109 Works

Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities

Carla Martins Lopes, Délio Baêta, Thais Sasso, Agustín Vanzetti, Kelly Zamudio, Pierre Taberlet & Célio Haddad
Leaf litter habitats shelter a great variety of organisms, which play an important role in ecosystem dynamics. However, monitoring species in leaf litter is challenging, especially in highly diverse environments such as tropical forests, because individuals may easily camouflage themselves or hide in the litter layer. Identifying species based on environmental DNA (eDNA) would allow us to assess biodiversity in this microhabitat, without the need for direct observation of individuals. We applied eDNA metabarcoding to...

Data from: Local prey shortages drive foraging costs and breeding success in a declining seabird, the Atlantic puffin

Annette L Fayet, Gemma V Clucas, Tycho Anker-Nilssen, Martyna Syposz & Erpur S Hansen
As more and more species face anthropogenic threats, understanding causes of population declines in vulnerable taxa is essential. However, long-term datasets, ideal to identify lasting or indirect effects on fitness measures such as those caused by environmental factors, are not always available. Here we use a single year but multi-population approach on populations with contrasting demographic trends to identify possible drivers and mechanisms of seabird population changes in the north-east Atlantic, using the Atlantic puffin,...

Cornell National Social Survey (CNSS), 2020

Cornell National Social Survey is a random-sample survey of adults aged 18 and over. In 2020, participants were asked their opinions on a range of topics.

Data from: Host population dynamics in the face of an evolving pathogen

Wesley Hochachka, Andrew Dobson, Dana Hawley & André Dhondt
1. Interactions between hosts and pathogens are dynamic at both ecological and evolutionary levels. In the resultant “eco-evolutionary dynamics” ecological and evolutionary processes affect each other. For example, the house finch (Haemorhous mexicanus) and its recently-emerged pathogen, the bacterium Mycoplasma gallisepticum, form a system in which evidence suggests that changes in bacterial virulence through time enhance levels of host immunity in ways that drive the evolution of virulence in an arms race. 2. We use...

Rapid recovery by fat- and muscle-depleted Blackpoll Warblers following trans-oceanic migration is driven by time-minimization

Nicholas J. Bayly, Kenneth V. Rosenberg, Ryan Norris, Philip D. Taylor & Keith A. Hobson
Non-stop endurance flights are a defining characteristic of many long-distance migratory birds but subsequent recovery phases are not typically distinguished from fueling phases (collectively ‘stopovers’), despite endurance flights inducing marked physiological changes including flight muscle atrophy and gastrointestinal tract reductions. Here, we hypothesize that recovery requires unique behavioral adaptations, leading to departures from the predictions of optimal migration theory for time-minimizing migrants. We predict that recovering birds will 1) select (moist) food-rich habitats on arrival;...

Value of Curation Survey, January 2021

Lisa R Johnston, Renata Gonçalves Curty, Sophia Lafferty-Hess, Hannah Hadley, Jonathan Petters, Hoa Luong, Susan Braxton, Jake Carlson & Wendy A Kozlowski
This dataset includes the raw and augmented survey results from the January 2021 Value of Curation survey run by the Data Curation Network. Distributed to US data repository staff and directors via email listservs the survey received a total of 120 responses. 22 responses were for non-US repositories and three did not provide a repository of reference. A majority of the participants self-identified as staff members with 52 staff and 34 repository directors. The remaining...

Population assignment tests uncover rare long-distance larval dispersal events

Cassidy D'Aloia, Steven Bogdanowicz, Jose Andres & Peter Buston
Long-distance dispersal (LDD) is consequential to metapopulation ecology and evolution. In systems where dispersal is undertaken by small propagules, such as larvae in the ocean, documenting LDD is especially challenging. Genetic parentage analysis has gained traction as a method for measuring larval dispersal, but such studies are generally spatially limited, leaving LDD understudied in marine species. We addressed this knowledge gap by uncovering LDD with population assignment tests in the coral reef fish Elacatinus lori—a...

