55 Works

Phylogenomics, introgression, and demographic history of South American true toads (Rhinella)

Danielle Rivera, Ivan Prates, Thomas Firneno, Miguel Rodrigues, Janalee Caldwell & Matthew Fujita
The effects of genetic introgression on species boundaries and how they affect species’ integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (Rhinella), we assess...

Phylogenetic conflicts, combinability, and deep phylogenomics in plants

Stephen Smith, Joseph Walker, Joseph Brown & Nathanael Hale
Studies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a dataset in order to resolve recalcitrant relationships and, importantly, identify what the dataset is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error...

Data from: New forms of structure in ecosystems revealed with the Kuramoto model

John Vandermeer
This is the general Mathematica code for the article, "New forms of structure in ecosystems revealed with the Kuramoto model" by Vandermeer, Hajian-Forooshani, Medina and Perfecto. All results presented in the article can be obtained by running the code with appropriate parameter settings.

Habitat structure mediates vulnerability to climate change through its effects on thermoregulatory behavior

Lauren Neel, Michael Logan, Daniel Nicholson, Christina Miller, Albert Chung, Inbar Maayan, Zach Degon, Madeline DuBois, John David Curlis, Q Taylor, Kaitlin Keegan, Owen McMillan, Jonathan Losos & Christian Cox
Tropical ectotherms are thought to be especially vulnerable to climate change because they are thermal specialists, having evolved in aseasonal thermal environments. However, even within the tropics, habitat structure can influence opportunities for behavioral thermoregulation. Open (and edge) habitats likely promote more effective thermoregulation due to the high spatial heterogeneity of the thermal landscape, while forests are thermally homogenous and may constrain opportunities for behavioral buffering of environmental temperatures. Nevertheless, the ways in which behavior...

Comparison of adult census size and effective population size support the need for continued protection of two Solomon Island endemics

Sarah A. Cowles, Brian C. Weeks, Lindsey Perrin, Nancy Chen & J. Albert C. Uy
Because a population’s ability to respond to rapid change is dictated by standing genetic variation, we can better predict a population’s long-term viability by estimating and then comparing adult census size (N) and effective population size (Ne). However, most studies only measure N or Ne, which can be misleading. Using a combination of field and genomic sequence data, we here estimate and compare N and Ne in two range-restricted endemics of the Solomon Islands. Two...

Data from: Long-term trends in the occupancy of ants revealed through use of multi-sourced datasets

Julie Sheard, Carsten Rahbek, Robert Dunn, Nathan Sanders & Nick Isaac
We combined participatory science data and museum records to understand long-term changes in occupancy for 29 ant species in Denmark over 119 years. Bayesian occupancy modelling indicated change in occupancy for 15 species: five increased, four declined and six showed fluctuating trends. We consider how trends may have been influenced by life-history and habitat changes. Our results build on an emerging picture that biodiversity change in insects is more complex than implied by the simple...

Behavioural plasticity in a native species is related to foraging resilience in the presence of an aggressive invader

Marian Wong, Melinda Keiller, Laura Lopez & Kai Paijmans
Competition between invasive and native species can result in exploitation of resources by the invader, reducing foraging rates of natives. However, it is increasingly recognised that multiple factors can enhance the resilience of native species competing for limiting resources with invaders. Although extensively studied in terrestrial species, little research has focused on behavioural plasticity in the aquatic realm and how this influences native species resilience. Here we examined the role of behavioural plasticity in interactions...

Living in the concrete jungle: carnivore spatial ecology in urban parks

Siria Gámez & Nyeema C. Harris
People and wildlife are living in an increasingly urban world, replete with unprecedented human densities, sprawling built environments, and altered landscapes. Such anthropogenic pressures can affect multiple processes within an ecological community, from spatial patterns to interspecific interactions. We tested two competing hypotheses, human shields versus human competitors, to characterize how humans affect the carnivore community using multi-species occupancy models. From 2017-2020, we conducted the first camera survey of city parks in Detroit, Michigan, and...

