34 Works

Ferrofluid displacement in a simple 2.5D micromodel

Ningyu Wang, Yifei Liu, Luming Cha, Masa Prodanovic & Matthew Balhoff
The dataset contains a series of images of a varying-depth converging-diverging single-channel micromodel during ferrofluid flooding without and then with an external magnetic field. One image shows the initial oil saturation after ferrofluid flooding without a magnetic field, and twelve images show the oil saturation after the magnetic field was turned on. Only eight pores in the flow channel are shown in these images, while there are more than 100 pores in the flow channel....

No sex differences in learning in wild bumblebees

Felicity Muth
Females and males often face different sources of selection, resulting in dimorphism in morphological, physiological, and even cognitive traits. Sex differences are often studied in respect to spatial cognition, yet the different ecological roles of males and females might shape cognition in multiple ways. For example, in dietary generalist bumblebees (Bombus), the ability to learn associations is critical to female workers, who face informationally-rich foraging scenarios as they collect nectar and pollen from thousands of...

Estimating the distribution of carotenoid coloration in skin and integumentary structures of birds and extinct dinosaurs

Sarah Davis & Julia Clarke
Carotenoids are pigments responsible for most bright yellow, red, and orange hues in birds. Their distribution has been investigated in avian plumage, but the evolution of their expression in skin and other integumentary structures has not been approached in detail. Here, we investigate the expression of carotenoid-consistent coloration across tissue types in all extant, non-passerine species (n= 4,022) and archelosaur outgroups in a phylogenetic framework. We collect dietary data for a subset of birds and...

Season of prescribed fire determines grassland restoration outcomes after fire exclusion and overgrazing

Erin N. Novak, Michelle Bertelsen, Dick Davis, Devin M. Grobert, Kelly G. Lyons, Jason P. Martina, W. Matt McCaw, Matthew O'Toole & Joseph W. Veldman
Fire exclusion and mismanaged grazing are globally important drivers of environmental change in mesic C4 grasslands and savannas. Although interest is growing in prescribed fire for grassland restoration, we have little long-term experimental evidence of the influence of burn season on the recovery of herbaceous plant communities, encroachment by trees and shrubs, and invasion by exotic grasses. We conducted a prescribed fire experiment (seven burns between 2001 and 2019) in historically fire-excluded and overgrazed grasslands...

Cytotype and genotype predict mortality and recruitment in Colorado quaking aspen (Populus tremuloides)

Benjamin Blonder, Courtenay Ray, James Walton, Marco Castaneda, K. Dana Chadwick, Michael Clyne, Pierre Gaüzere, Lars Iversen, Madison Lusk, G. Richard Strimbeck, Savannah Troy & Karen Mock
Species responses to climate change depend on environment, genetics, and interactions among these factors. Intraspecific cytotype (ploidy level) variation is a common type of genetic variation in many species. However, the importance of intraspecific cytotype variation in determining demography across environments is poorly known. We studied the tree species quaking aspen (Populus tremuloides), which occurs in diploid and triploid cytotypes. This widespread species is experiencing contractions in its western range, which could potentially be linked...

Defensive hypervariable regions confer superinfection exclusion in microviruses

Paul Kirchberger
Single-stranded DNA phages of the family Microviridae have fundamentally different evolutionary origins and dynamics than the more frequently studied double-stranded DNA phages. Despite their small size (generally <5kb), which imposes extreme constraints on genomic innovation, they have adapted to become prominent members of viromes in numerous ecosystems and hold a dominant position among viruses in the human gut. We show that multiple, divergent lineages in the family Microviridae have independently become capable of lysogenizing hosts...

Differences in bee community composition between restored and remnant prairies are more strongly linked to forb community differences than landscape differences

Ian Lane, Zachary Portman, Christina Herron-Sweet, Gabriella Pardee & Daniel Cariveau
1. Grassland restoration is an important tool for conserving bee biodiversity within agricultural landscapes. Restorations foster increases in local bee abundance and α-diversity, however, these measures are insufficient for understanding if remnant communities are being conserved. We compared native bee α-diversity, β-diversity, and community composition between restored and remnant prairies in Minnesota, USA. We then investigated two potential drivers of bee community dissimilarity between restored and remnant prairies: proportion of agricultural land surrounding a restoration...

The early life of a leaf-cutter colony constrains symbiont vertical transmission

Zachary Phillips, Luke Reding & Caroline Farrior
The early life of a leaf-cutter colony is characterized by the dispersal of a female alate (winged “queen”) carrying a fungal pellet, and the subsequent establishment of a foundress (workerless “queen”) raising her incipient fungal garden and colony. The symbiotic roach Attaphila fungicola hitchhikes on female alates during leaf-cutter nuptial flights, which strongly suggests that roaches are vertically transmitted to foundresses and their incipient colonies; however, weak compatibility between roaches and incipient gardens may constrain...

