247 Works

Capillary rise in vuggy porous media

Hasan J Khan, Masa Prodanovic, Ayaz Mehmani, David DiCarlo & Dayeed Khan
Capillary rise in vuggy porous media

Mudrock images from Nankai Trough

Abhishek Bihani, Hugh Daigle, Masa Prodanovic, Kitty Milliken & Javier E. Santos
An image analysis workflow was used to study the electron microscopy images of uncemented muds obtained at various depths (< 1.1 km burial) in the Kumano Basin of Nankai Trough offshore Japan for studying the silt bridging phenomenon. Forty-nine images from five core samples at different depths of Site C0002 obtained during Integrated Ocean Drilling Program (IODP) Expeditions 315 and 338 were used for the study. The original image set can be found at https://www.digitalrocksportal.org/projects/42....

Data from: Isolation by instability: historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna

Mariana M. Vasconcellos, Guarino R. Colli, Jesse N. Weber, Edgardo M. Ortiz, T. Rodrigues Miguel & David C. Cannatella
Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the...

Data from: Impact of the Late Triassic mass extinction on functional diversity and composition of marine ecosystems

Alexander M. Dunhill, William J. Foster, James Sciberras & Richard J. Twitchett
Mass extinctions have profoundly influenced the history of life, not only through the death of species but also through changes in ecosystem function and structure. Importantly, these events allow us the opportunity to study ecological dynamics under levels of environmental stress for which there are no recent analogues. Here, we examine the impact and selectivity of the Late Triassic mass extinction event on the functional diversity and functional composition of the global marine ecosystem, and...

Data from: Mating status correlates with dorsal brightness in some but not all poison frog populations

Corinna E. Dreher, Ariel Rodríguez, Molly E. Cummings & Heike Pröhl
Sexual signals are important for intraspecific communication and mate selection, but their evolution may be driven by both natural and sexual selection, and stochastic processes. Strawberry poison frogs (Oophaga pumilio) show strong color divergence among populations, but coloration also varies among individuals of the same population. The importance of coloration for female mate choice has been studied intensely, and sexual selection seems to affect color divergence in strawberry poison frogs. However, the effect of coloration...

Data from: Chromosomal speciation in the genomics era: disentangling phylogenetic evolution of rock-wallabies

Sally Potter, Jason G. Bragg, Mozes P. Blom, Janine E. Deakin, Mark Kirkpatrick, Mark D. Eldridge, Craig Moritz, Mozes P. K. Blom & Mark D. B. Eldridge
The association of chromosome rearrangements with speciation is well established, and there is a long history of theory and evidence relating to “chromosomal speciation”. Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about...

Data from: Plasticity contributes to a fine-scale depth gradient in sticklebacks’ visual system

Thor Veen, Chad Brock, Diana Rennison & Daniel Bolnick
The light environment influences an animal’s ability to forage, evade predators, and find mates, and consequently is known to drive local adaptation of visual systems. However, the light environment may also vary over fine spatial scales at which genetic adaptation is difficult. For instance, in aquatic systems the available wavelengths of light change over a few meters depth. Do animals plastically adjust their visual system to such small-scale environmental light variation? Here, we show that...

Data from: Development of an adrenocortical cancer humanized mouse model to characterize anti-PD1 effects on tumor microenvironment

Julie Lang, Anna Capasso, Kimberly R. Jordan, Jena D. French, Adwitiya Kar, Stacey M. Bagby, Jacob Barbee, Betelehem W. Yacob, Lia S. Head, Kenneth D. Tompkins, Brian M. Freed, Hilary Somerset, Toshimasa J. Clark, Todd M. Pitts, Well A. Messersmith, S. Gail Eckhardt, Margaret E. Wierman, Stephen Leong & Katja Kiseljak-Vassiliades
Context: While the development of immune checkpoint inhibitors has transformed treatment strategies of several human malignancies, research models to study immunotherapy in ACC are lacking. Objective: To explore the effect of anti-PD1 immunotherapy on the alteration of the immune milieu in ACC in a newly generated preclinical model and correlate with the response of the matched patient. Design, Setting and Intervention: To characterize the CU-ACC2-M2B patient-derived xenograft in a humanized mouse model, evaluate the effect...

Data from: Fine-scale environmental specialization of reef- building corals might be limiting reef recovery in the Florida Keys

Carly D. Kenkel, Albert T. Almanza & Mikhail V. Matz
Despite decades of monitoring global reef decline, we are still largely unable to explain patterns of reef deterioration at local scales, which precludes the development of effective management strategies. Offshore reefs of the Florida Keys, USA, experience milder temperatures and lower nutrient loads in comparison to inshore reefs yet remain considerably more degraded than nearshore patch reefs. A year-long reciprocal transplant experiment of the mustard hill coral (Porites astreoides) involving four source and eight transplant...