Sex, age, and acoustic mating interactions affect the immunity of Aedes aegypti offspring

Courtney Murdock, Christine Reitmayer, Ashutosh Pathak, Laura Harrington, Melinda Brindley & Lauren Cator
Aedes aegypti is an important vector of several pathogenic arboviruses including dengue, chikungunya and Zika. Innovative approaches to control Aedes populations, involving synthetic transgenic modifications as well as Wolbachia bacteria, appear promising. For the various techniques requiring offspring inheritance of a trait, released males must successfully compete for mating partners against wildtype males. However, very little is known about mechanisms of mate selection in mosquitoes in general and in particular about potential correlations between mating...

Molecular assays of pollen use consistently reflect pollinator visitation patterns in a system of flowering plants

Aubrie James, Monica Geber & David Toews
Determining how pollinators visit plants versus how they carry and transfer pollen is an ongoing project in pollination ecology. The current tools for identifying the pollens that bees carry have different strengths and weaknesses when used for ecological inference. In this study we use three methods to better understand a system of congeneric, co-flowering plants in the genus Clarkia and their bee pollinators: observations of plant-pollinator contact in the field, and two different molecular methods...

Large herbivores suppress liana infestation in an African savanna

Tyler C. Coverdale, Ryan D. O'Connell, Matthew C. Hutchinson, Amanda Savagian, Tyler R. Kartzinel, Todd M. Palmer, Jacob R. Goheen, David J. Augustine, Mahesh Sankaran, Corina E. Tarnita & Robert M. Pringle
African savannas are the last stronghold of diverse large-mammal communities, and a major focus of savanna ecology is to understand how these animals affect the relative abundance of trees and grasses. However, savannas support diverse plant life-forms, and human-induced changes in large-herbivore assemblages—declining wildlife populations and their displacement by livestock—may cause unexpected shifts in plant community composition. We investigated how herbivory affects the prevalence of lianas (woody vines) and their impact on trees in an...

Proboscis curling in a pollinator causes extensive pollen movement and loss

Gordon Smith
1. Precise pollen placement on floral visitors can improve pollen transfer, but in many plant species, pollen is deposited onto the flexible proboscises of long-tongued insects. These proboscises are curled and uncurled between floral visits, potentially causing pollen to be lost or displaced. Rates of pollen movement and loss resulting from proboscis curling, and hence the potential quality of long-tongued insects as pollinators, are unknown. 2. Here we experimentally measure pollen loss and movement on...

A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations

Laxman Adhikari, Jesse Poland, Sandesh Shrestha, Shuanyge Wu, Jared Crain, Lianglian Gao, Byron Evers, Duane Wilson, Yoonha Ju, Dal-Hoe Koo, Pierre Hulc, Curtis Pozniak, Sean Walkowiak, Xiaoyun Wang, Jing Wu, Jeffrey Glaubitz, Lee DeHaan & Bernd Friebe
An optimized, high-throughput and cost-effective genotyping method applicable to various crop breeding populations is very important in this genomic era. We have developed an optimized Nextera skim-sequencing (skim-seq) approach to genotype different populations that can be used for genetics studies and genomics-assisted breeding. We performed skim-seq on a variety of populations developed through doubled haploid (DH) technology, inter-specific recombinants developed through introgression, amphidiploid developed through wide crosses, and on known monosomic samples. 1. A doubled...

Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization

Qing-Hui Sun, Diego F. Morales-Briones, Hong-Xin Wang, Jacob Landis, Jun Wen & Hua-Feng Wang
• Background and Aims Abelia (Caprifoliaceae) is a small genus with five species, including one man-made hybrid and several natural hybrids. The genus has a discontinuous distribution in Mainland China, the Taiwan Island, and the Ryukyu Islands, providing a model system to explore mechanisms of species dispersal in the East Asian flora. However, the current phylogenetic relationships within Abelia remain uncertain. • Methods In this study, we reconstructed the phylogenetic relationships within Abelia using nuclear...