Diversity-stability cascade in pond plankton experiments

Chase Rakowski, Caroline Farrior, Schonna Manning & Mathew Leibold
This collection of files consists of freshwater plankton biomass data from a laboratory microcosm experiment and an accompanying field mesocosm experiment in which we manipulated the presence of two heteropteran predators. In the laboratory experiment, we incubated 20 large microcosms with phytoplankton and zooplankton, fully crossing a 1x vs. 2x zooplankton density treatment with presence or absence of a single Notonecta undulata adult. Two of these microcosms were lost, resulting in data for 18 of...

Data For: The developing bird pelvis passes through ancestral Archosaurian and Dinosaurian conditions

Christopher Griffin, João Botelho, Michael Hanson, Matteo Fabbri, Daniel Smith-Paredes, Ryan Carney, Mark Norell, Shiro Egawa, Stephen Gatesy, Timothy Rowe, Ruth Elsey, Sterling Nesbitt & Bhart-Anjan Bhullar
Living birds (Aves) have bodies dramatically modified from the ancestral reptilian condition. The avian pelvis in particular experienced dramatic changes during the transition from early archosaurs to living birds. This stepwise transformation is well documented by an excellent fossil record; however, the ontogenetic alterations that underly it are less well-understood. We used embryological imaging techniques to examine the morphogenesis of avian pelvic tissues in three dimensions, allowing direct comparison with the fossil record. Many ancestral...

The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes

Chaehee Lee, In-Su Choi, Domingos Cardoso, Haroldo De Lima, Luciano De Queiroz, Martin Wojciechowski, Robert Jansen & Tracey Ruhlman
The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused...

Cognitive maps in the wild: Revealing the use of metric information in black howler monkeys' route navigation

Miguel De Guinea, Alejandro Estrada, Anna Isola K. Nekaris & Sarie Van Belle
When navigating, wild animals rely on internal representations of the external world to take movement decisions – called “cognitive maps”. As a rule, flexible navigation is hypothesized to be supported by sophisticated spatial skills (i.e., Euclidean cognitive maps); however, constrained movements along habitual routes is the most commonly reported navigation strategy. Even though incorporating metric information (i.e., distances and angles between locations) in route-based cognitive maps would likely enhance an animal’s navigation efficiency, there has...

Heterogeneous histories of recombination suppression on stickleback sex chromosomes

Mark Kirkpatrick
How consistent are the evolutionary trajectories of sex chromosomes shortly after they form? Insights into the evolution of recombination, differentiation, and degeneration can be provided by comparing closely related species with homologous sex chromosomes. The sex chromosomes of the threespine stickleback (Gasterosteus aculeatus) and its sister species, the Japan Sea stickleback (G. nipponicus), have been well characterized. Little is known, however, about the sex chromosomes of their congener, the blackspotted stickleback (G. wheatlandi). We used...

Sensory ecology of the frog-eating bat, Trachops cirrhosus, from DNA metabarcoding and behavior

Patricia L Jones, Timothy Divoll, M. May Dixon, Dineilys Aparicio, Gregg Cohen, Ulrich Mueller, Michael Ryan & Rachel Page
Metabarcoding of prey DNA from fecal samples can be used to design behavioral experiments to study the foraging behavior and sensory ecology of predators. The frog-eating bat, Trachops cirrhosus, eavesdrops on the mating calls of its anuran prey. We captured wild T. cirrhosus and identified prey remains in the bats' fecal samples using DNA metabarcoding of two gene regions (CO1, 16S). Bats were preying on frogs previously unknown in their diet, such as species in...

Data from: Divergent pathways of nitrogen-fixing trees through succession depend on starting nitrogen supply and priority effects

Thomas Bytnerowicz & Duncan Menge
Nitrogen-fixing trees are a major potential source of nitrogen into terrestrial ecosystems. The degree to which they persist into older forests has considerable implications for forest nitrogen budgets. We characterized nitrogen-fixing tree abundance across stand age in the contiguous United States and analyzed a theoretical model to help understand competitive outcomes and successional trajectories of nitrogen-fixing and nonfixing trees. Nitrogen-fixing tree abundance is bimodal in all regions except the northeastern United States, even in older...

Decrypting cryptic crosswords: Semantically complex wordplay puzzles as a target for NLP

Joshua Rozner, Christopher Potts & Kyle Mahowald
Cryptic crosswords, the dominant crossword variety in the UK, are a promising target for advancing NLP systems that seek to process semantically complex, highly compositional language. Cryptic clues read like fluent natural language but are adversarially composed of two parts: a definition and a wordplay cipher requiring character-level manipulations. Expert humans use creative intelligence to solve cryptics, flexibly combining linguistic, world, and domain knowledge. In this paper, we make two main contributions. First, we present...