Density, parasitism, and sexual reproduction are strongly correlated in lake Daphnia populations

Meghan A. Duffy, Camden D. Gowler, Mary A. Rogalski, Clara L. Shaw & Katherine K. Hunsberger
Many organisms can reproduce both asexually and sexually. For cyclical parthenogens, periods of asexual reproduction are punctuated by bouts of sexual reproduction, and the shift from asexual to sexual reproduction has large impacts on fitness and population dynamics. We studied populations of Daphnia dentifera to determine the amount of investment in sexual reproduction as well as the factors associated with variation in investment in sex. To do so, we tracked host density, infections by nine...

Retention fraction of 15N-labelled deposited ammonium and nitrate in forests

Geshere Abdisa Gurmesa, Ang Wang, Shanlong Li, Shushi Peng, Wim De Vries, Per Gundersen, Philippe Ciais, Oliver L Phillips, Erik Hobbie, Weixing Zhu, Knute Nadelhoffer, Yi Xi, Edith Bai, Tao Sun, Dexiang Chen, Wenjun Zhou, Yiping Zhang, Yingrong Guo, Jiaojun Zhu, Lei Duan, Dejun Li, Keisuke Koba, Enzai Du, Guoyi Zhou, Xingguo Han … & Yunting Fang
The impacts of enhanced nitrogen (N) deposition on global forest carbon (C) sink and other ecosystem services may depend on whether N is deposited in reduced (mainly as ammonium) or oxidized forms (mainly as nitrate) and the subsequent fate of each. However, the fates of the two key reactive N forms and its contribution to forest C sink is unclear. We conducted ecosystem-scale paired 15N-labelling experiments in nine forests across China to quantify N retention...

2019 Survey of Florida Residents to Evaluate Public Comprehension of the “Cone of Uncertainty” Graphic

Scotney Evans, Kenneth Broad, Alberto Cairo, Sharanya Majumdar, Brian McNoldy, Barbara Millet & Leigh Rauk
This data set contains results from an online survey targeting a sample of 2,847 Florida residents in 2019. Unlike previous public surveys that focused more on evacuation decisions, forecast usage, and perception of hurricane risk, our approach specifically pays attention to the details of design elements of the forecast graphics with the long-term goal of minimizing misinterpretation of future graphics. The survey comprised 55 mostly multiple-choice and True/False questions, including demographic information and a series...

Detection histories for Lycalopex griseus, Lycalopex culpaeus, Leopardus guigna, and Canis familiaris and habitat destruction covariate data for Los Lagos Chile (2019)

Rumaan Malhotra, Jaime Jiménez & Nyeema Harris
In an increasingly anthropogenic world, species face multiple interacting threats. Habitat fragmentation and domestic dogs are two perturbations threatening terrestrial mammals globally. Our aim was to determine if (1) the spatial use of domestic dogs increases with habitat destruction and (2) whether domestic dogs and habitat destruction drive the spatial use of native carnivores in a heavily degraded agricultural landscape in the central valley/Andean foothills transition of Los Lagos, Chile. We implemented a camera trap...

ddRAD-seq alignment data for Unionid mussels

Trevor Hewitt, Amanda Haponski & Diarmaid Ó Foighil
North American watersheds contain the world’s highest diversity of freshwater mussels (Unionoida), and up to 40 species can co-occur in a single riffle. They collectively exhibit little evidence for ecological differentiation during the long-lived, benthic phase of their life cycle. In contrast, their brief parasitic larval phase involves the infection of a wide diversity of fish hosts. Gravid female mussels have evolved multiple methods for increasing the probability of infecting a host fish. Some species...

Inbreeding depression in artificial selection lines of Ipomoea purpurea

Megan Van Etten, Anah Soble & Regina Baucom
Inbreeding depression is a central parameter underlying mating system variation in nature and one that can be altered by environmental stress. Although a variety of systems show that inbreeding depression tends to increase under stressful conditions, we have very little understanding across most organisms how the level of inbreeding depression may change as a result of adaptation to stressors. In this work we examined the potential that inbreeding depression varied among lineages of Ipomoea purpurea...