Data from: Estimating tempo and mode of Y chromosome turnover: explaining Y chromosome loss with the fragile Y hypothesis

Heath Blackmon & Jeffery P. Demuth
Chromosomal sex determination is phylogenetically widespread, having arisen independently in many lineages. Decades of theoretical work provide predictions about sex chromosome differentiation that are well supported by observations in both XY and ZW systems. However, the phylogenetic scope of previous work gives us a limited understanding of the pace of sex chromosome gain and loss and why Y or W chromosomes are more often lost in some lineages than others, creating XO or ZO systems....

Data from: Ecological fidelity of functional traits based on species presence-absence in a modern mammalian bone assemblage (Amboseli, Kenya)

Joshua H. Miller, Anna Kay Behrensmeyer, Andrew Du, S. Kathleen Lyons, David Patterson, Anikó Tóth, Amelia Villaseñor, Erustus Kanga, Denné Reed & Anna K. Behrensmeyer
Comparisons between modern death assemblages and their source communities have demonstrated fidelity to species diversity across a variety of environments and taxonomic groups. However, differential species preservation and collection (including body-size bias) in both modern and fossil death assemblages may still skew the representation of other important ecological characteristics. Here, we move beyond live-dead taxonomic fidelity and focus on the recovery of functional ecology (how species interact with their ecosystem) at the community level for...

A Test of the Repeatability of Measurements of Relative Fitness in the Long-Term Evolution Experiment with Escherichia coli

Jeffrey E. Barrick, Daniel E. Deatherage & Richard E. Lenski
Experimental studies of evolution using microbes have a long tradition, and these studies have increased greatly in number and scope in recent decades. Most such experiments have been short in duration, typically running for weeks or months. A venerable exception, the long-term evolution experiment (LTEE) with Escherichia coli has continued for 30 years and 70,000 bacterial generations. The LTEE has become one of the cornerstones of the field of experimental evolution, in general, and the...

Data from: A growth-defense trade-off is general across native and exotic grasses

Robert W. Heckman, Fletcher W. Halliday & Charles E. Mitchell
High-resource environments typically favor quick-growing, poorly-defended plants, while resource-poor environments typically favor slow-growing, well-defended plants. The prevailing hypothesis explaining this pattern states that, as resource availability increases, well-defended, slow-growing species are replaced by poorly defended, fast-growing species. A second hypothesis states that greater resource availability increases allocation to growth at the expense of defense, within species. Regardless of mechanism, if exotic species are released from enemies relative to natives, shifts in allocation to growth and...

Data from: Divergence in coloration and the evolution of reproductive isolation in the Anolis marmoratus species complex

Martha M. Muñoz, Nicholas G. Crawford, , Nicholas J. Messana, Rebecca D. Tarvin, Liam J. Revell, Rosanne M. Zandvliet, Juanita M. Hopwood, Elbert Mock, André L. Schneider, Chris J. Schneider, Thomas J. McGreevy & Christopher J. Schneider
Adaptive divergence in coloration is expected to produce reproductive isolation in species that use colorful signals in mate choice and species recognition. Indeed, many adaptive radiations are characterized by differentiation in colorful signals, suggesting that divergent selection acting on coloration may be an important component of speciation. Populations in the Anolis marmoratus species complex from the Caribbean island of Guadeloupe display striking divergence in adult male color and pattern that occurs over small geographic distances,...

Data from: Independent acquisition of sodium selectivity in bacterial and animal sodium channels

Benjamin J. Liebeskind, David M. Hillis & Harold H. Zakon
Electrical signaling in animal nerves and muscles is largely carried out by proteins in the superfamily of voltage-gated ion channels. These proteins are based on a single homologous domain, but different types exist as single-domain tetramers, two-domain dimers, or four-domain proteins that comprise the whole pore-forming structure. Four-domain channels are hypothesized to have evolved from a single-domain ancestor by two rounds of internal duplication. The role that a channel plays in a cell’s physiology is...

Data from: Diagnostic gene expression biomarkers of coral thermal stress

Carly D. Kenkel, Christopher Sheridan, Miguel C. Leal, Ranjeet Bhagooli, Karl D. Castillo, Naoko Kurata, Elizabeth McGinty, Tamar L. Goulet, Mikhail V. Matz, C. D. Kenkel, M. V. Matz, M. C. Leal, E. McGinty, T. L. Goulet, K. D. Castillo, C. Sheridan, N. Kurata & R. Bhagooli
Gene expression biomarkers can enable rapid assessment of physiological conditions in situ, providing a valuable tool for reef managers interested in linking organism physiology with large-scale climatic conditions. Here, we assessed the ability of quantitative PCR (qPCR) based gene expression biomarkers to evaluate (1) the immediate cellular stress response (CSR) of Porites astreoides to incremental thermal stress and (2) the magnitude of CSR and cellular homeostasis response (CHR) during a natural bleaching event. Expression levels...