Data from: Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize

Anju Giri, Merritt Burch, Edward Buckler & Guillaume Ramstein
Genomic prediction typically relies on associations between single-site polymorphisms and traits of interest. This representation of genomic variability has been successful for prediction within populations. However, it usually cannot capture the complex effects due to combination of alleles in haplotypes. Therefore, accuracy across populations has usually been low. Here we present a novel and cost-effective method for imputing cis haplotype associated RNA expression (HARE, RNA expression of genes by haplotype), studied their transferability across tissues,...

Sex-specific plasticity and the nutritional geometry of insulin-signaling gene expression in Drosophila melanogaster

Alexander Shingleton, Jeanne McDonald, Pegah Nabili, Lily Thorsen & Sohee Joen
Background Sexual-size dimorphism (SSD) is replete among animals, but while the selective pressures that drive the evolution of SSD have been well studied, the developmental mechanisms upon which these pressures act are poorly understood. Ours and others’ research has shown that SSD in D. melanogaster reflects elevated levels of nutritional plasticity in females versus males, such that SSD increases with dietary intake and body size, a phenomenon called sex-specific plasticity (SSP). Additional data indicate that...

Sex differences in the foraging behavior of a generalist hawkmoth

Gordon Smith
Within-species variation in pollinator behavior is widely observed, but itscauses have been minimally investigated. Pollinator sex is associated with large differ-ences in behavior that may lead to predictable differences in flower foraging, but thisexpectation has not been explicitly tested. We investigate sex-associated differences innectar-foraging behavior of the hawkmothHyles lineata, using pollen on the proboscisas a proxy for flower visitation. We tested two predictions emerging from the literature:(1) the sexes differ in the flower species they...

Comprehensive analysis of PPPCs family reveals the clinical significance of PPP1CA and PPP4C in breast cancer

Wenjun Xie, Ying Sun, Yu Zeng, Linfei Hu, Jingtai Zhi, Hang Ling, Xiangqian Zheng, Xianhui Ruan & Ming Gao
The phosphoprotein phosphatase catalytic subunit (PPPCs) family has been shown to play an important role in the development and progression of various malignancies, but its expression patterns and biological functions in breast cancer (BC) remain unclear. Therefore, we aimed to investigate the clinical significance and biological functions of the PPPCs family to understand its possible significance in the diagnosis, prognosis and treatment of breast cancer. We comprehensively investigated the expression levels, diagnostic accuracy, prognostic outcomes,...

Clinical significance of long noncoding RNA MNX1-AS1 in human cancers: a meta-analysis of cohort studies and bioinformatics analysis based on TCGA datasets

Kang Chen, Jian-Xin Gan, Ze-Ping Huang, Jun Liu & Hai-Peng Liu
MNX1-AS1 expression has been proposed to be abnormally upregulated in multiple human malignancies and be linked with the survival outcome of patients. However, relevant conclusions were yielded based on the limited samples. Therefore, we herein implemented a meta-analysis of the published cohort studies to further decipher the relationship of MNX1-AS1 level to prognosis and clinicopathological features in various cancers. Additionally, using The Cancer Genome Atlas (TCGA) datasets we carried out a bioinformatics analysis to make...

Clinical significance of long noncoding RNA MNX1-AS1 in human cancers: a meta-analysis of cohort studies and bioinformatics analysis based on TCGA datasets

Kang Chen, Jian-Xin Gan, Ze-Ping Huang, Jun Liu & Hai-Peng Liu
MNX1-AS1 expression has been proposed to be abnormally upregulated in multiple human malignancies and be linked with the survival outcome of patients. However, relevant conclusions were yielded based on the limited samples. Therefore, we herein implemented a meta-analysis of the published cohort studies to further decipher the relationship of MNX1-AS1 level to prognosis and clinicopathological features in various cancers. Additionally, using The Cancer Genome Atlas (TCGA) datasets we carried out a bioinformatics analysis to make...