Data from: Virulent disease epidemics can increase host density by depressing foraging of hosts

Rachel Penczykowski, Marta Shocket, Jessica Housley Ochs, Brian Lemanski, Hema Sundar, Meghan Duffy & Spencer Hall
All else equal, parasites that harm host fitness should depress densities of their hosts. However, parasites that alter host traits may increase host density via indirect ecological interactions. Here, we show how depression of foraging rate of infected hosts can produce such a hydra effect. Using a foraging assay, we quantified reduced foraging rates of a zooplankton host infected with a virulent fungal parasite. We then parameterized a dynamical model of hosts, parasites, and resources...

Balancing selection and drift in a polymorphic salamander metapopulation

Sean Giery, Marketa Zimova, Dana Drake & Mark Urban
Understanding how genetic variation is maintained in a metapopulation is a longstanding problem in evolutionary biology. Historical resurveys of polymorphisms have offered efficient insights about evolutionary mechanisms, but are often conducted on single, large populations, neglecting the more comprehensive view afforded by considering all populations in a metapopulation. Here, we resurveyed a metapopulation of spotted salamanders (Ambystoma maculatum) to understand the evolutionary drivers of frequency variation in an egg mass colour polymorphism. We found that...

Supplemental Materials: Duration of poverty and subsequent cognitive function and decline among older adults in China, 2005-2018

Xuexin Yu, Wei Zhang & Lindsay Kobayashi
Objective To investigate the relationship between late-life duration of poverty exposure and cognitive function and decline among older adults in China. Methods Data were from 3,209 participants aged ≥64 in the Chinese Longitudinal Healthy Longevity Survey (CLHLS). Duration of poverty, defined according to urban and rural regional standards from the China Statistical Yearbook, was assessed from 2005-2011 (never in poverty; 1/3 of the period in poverty; ≥2/3 of the period in poverty). Cognitive function was...

Stage-structured ontogeny in resource populations generates non-additive stabilizing and de-stabilizing forces in populations and communities

Paul Glaum & John Vandermeer
Demographic heterogeneity influences how populations respond to density dependent intraspecific competition and trophic interactions. Distinct stages across an organism’s development, or ontogeny, are an important example of demographic heterogeneity. In consumer populations, ontogenetic stage structure has been shown to produce categorical differences in population dynamics, community dynamics, and even species coexistence compared to models lacking explicit ontogeny. The study of consumer-resource interactions must also consider the ontogenetic stage structure of the resource itself, particularly plants,...

Isotopic data from: Coupled shifts in ectomycorrhizal communities and plant uptake of organic nitrogen along a soil gradient: an isotopic perspective

Peter Pellitier
Plants associating with mutualistic ectomycorrhizal (ECM) fungi may directly obtain nitrogen (N) bound in soil organic matter (N-SOM). However, the contribution of N-SOM to plant growth under field conditions remains poorly constrained. We tested the hypothesis that turnover in ECM communities along soil inorganic N gradients mediates a functional transition from plant reliance on N-SOM in low inorganic N soils, to primarily inorganic N uptake in inorganic N rich condition soils. We quantified the d15N...

Supplementary files for \"Creating a Universal Depth-To-Load Conversion Technique for the Conterminous United States using Random Forests\"

Jesse Wheeler, Brennan Bean & Marc Maguire
As part of an ongoing effort to update the ground snow load maps in the United States, this paper presents an investigation into snow densities for the purpose of predicting ground snow loads for structural engineering design with ASCE 7. Despite their importance, direct measurements of snow load are sparse when compared to measurements of snow depth. As a result, it is often necessary to estimate snow load using snow depth and other readily accessible...