Data from: Convergent regulatory evolution and loss of flight in palaeognathous birds

Timothy B. Sackton, Phil Grayson, Alison Cloutier, Zhirui Hu, Jun S. Liu, Nicole E. Wheeler, Paul P. Gardner, Julia A. Clarke, Allan J. Baker, Michele Clamp & Scott V. Edwards
A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which...

Data from: Red fluorescence in coral larvae is associated with a diapause-like state

Marie E. Strader, Galina V. Aglyamova & Mikhail V. Matz
Effective dispersal across environmental gradients is the key to species resilience to environmental perturbation, including climate change. Coral reefs are among the most sensitive ecosystems to global warming, but factors predicting coral dispersal potential remain unknown. In a reef-building coral Acropora millepora, larval fluorescence emerged as a possible indicator of dispersal potential since it correlates with responsiveness to a settlement cue. Here we show that gene expression in red fluorescent larvae of A. millepora is...

Data from: Species richness mediates within-species nutrient resorption: implications for the biodiversity-productivity relationship

Xiao-Tao Lü, Yan-Yu Hu, Amelia A. Wolf & Xingguo Han
1.Between-species variation in nutrient resorption is one of the mechanisms explaining the positive relationship between biodiversity and primary productivity. Yet, the role of within-species variations in nutrient resorption in mediating the relationship between biodiversity and productivity remains unclear. 2.We examined how within-species nutrient resorption, and ultimately productivity, respond to changes in species richness by using four traits related to nitrogen and phosphorus use in four dominant species from different plant functional groups in a biodiversity...

Data from: phenotools: an R package for visualizing and analyzing phenomic datasets

Chad M. Eliason, Scott V. Edwards & Julia A. Clarke
1.Phenotypic data is crucial for understanding genotype–phenotype relationships, assessing the tree of life, and revealing trends in trait diversity over time. Large‐scale description of whole organisms for quantitative analyses (phenomics) presents several challenges, and technological advances in the collection of genomic data outpace those for phenomic data. Reasons for this disparity include the time‐consuming and expensive nature of collecting discrete phenotypic data and mining previously‐published data on a given species (both often requiring anatomical expertise...

Data from: Methods for the quantitative comparison of molecular estimates of clade age and the fossil record

Julia A. Clarke & Clint A. Boyd
Approaches quantifying relative congruence, or incongruence, of molecular divergence estimates and the fossil record have been limited. Previously proposed methods are largely node specific, assessing incongruence at particular nodes for which both fossil data and molecular divergence estimates are available. These existing metrics, and other methods that quantify incongruence across topologies including entirely extinct clades, have so far not taken into account uncertainty surrounding both the divergence estimates and the ages of fossils. They have...

Data from: SuperFine: fast and accurate supertree estimation

M. Shel Swenson, Rahul Suri, C. Randal Linder & Tandy Warnow
Many research groups are estimating trees containing anywhere from a few thousand to hundreds of thousands of species, towards the eventual goal of the estimation of a Tree of Life, containing perhaps as many as several million leaves. These phylogenetic estimations present enormous computational challenges, and current computational methods are likely to fail to run even on datasets in the low end of this range. One approach to estimate a large species tree is to...

Data from: Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

Yan-Jie Feng, David C. Blackburn, Dan Liang, David M. Hillis, David B. Wake, David C. Cannatella & Peng Zhang
Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with...

Data from: Does biomass growth increase in the largest trees? Flaws, fallacies and alternative analyses

Douglas Sheil, Chris S. Eastaugh, Mart Vlam, Pieter A. Zuidema, Peter Groenendijk, Peter Van Der Sleen, Alex Jay & Jerome Vanclay
The long-standing view that biomass growth in trees typically follows a rise-and-fall unimodal pattern has been challenged by studies concluding that biomass growth increases with size even among the largest stems in both closed forests and in open competition-free environments. We highlight challenges and pitfalls that influence such interpretations. The ability to observe and calibrate biomass change in large stems requires adequate data regarding these specific stems. Data checking and control procedures can bias estimates...

Data from: Interactions of multisensory components perceptually rescue túngara frog mating signals

Ryan C. Taylor & Michael J. Ryan
Sexual signals are often complex and perceived by multiple senses. How animals integrate signal components across sensory modalities can influence signal evolution. Here we show that two relatively unattractive signals that are perceived acoustically and visually can be combined in a pattern to form a signal that is attractive to female túngara frogs. Such unanticipated perceptual effects suggest that the evolution of complex signals can occur by alteration of the relationships among already-existing traits.

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