events and artificial selection. However, existing genetic studies have not explored variance in the number of reproducing males and females, and whether it has changed across evolutionary time. While male-biased mating practices, such as male-biased migration and multiple paternity, have been observed in wolves, recent breeding practices could have led to female-biased mating patterns in breed dogs. For example, breed dogs are thought to...

Menin Associates with the Mitotic Spindle and is Important for Cell Division

Jorge Torres, Mark Sawicki & Ankur Gholkar
Menin is the protein mutated in patients with multiple endocrine neoplasia type 1 (MEN1) syndrome and their corresponding sporadic tumor counterparts. Here, we have uncovered a novel function for menin in promoting proper cell division. We show that menin localizes to the mitotic spindle poles and the mitotic spindle during early mitosis and to the intercellular bridge microtubules during cytokinesis in HeLa cells. Menin depletion led to defects in spindle assembly and chromosome congression during...

Data from: Better safe than sorry: spider societies mitigate risk by prioritizing caution

Colin M. Wright, James L.L. Lichtenstein, Lauren P. Luscuskie, Graham A. Montgomery, Noa Pinter-Wollman & Jonathan N. Pruitt
Group members often vary in the information that they have about their environment. In this study, we evaluated the relative contribution of information held by the population majority vs. new immigrants to groups in determining group function. To do so we created experimental groups of the social spider Stegodyphus dumicola that were either iteratively exposed to a dangerous predator, the ant Anoplopepis custodiens, or kept in safety. We then seeded these groups (i.e., the population...

Data from: Temperature shapes opposing latitudinal gradients of plant taxonomic and phylogenetic β diversity

Ian R. McFadden, Brody Sandel, Constantinos Tsirogiannis, Naia Morueta-Holme, Jens-Christian Svenning, Brian J. Enquist & Nathan J. B. Kraft
Latitudinal and elevational richness gradients have received much attention from ecologists but there is little consensus on underlying causes. One possible proximate cause is increased levels of species turnover, or β diversity, in the tropics compared to temperate regions. Here, we leverage a large botanical dataset to map taxonomic and phylogenetic β diversity, as mean turnover between neighboring 100 × 100 km cells, across the Americas and determine key climatic drivers. We find taxonomic and...

BCI 50-ha Plot Taxonomy

Richard Condit, Rolando Pérez, Salomón Aguilar, Suzanne Lao, Robin Foster & Hubbell Stephen
BCI 50-ha Plot Taxonomy The 50-ha plot at Barro Colorado Island was initially demarcated and fully censused in 1982, and has been fully censused 7 times since, every 5 years from 1985 through 2015 (Hubbell and Foster 1983, Hubbell et al. 1990, Condit et al. 2012, Condit et al. 2017). The taxonomic component required repeated collecting and sorting so that every individual could be matched to a previously described species from Croat (1978). Over 300...

Myotubularin related protein 7 is essential for the spermatogonial stem cell homeostasis via PI3K/AKT signaling

Dan Zhao, Cong Shen, Tingting Gao, Hong Li, Yueshuai Guo, Feng Li, Chenchen Liu, Yuanyuan Liu, Xia Chen, Xi Zhang, Yangyang Wu, Yi Yu, Meng Lin, Yan Yuan, Xiaofang Chen, Xiaoyan Huang, Shenmin Yang, Jun Yu, Jun Zhang & Bo Zheng
Myotubularin related protein 7 (MTMR7), a key member of the MTMR family, depicts phosphatase activity and is involved in myogenesis and tumor growth. We have previously identified MTMR7 in the proteomic profile of mouse spermatogonial stem cell (SSC) maturation and differentiation, implying that MTMR7 is associated with neonatal testicular development. In this study, to further explore the distribution and function of MTMR7 in mouse testis, we studied the effect of Mtmr7 knockdown on neonatal testicular...

High-frequency measurements of aeolian saltation flux: time series data

Raleigh L. Martin, Jasper F. Kok, Chris H. Hugenholtz, Thomas E. Barchyn, Marcelo Chamecki & Jean T. Ellis
High-frequency (25-50 Hz) coupled observations of wind speed and aeolian saltation flux (i.e, the wind-blown movement of sand) were measured at three field sites: Jericoacoara, Brazil; Rancho Guadalupe, California; and Oceano, California. The dataset provided here contains the full record of raw and processed time series of saltation flux and wind speed measured at multiple heights above the sediment surface.

Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission

Chelsea Wood, Susanne Sokolow, Isabel Jones, Andrew Chamberlin, Kevin Lafferty, Armand Kuris, Merlijn Jocque, Skylar Hopkins, Grant Adams, Julia Buck, Andrea Lund, Ana Garcia-Vedrenne, Evan Fiorenza, Jason Rohr, Fiona Allan, Bonnie Webster, Muriel Rabone, Joanne Webster, Lydie Bandagny, Raphael Ndione, Simon Senghor, Anne-Marie Schacht, Nicolas Jouanard, Gilles Riveau & Giulio De Leo
Recently, the World Health Organization recognized that efforts to interrupt schistosomiasis transmission through mass drug administration have been ineffective in some regions; one of their new recommended strategies for global schistosomiasis control emphasizes targeting the freshwater snails that transmit schistosome parasites. We sought to identify robust indicators that would enable precision targeting of these snails. At the site of the world’s largest recorded schistosomiasis epidemic—the Lower Senegal River Basin in Senegal—intensive sampling revealed positive relationships...

Data from: Aβ42 fibril formation from predominantly oligomeric samples suggests a link between oligomer heterogeneity and fibril polymorphism

Christine Xue, Joyce Tran, Hongsu Wang, Giovanna Park, Frederick Hsu & Zhefeng Guo
Aβ oligomers play a central role in the pathogenesis of Alzheimer’s disease. Oligomers of different sizes, morphology, and structures have been reported in both in vivo and in vitro studies, but there is a general lack of understanding about where to place these oligomers in the overall process of Aβ aggregation and fibrillization. Here we show that Aβ42 spontaneously forms oligomers with a wide range of sizes in the same sample. These Aβ42 samples contain...

Data from: Patterns of nitrogen-fixing tree abundance in forests across Asia and America

Duncan N. L. Menge, Ryan A. Chisholm, Stuart J. Davies, Kamariah Abu Salim, David Allen, Mauricio Alvarez, Norm Bourg, Warren Y. Brockelman, Sarayudh Bunyavejchewin, Nathalie Butt, Min Cao, Wirong Chanthorn, Wei-Chun Chao, Keith Clay, Richard Condit, Susan Cordell, João Batista Da Silva, H. S. Dattaraja, Ana Cristina Segalin De Andrade, Alexandre A. Oliveira, Jan Den Ouden, Michael Drescher, Christine Fletcher, Christian P. Giardina, C. V. Savitri Gunatilleke … & Tak Fung
Symbiotic nitrogen (N)‐fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N‐fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N‐fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America...

Data from: D2 dopamine receptor activation induces female preference for male song in the monogamous zebra finch

Nancy F. Day, David Saxon, Anastasia Robbins, Lily Harris, Emily Nee, Naomi Shroff-Mehta, Kaeley Stout, Julia Sun, Natalie Lillie, Mara Burns, Clio Korn & Melissa J. Coleman
The evolutionary conservation of neural mechanisms for forming and maintaining pair bonds is unclear. Oxytocin, vasopressin, and dopamine (DA) transmitter systems have been shown to be important in pair-bond formation and maintenance in several vertebrate species. We examined the role of dopamine in formation of song preference in zebra finches, a monogamous bird. Male courtship song is an honest signal of sexual fitness; thus we measured female song preference to evaluate the role of DA...

Data from: Hierarchy in adaptive radiation: a case study using the Carnivora (Mammalia)

Graham J Slater & Anthony R Friscia
Simpson’s “early burst” model of adaptive radiation was intended to explain the early proliferation of morphological and functional variation in diversifying clades. Yet, despite much empirical testing, questions remain regarding its frequency across the tree of life. Here, we evaluate the support for an early burst adaptive radiation in 14 ecomorphological traits plus body mass for the extant mammalian order Carnivora and its constituent families. We find strong support for an early burst of evolution...

Data from: Continent‐scale phenotype mapping using citizen scientists’ photographs

Jonathan P. Drury, Morgan Barnes, Ann E. Finneran, Maddie Harris & Gregory F. Grether
Field investigations of phenotypic variation in free‐living organisms are often limited in scope owing to time and funding constraints. By collaborating with online communities of amateur naturalists, investigators can greatly increase the amount and diversity of phenotypic data in their analyses while simultaneously engaging with a public audience. Here, we present a method for quantifying phenotypes of individual organisms in citizen scientists’ photographs. We then show that our protocol for measuring wing phenotypes from photographs...

Data from: Reversing the effects of evolutionary prey naiveté through controlled predator exposure

Alexandra K. Ross, Mike Letnic, Daniel T. Blumstein & Katherine E. Moseby
1. Inappropriate anti-predator responses (naiveté) towards introduced predators is a key factor contributing to the extinction and endangerment of prey species worldwide and the failure of wildlife reintroductions. Here, we test the idea that reintroduction success can be improved by exposing a predator naïve prey species to introduced predators under controlled conditions (in situ predation) prior to reintroduction, such that prey adopt increased wary behaviours to aid in survival. 2. We exposed a population of...