Data from: Genetic and ecogeographic controls on species cohesion in Australia’s most diverse lizard radiation

Ivan Prates, Sonal Singhal, M. Raquel Marchán-Rivadeneira, Maggie R. Grundler, Craig C. Moritz, Steve Donnellan & Daniel L. Rabosky
Species vary extensively in geographic range size and climatic niche breadth. If range limits are primarily determined by climatic factors, species with broad climatic tolerances and those that track geographically widespread climates should have large ranges. However, large ranges might increase the probability of population fragmentation and adaptive divergence, potentially decoupling climatic niche breadth and range size. Conversely, ecological generalism in widespread species might lead to higher gene flow across climatic transitions, increasing species’ cohesion...

Rare missense functional variants at COL4A1 and COL4A2 in sporadic intracerebral hemorrhage

Jaeyoon Chung, Graham Hamilton, Minsup Kim, Sandro Marini, Bailey Montgomery, Jonathan Henry, Art Cho, Devin Brown, Bradford Worrall, James Meschia, Scott Silliman, Magdy Selim, David Tirschwell, Chelsea Kidwell, Brett Kissela, Steven Greenberg, Anand Viswanathan, Joshua Goldstein, Carl Langefeld, Kristiina Rannikmae, Catherine Sudlow, Neshika Samarasekera, Mark Rodrigues, Rustam Salman, James Prendergast … & Christopher Anderson
Objective To test the genetic contribution of rare missense variants in COL4A1 and COL4A2 in which common variants are genetically associated with sporadic intracerebral hemorrhage (ICH), we performed rare variant analysis in multiple sequencing data for the risk for sporadic ICH. Methods We performed sequencing across 559Kbp at 13q34 including COL4A1 and COL4A2 among 2,133 individuals (1,055 ICH cases; 1,078 controls) in US-based and 1,492 individuals (192 ICH cases; 1,300 controls) from Scotland-based cohorts, followed...

Dose relationships can exacerbate, mute, or reverse the impact of heterospecific host density on infection prevalence

Patrick Clay, Michael Cortez & Meghan Duffy
The likelihood an individual becomes infected depends on the community in which it is embedded. For environmentally transmitted parasites, host community composition can alter host density, the density of parasites that hosts encounter in the environment, and the dose to which hosts are subsequently exposed. While some multi-host theory incorporates some of these factors (e.g., competition among hosts), it does not currently consider the nonlinear relationships between parasite exposure dose and per-propagule infectivity (dose-infectivity relationships),...

Thermal ecology and baseline energetic requirements of a large-bodied ectotherm suggest resilience to climate change

Hayley Crowell, Katherine King, James Whelan, Mallory Harmel, Gennesee Garcia, Sebastian Gonzales, Paul Maier, Heather Neldner, Thomas Nhu, John Nolan & Emily Taylor
Most studies on how rising temperatures will impact terrestrial ectotherms have focused on single populations or multiple sympatric species. Addressing the thermal and energetic implications of climatic variation on multiple allopatric populations of a species will help us better elucidate how a species may be impacted by altered climates. We used eight years of thermal and behavioral data collected from four populations of Pacific rattlesnakes (Crotalus oreganus) living in climatically distinct habitat types (inland and...

Data for: Freeze tolerance influenced forest cover and hydrology during the Pennsylvanian

William Matthaeus, Sophia I. Macarewich, Jon D. Richey, Jonathan P. Wilson, Jennifer C. McElwin, Isabel P. Montañez, William A. DiMichele, Michael T. Hren, Christopher J. Poulsen & Joseph D. White
Global forest cover affects the Earth system by altering surface mass and energy exchange. Physiology determines plant environmental limits and influences geographical vegetation distribution. Ancient plant physiology, therefore, likely affected vegetation-climate feedbacks. We combine climate modeling and ecosystem-process modeling to simulate arboreal vegetation in the late Paleozoic ice age. Using GENESIS V3 GCM simulations, varying pCO2, pO2, and ice extent for the Pennsylvanian, and fossil-derived leaf C:N, maximum stomatal conductance, and specific conductivity for several...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Michigan-Ann Arbor
  • University of Michigan–Ann Arbor
  • Pennsylvania State University
  • University of California, Berkeley
  • University of Florida
  • University of Kansas
  • University of Cambridge
  • University of Minnesota
  • University of Nevada Reno
  • Florida International University