363 Works

Data from: Inducible versus constitutive social immunity: examining effects of colony infection on glucose oxidase and defensin-1 production in honeybees

Margarita M. López-Uribe, Andrea Fitzgerald & Michael Simone-Finstrom
Honeybees use a variety of defence mechanisms to reduce disease infection and spread throughout the colony. Many of these defences rely on the collective action of multiple individuals to prevent, reduce or eradicate pathogens—often referred to as ‘social immunity’. Glucose oxidase (GOX) and some antimicrobial peptides (e.g. defensin-1 or Def1) are secreted by the hypopharyngeal gland of adult bees on larval food for their antiseptic properties. Because workers secrete these compounds to protect larvae, they...

Data from: Rapid human-induced divergence of life-history strategies in Bahamian livebearing fishes (family Poeciliidae)

Rüdiger Riesch, Tara Easter, Craig A. Layman & Randall Brian Langerhans
1. Human-induced rapid environmental change (HIREC) can have dramatic impacts on ecosystems, leading to rapid trait changes in some organisms and extinction in others. Such changes in traits signify that human actions can lead to cases of increased phenotypic diversity and consequently can strongly impact population-, community- and ecosystem-level dynamics. 2. Here, we examine whether the ecological consequences of habitat fragmentation have led to changes in the life histories of three native species of mosquitofish...

Data from: Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing

Andrew L. Pais, Ross W. Whetten & Qiu-Yun Jenny Xiang
Discovering local adaptation, its genetic underpinnings, and environmental drivers is important for conserving forest species. Ecological genomic approaches coupled with next-generation sequencing are useful means to detect local adaptation and uncover its underlying genetic basis in nonmodel species. We report results from a study on flowering dogwood trees (Cornus florida L.) using genotyping by sequencing (GBS). This species is ecologically important to eastern US forests but is severely threatened by fungal diseases. We analyzed subpopulations...

Data from: Protein and carbohydrate intake influence sperm number and male fertility in male cockroaches but not sperm viability

Harriet Bunning, James Rapkin, Catharine Ruth Archer, Kim Jensen, John Hunt & Laurence Belcher
It is commonly assumed that because males produce many, tiny sperm, they are cheap to produce. Recent work, however, suggests that sperm production is not cost-free. If sperm are costly to produce, sperm number and/or viability should be influenced by diet, and this has been documented in numerous species. Yet few studies have examined the exact nutrients responsible for mediating these effects. Here, we quantify the effects of protein (P) and carbohydrate (C) intake on...

Data from: Allopolyploidy and the evolution of plant virus resistance

John W. Gottula, Ramsey Lewis, Seiya Saito & Marc Fuchs
Background: The relationship between allopolyploidy and plant virus resistance is poorly understood. To determine the relationship of plant evolutionary history and basal virus resistance, a panel of Nicotiana species from diverse geographic regions and ploidy levels was assessed for resistance to non-coevolved viruses from the genus Nepovirus, family Secoviridae. The heritability of resistance was tested in a panel of synthetic allopolyploids. Leaves of different positions on each inoculated plant were tested for virus presence and...

Data from: Phylogenetic structure and host abundance drive disease pressure in communities

Ingrid M. Parker, Megan Saunders, Megan Bontrager, Andrew P. Weitz, Rebecca Hendricks, Roger Magarey, Karl Suiter & Gregory S. Gilbert
Pathogens play an important part in shaping the structure and dynamics of natural communities, because species are not affected by them equally. A shared goal of ecology and epidemiology is to predict when a species is most vulnerable to disease. A leading hypothesis asserts that the impact of disease should increase with host abundance, producing a ‘rare-species advantage. However, the impact of a pathogen may be decoupled from host abundance, because most pathogens infect more...

Data from: Effects of plant functional group loss on soil biota and net ecosystem exchange: a plant removal experiment in the Mongolian grassland

Dima Chen, Qingmin Pan, Yongfei Bai, Shuijin Hu, Jianhui Huang, Qibing Wang, Shahid Naeem, James J. Elser, Jianguo Wu & Xingguo Han
1. The rapid loss of global biodiversity can greatly affect the functioning of above-ground components of ecosystems. However, how such biodiversity losses affect below-ground communities and linkages to soil carbon (C) sequestration is unclear. Here we describe how losses in plant functional groups (PFGs) affect soil microbial and nematode communities and net ecosystem exchange (NEE) in a 4-year removal experiment conducted on the Mongolian plateau, the world's largest remaining natural grassland. 2. Our results demonstrated...

Data from: Male courtship preference during seasonal sympatry may maintain population divergence

Abigail A. Kimmitt, Samantha L. Dietz, Dustin G. Reichard & Ellen D. Ketterson
Animal migration can lead to a population distribution known as seasonal sympatry, in which closely related migrant and resident populations of the same species co-occur in sympatry during part of the year, but are otherwise allopatric. During seasonal sympatry in early spring, residents may initiate reproduction before migrants depart, presenting an opportunity for gene flow. Differences in reproductive timing between migrant and resident populations may favor residents that exhibit preferences for potential mates of similar...

Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality

Mark C Harrison, Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Johannes Gowin, Carolin Greiner, Yi Han, Haofu Hu, Daniel S.T. Hughes, Ann-Kathrin Huylmans, Carsten Kemena, Lukas P.M. Kremer, Sandra L. Lee, Alberto Lopez-Ezquerra, Ludovic Mallet, Jose M. Monroy-Kuhn, Annabell Moser, Shwetha C. Murali, Donna M. Muzny … & Erich Bornberg-Bauer
Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects....

Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta

Maggie R. Wagner & Thomas Mitchell-Olds
Phenotypic plasticity is thought to impact evolutionary trajectories by shifting trait values in a direction that is either favored by natural selection (“adaptive plasticity”) or disfavored (“nonadaptive” plasticity). However, it is unclear how commonly each of these types of plasticity occurs in natural populations. To answer this question, we measured glucosinolate defensive chemistry and reproductive fitness in over 1,500 individuals of the wild perennial mustard Boechera stricta, planted in four common gardens across central Idaho,...

Data from: Best practices for justifying fossil calibrations

James F. Parham, Philip C. J. Donoghue, Christopher J. Bell, Tyler D. Calway, Jason J. Head, Patricia A. Holroyd, Jun G. Inoue, Randall B. Irmis, Walter G. Joyce, Daniel T. Ksepka, José S. L. Patané, Nathan D. Smith, James E. Tarver, Marcel Van Tuinen, Ziheng Yang, Kenneth D. Angielczyk, Jenny M. Greenwood, Christy A. Hipsley, Jacobs Louis, Peter J. Makovicky, Johannes Müller, Krister T. Smith, Jessica M. Theodor, Rachel C. M. Warnock, Michael J. Benton … & Louis Jacobs
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule; with replacement rates established (calibrated) using inaccurate paleontological age estimates...

Copper and zinc generated by the Aquascape IonGen pond clarifier system can be detrimental to koi (Cyprinus carpio) health

Emily Tucker, Jamie Gerlach, Azais Curtean, Kent Passingham, Lisa Murphy & Gregory Lewbart
BackgroundCopper is frequently used as an algicide, and copper ion generators such as the Aquascape IonGen claim to be safe for use in systems containing fish. In 2012, a die-off of koi (Cyprinus carpio) in a pond in Raleigh, North Carolina, occurred after the IonGen was added to the system.MethodsPhysical and postmortem examinations suggested that heavy metal toxicity was the likely cause of morbidity and mortality. This was supported by a heavy metal screening of...

The magnitude of large-scale tree mortality caused by the invasive pathogen Phytophthora ramorum

Richard Cobb, Sarah Haas, Nicholas Kruskamp, Whalen Dillon, Tedmund Swiecki, David Rizzo, Susan Frankel & Ross Meentemeyer
Forest pathogens are important drivers of tree mortality across the globe but it is exceptionally challenging to gather and build unbiased quantitative models of their impacts, which has resulted in few estimates matching the scale of disease. Here we harness the rare dataset matching the spatial scale of pathogen invasion, host, and disease heterogeneity to estimate infection and mortality for the four most susceptible host species of Phytophthora ramorum, an invasive pathogen that drives the...

A new pipeline for removing paralogs in target enrichment data

Wenbin Zhou, John Soghigian &
Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper...

Data From: Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae)

Xuankun Li, Luisa C. Teasdale, Keith M. Bayless, Allan G. Ellis, Brian M. Wiegmann, Carlos José E. Lamas, Christine L. Lambkin, Neal L. Evenhuis, James A. Nicholls, Diana Hartley, Seunggwan Shin, Michelle Trautwein, Andreas Zwick, Bryan D. Lessard & David K. Yeates
Bombyliidae is a very species-rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present-day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the...

Gestational Cd exposure in the CD-1 mouse induces sex-specific hepatic insulin insensitivity, obesity and metabolic syndrome in adult female offspring

Thomas Jackson, Garret Ryherd, Chris Scheibly, Aubrey Sasser, T. C. Guillette & Scott Belcher
There is compelling evidence that developmental exposure to some toxic metals increases risk for obesity and obesity-related morbidity including cardiovascular disease and type 2 diabetes in adults. To explore the hypothesis that developmental Cd exposure increased risk of obesity later in life, male and female CD-1 mice were maternally exposed to 500 ppb CdCl2 in drinking water during a human gestational equivalent period (GD0 - PND10). Hallmark indicators of metabolic disruption, hepatic steatosis, and metabolic...