Data from: The advantages of going large: genome‐wide SNPs clarify the complex population history and systematics of the threatened western pond turtle

Phillip Q. Spinks, Robert C. Thomson & H. Bradley Shaffer
As the field of phylogeography has matured, it has become clear that analyses of one or a few genes may reveal more about the history of those genes than the populations and species that are the targets of study. To alleviate these concerns, the discipline has moved towards larger analyses of more individuals and more genes, although little attention has been paid to the qualitative or quantitative gains that such increases in scale and scope...

Association of EGLN1 gene with high aerobic capacity of Peruvian Quechua at high altitude

Abigail W. Bigham, Tom D. Brutsaert, Melisa Kiyamu, Gianpietro Elias Revollendo, Jenna L. Isherwood, Frank S. Lee, Maria Rivera-Ch., Fabiola Leon-Velarde & Sudipta Ghosh
Highland native Andeans have resided at altitude for millennia. They display high aerobic capacity (VO2max) at altitude and this may be a reflection of genetic adaptation to chronic hypoxia. Previous genome-wide (GW) scans for natural selection have nominated EGLN1 as a candidate gene. The encoded protein, EGLN1/PHD2, is an O2 sensor that controls levels of the Hypoxia Inducible Factor-a (HIF-a), which regulates the cellular response to hypoxia. From GWAS and ANCOVA performed on a total...

Data from: Leaf drought tolerance cannot be inferred from classic leaf traits in a tropical rainforest

Isabelle Maréchaux, Laurent Saint-André, Megan K. Bartlett, Lawren Sack & Jérôme Chave
Plants are enormously diverse in their traits and ecological adaptation, even within given ecosystems, such as tropical rainforests. Accounting for this diversity in vegetation models poses serious challenges. Global plant functional trait databases have highlighted general trait correlations across species that have considerably advanced this research program. However, it remains unclear whether trait correlations found globally hold within communities, and whether they extend to drought tolerance traits. For 134 individual plants spanning a range of...

Empirically estimated electron lifetimes in the Earth's radiation belts: 2. Comparison with theory

Seth Claudepierre
These data are provided as supporting information for the manuscript "Empirically estimated electron lifetimes in the Earth's radiation belts: 2. Comparison with theory" by Claudepierre et al. These data include electron flux measurements in the Earth's radiation belt obtained with the MagEIS instrument on the NASA Van Allen Probe B satellite, along with the theoretical decay timescale estimates described in the manuscript. The contents of the data files are described in greater detail in the...

MiR-150-5p retards the progression of myocardial fibrosis by targeting EGR1

Jie Shen, Wanhong Xing, Fangqi Gong, Wei Wang, Yufeng Yan, Yiying Zhang, Chunhong Xie & Songling Fu
To investigate the differential expression of microRNA-150-5p (miR-150-5p) and early growth response 1 (EGR1) in myocardial fibrosis (MF) cells, and determine the effect between miR-150-5p and EGR1 on MF. Human MF cells were generated via Trypanosoma cruzi (T. cruzi) infection, a mouse model of MF was generated via angiotensin II. The expression levels of miR-150-5p and EGR1 were detected by quantitative real-time polymerase chain reaction (qRT-PCR) and western blot assay. The correlation between miR-150-5p and...

MiR-150-5p retards the progression of myocardial fibrosis by targeting EGR1

Jie Shen, Wanhong Xing, Fangqi Gong, Wei Wang, Yufeng Yan, Yiying Zhang, Chunhong Xie & Songling Fu
To investigate the differential expression of microRNA-150-5p (miR-150-5p) and early growth response 1 (EGR1) in myocardial fibrosis (MF) cells, and determine the effect between miR-150-5p and EGR1 on MF. Human MF cells were generated via Trypanosoma cruzi (T. cruzi) infection, a mouse model of MF was generated via angiotensin II. The expression levels of miR-150-5p and EGR1 were detected by quantitative real-time polymerase chain reaction (qRT-PCR) and western blot assay. The correlation between miR-150-5p and...

Data from: Safety cues can give prey more valuable information than danger cues

Barney Luttbeg, Maud C O Ferrari, Daniel T Blumstein & Douglas P Chivers
The ability of prey to assess predation risk is fundamental to their success. It is routinely assumed predator cues do not vary in reliability across levels of predation risk. We propose that cues can differ in how precisely they indicate different levels of predation risk. What we call danger cues precisely indicate high risk levels, while safety cues precisely indicate low risk levels. Using optimality modeling, we find that prey fitness is increased when prey...

Registration Year

  • 2019

Resource Types

  • Dataset


  • University of California Los Angeles
  • Sun Yat-sen University
  • Zhejiang University
  • Air Force Medical University
  • Fudan University Shanghai Cancer Center
  • Huazhong University of Science and Technology
  • Fudan University
  • Field Museum of Natural History
  • Wenzhou Medical University
  • Taiwan Forestry Research Institute