Visual tracking of animals in three-dimensions using mobile handheld independent GoPro cameras and VSLAM software

Parrish Brady
I present the system PATMOS (Paths And Tessellated Meshes from ORB_SLAM2) for measuring three-dimensional paths of animals in situ using two handheld GoPro cameras and a small spatial reference object. Animal paths were triangulated from mobile camera positions obtained from a modified version of ORB_SLAM2, an open-source visual simultaneous localization and mapping software package. In addition to path calculation, this process provided a virtual three-dimensional surface approximation to the environment from which path to environment...

Effects on Digital Rock Physics Models from Variable Computed Tomography Scans Settings

Eric Goldfarb, Ken Ikeda, Masa Prodanovic, Richard Ketcham & Nicola Tisato
The present contribution aims to understand the effect of Computed Tomography (CT) acquisition settings on digital rock physics models. We conducted 32 scans of 4 Berea Sandstone samples. In order to understand the effects of setup parameters on the calculated density of the samples, each scan had different set up conditions. We also varied post acquisition filtering, including applying different beam hardening corrections, and various noise filters. We observe that by using phantoms of known...

Drainage experiment in an intermediate-scale beadpack

Hailun Ni & Timothy Meckel

De novo genome assembly of Leptodactylus fuscus

Lu Yang, Peter Andolfatto, Andrew Crawford, Santiago Herrera-Álvarez, Maríadel Pilar Rodríguez-Ordoñez, Julie Peng, Shabnam Mohammadi, Jay Storz, Arbel Harpak & Susanne Dobler
This presents a de novo genome assembly of Leptodactylus fuscus. High molecular weight DNA was extracted from a L. fuscus embryo which had been preserved in ethanol upon collection in Garzón, Huila, Colombia. The library was prepared and sequenced with 10X Genomics Chromium. Linked reads were processed by Long Ranger basic v2.2.2 and assembled with Supernova v2.1.1. The assembled genome is 2.42 Gb with 16,530 scaffolds >=10 kb, and scaffold N50 = 363 kb. The...

Personality predicts innovation and social learning in children; Implications for cultural evolution

Bruce Rawlings
Innovation and social learning are the pillars of cultural evolution, allowing cultural behaviours to cumulatively advance over generations. Yet, little is known about individual differences in the use of social and asocial information. We examined whether personality influenced children’s propensity to observe others or independently generate solutions to novel problems. Conscientiousness was associated with electing for no demonstrations, while agreeableness was associated with opting for demonstrations. For children receiving demonstrations, openness to experience consistently predicted...

Dispersal patterns in black howler monkeys (Alouatta pigra): Integrating multi-year demographic and molecular data

Sarie Van Belle & Anthony Di Fiore
Dispersal is a fundamental process in the functioning of animal societies as it regulates the degree to which closely related individuals are spatially concentrated. A species’ dispersal pattern can be complex as it emerges from individuals’ decisions shaped by the cost-benefit tradeoffs associated with either remaining in the natal group or dispersing. Given the potential complexity, combining long-term demographic information with molecular data can provide important insights into dispersal patterns of a species. Based on...

Data from: Intra-specific differences in cognition: Bumblebee queens learn better than workers

Felicity Muth
Species’ cognitive traits are shaped by their ecology, and even within a species, cognition can reflect the behavioural requirements of individuals with diffferent roles. Social insects have a number of discrete roles (castes) within a colony, and thus offer a useful system to determine how ecological requirements shape cognition. Bumblebee queens are a critical point in the lifecycle of their colony, since its future success is reliant on a single individual’s ability to learn about...

DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity

Jordan M Casey, Emma Ransome, Allen G Collins, Angka Mahardini, Eka M Kurniasih, Andrianus Sembiring, Nina M D Schiettekatte, Ni Kadek Dita Cahyani, Aji Wahyu Anggoro, Mikaela Moore, Abby Uehling, Mahdi Belcaid, Paul H Barber, Jonathan B Geller & Christopher P Meyer
DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome c oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed “universal” markers for eukaryotes, but the extent of taxonomic biases introduced by these markers and how such biases may impact metabarcoding performance is not well quantified. Here, focusing on macro-eukaryotes, we use standardized sampling from...

How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake

Thomas Marshall, E. Anne Chambers, Mikhail Matz & David Hillis
As DNA sequencing technologies and methods for delimiting species with genomic data become more accessible and numerous, researchers have more tools than ever to investigate questions in systematics and phylogeography. However, easy access to sophisticated computational tools is not without its drawbacks. Choosing the right approach for one’s question can be challenging when presented with multitudinous options, some of which fail to distinguish between species and intraspecific population structure. Here, we employ a methodology that...

Registration Year

  • 2021

Resource Types

  • Dataset


  • The University of Texas at Austin
  • Columbia University
  • Stanford University
  • Universität Hamburg
  • Princeton University
  • University of Chicago
  • Arizona State University
  • University of Paris-Saclay
  • Universidad de Los Andes
  • Wellcome Sanger Institute