Supporting Data for: Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae)

Norman Wickett, Lindsey Bechen, Geoffrey Broadhead, Rachel Levin, Rick Overson, Tania Jogesh, Jeremie Fant, Robert Raguso & Krissa Skogen
Background: Plant volatiles play an important role in both plant-pollinator and plant-herbivore interactions. Intraspecific polymorphisms in volatile production are ubiquitous, but studies that explore underlying differential gene expression are rare. Oenothera harringtonii populations are polymorphic in floral emission of the monoterpene (R)-(-)-linalool; some plants emit (R)-(-)-linalool (linalool+ plants) while others do not (linalool- plants). However, the genes associated with differential production of this floral volatile in Oenothera are unknown. We used RNA-Seq to broadly characterize...

Social Interaction and Pain Threshold in Virtual Reality

Andrea Stevenson Won, Swati Pandita & Kaylee Payne Kruzan
This experiment examined the effects of social presence and perceived location of a virtual environment on participants’ pain thresholds in a pre-registered, within-subjects experiment. First, we examined the effects of social interaction vs being alone in a virtual environment. Second, we compared a virtual environment representing a remote location to a replication of the lab environment. While the "location" of the virtual environment did affect social presence, such that participants reported greater social presence with...

Differential geographic patterns in song components of male Albert’s lyrebirds

Fiona Backhouse, Anastasia Dalziell, Robert Magrath, Aaron Rice, Taylor Crisologo & Justin Welbergen
Geographic variation in bird song has received much attention in evolutionary studies, yet few consider components within songs that may be subject to different constraints and follow different evolutionary trajectories. Here we quantify patterns of geographic variation in the socially-transmitted ‘whistle’ song of Albert’s lyrebirds (Menura alberti), an oscine passerine renowned for its remarkable vocal abilities. Albert’s lyrebirds are confined to narrow stretches of suitable habitat, allowing us to map likely paths of cultural transmission...

Did shell-crushing predators drive the evolution of ammonoid septal shape?

Erynn Johnson, Briana DiMarco, David Peterman, Aja Carter & Warren Allmon
For centuries, paleontologists have sought functional explanations for the uniquely complex internal walls (septa) of ammonoids, extinct shelled cephalopods. Ammonoid septa developed increasingly complex fractal margins, unlike any modern shell morphologies, throughout more than 300 million years of evolution. Some have suggested these morphologies provided increased resistance to shell-crushing predators. We perform the first physical compression experiments on model ammonoid septa using controlled, theoretical morphologies generated by computer-aided design and 3D printing. These biomechanical experiments...

Male-like female morphs in hummingbirds: the evolution of a widespread sex-limited plumage polymorphism

Eleanor Diamant, Jay J. Falk & Dustin R. Rubenstein
Differences in the way males and females look or behave are common in animals. However, discrete variation within sexes (sex-limited polymorphism) also occurs in several vertebrate and invertebrate lineages. In birds, female-limited polymorphism (FLP) in which some females resemble males in coloration is most prominent in hummingbirds, a group known for its morphological and behavioural sexual dimorphism. Yet, it remains unclear whether this intrasexual colour variation in hummingbirds arises through direct selection on females, or...

Bird Cams Lab Video Data

Rachael Mady, Peter Mason, Matthew Strimas-Mackey, Miyoko Chu, Tina Phillips, David Bonter, Charles Eldermire &

Registration Year

  • 2021

Resource Types

  • Dataset


  • Cornell University
  • Capital Medical University
  • Sun Yat-sen University
  • Shandong University
  • Xiamen University
  • Sichuan University
  • University of Florida
  • West China Hospital of Sichuan University
  • Tongren Hospital
  • Northeast Forestry University