Spine and dine: A key defensive trait promotes ecological success in spiny ants

Benjamin Blanchard, Akihiro Nakamura, Min Cao, Stephanie Chen & Corrie Moreau
A key focus of ecologists is explaining the origin and maintenance of morphological diversity and its association with ecological success. We investigate potential benefits and costs of a common and varied morphological trait, cuticular spines, for foraging behavior, interspecific competition, and predator-prey interactions in naturally co-occurring spiny ants (Hymenoptera: Formicidae: Polyrhachis) in an experimental setting. We expect that a defensive trait like spines might be associated with more conspicuous foraging, a greater number of workers...

Data from: A resurrection study reveals limited evolution of thermal performance in response to recent climate change across the geographic range of the scarlet monkeyflower

Rachel Wooliver & Seema Sheth
Evolutionary rescue can prevent populations from declining under climate change, and should be more likely at high-latitude, “leading” edges of species’ ranges due to greater temperature anomalies and gene flow from warm-adapted populations. Using a resurrection study with seeds collected before and after a seven-year period of record warming, we tested for thermal adaptation in the scarlet monkeyflower Mimulus cardinalis. We grew ancestors and descendants from northern-edge, central, and southern-edge populations across eight temperatures. Despite...

Supplementary information for: Using networks to identify structure in phylogenetic tree sets

Jeremy Brown, Melissa Marchand, Wen Huang, Guifang Zhou, Genevieve Mount, Jeremy Ash, Kyle Gallivan & James Wilgenbusch
Modern phylogenomic studies produce large sets of trees that can represent variation in inferred phylogenies across genes, uncertainty in estimated phylogenies for a given gene, or both. Standard practice is to condense this variation down to a small set of point estimates or consensus trees in order to facilitate display and interpretation. However, doing so results in the loss of enormous amounts of information about the structure of the underlying tree set. Here, we propose...

Detecting flying insects using car nets and DNA metabarcoding

Cecilie Svenningsen, Tobias Guldberg Frøslev, Jesper Bladt, Lene Bruhn Pedersen, Jonas Colling Larsen, Rasmus Ejrnæs, Camilla Fløjgaard, Anders Hansen, Jacob Heilmann-Clausen, Robert Dunn & Anders Tøttrup
Monitoring insects across space and time is challenging, due to their vast taxonomic and functional diversity. This study demonstrates how nets mounted on rooftops of cars (car nets) and DNA metabarcoding can be applied to sample flying insect richness and diversity across large spatial scales within a limited time period. During June 2018, 365 car net samples were collected by 151 volunteers during two daily time intervals on 218 routes in Denmark. Insect bulk samples...

Data from: Ecology of sleeping: the microbial and arthropod associates of chimpanzee beds

Megan S. Thoemmes, Fiona A. Stewart, R. Adriana Hernandez-Aguilar, Matthew A. Bertone, David A. Baltzegar, Russell J. Borski, Naomi Cohen, Kaitlin P. Coyle, Alexander K. Piel & Robert R. Dunn
The indoor environment created by the construction of homes and other buildings is often considered to be uniquely different from other environments. It is composed of organisms that are less diverse than those of the outdoors and strongly sourced by, or dependent upon, human bodies. Yet, no one has ever compared the composition of species found in contemporary human homes to that of other structures built by mammals, including those of non-human primates. Here we...

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas Buckley, Brett Calcott, Junqing Chen … & Xin Zhou
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight...

Data from: Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

W. Chris Funk, Robert E. Lovich, Paul A. Hohenlohe, Courtney A. Hofman, Scott A. Morrison, T. Scott Sillett, Cameron K. Ghalambor, Jesús E. Maldonado, Torben C. Rick, Mitch D. Day, Nicholas R. Polato, Sarah W. Fizpatrick, Timothy J. Coonan, Kevin R. Crooks, Adam Dillon, David K. Garcelon, Julie L. King, Christina L. Boser, Nicholas Gould, William F. Andelt & Sarah W. Fitzpatrick
The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each...

Data from: Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste

Stephanie L. Mathews, Mary J. Epps, Robert K. Blackburn, Michael B. Goshe, Amy M. Grunden & Robert R. Dunn
A citizen science project found that the greenhouse camel cricket (Diestrammena asynamora) is common in North American homes. Public response was to wonder “what good are they anyway?” and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for...

Data from: Genomics meets applied ecology: characterizing habitat quality for sloths in a tropical agroecosystem

Emily D. Fountain, Jung Koo Kang, Douglas J. Tempel, Per J. Palsbøll, Jonathan N. Pauli & M. Zachariah Peery
Understanding how habitat quality in heterogeneous landscapes governs the distribution and fitness of individuals is a fundamental aspect of ecology. While mean individual fitness is generally considered a key to assessing habitat quality, a comprehensive understanding of habitat quality in heterogeneous landscapes requires estimates of dispersal rates among habitat types. The increasing accessibility of genomic approaches, combined with field-based demographic methods, provides novel opportunities for incorporating dispersal estimation into assessments of habitat quality. In this...

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