390 Works

Data from: Contemporary evolution of plant growth rate following experimental removal of herbivores

Nash E. Turley, Walter C. Odell, Hanno Schaefer, Georg Everwand, Michael J. Crawley & Marc T. J. Johnson
Herbivores are credited with driving the evolutionary diversification of plant defensive strategies over macroevolutionary time. For this to be true, herbivores must also cause short-term evolution within plant populations, but few studies have experimentally tested this prediction. We addressed this gap using a long-term manipulative field experiment where exclosures protected 22 plant populations from natural rabbit herbivory for <1 to 26 years. We collected seeds of Rumex acetosa L. (Polygonaceae) from our plots and grew...

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...

Data from: Evidence that Egfr contributes to cryptic genetic variation for photoreceptor determination in natural populations of Drosophila melanogaster

Ian Dworkin, Arnar Palsson, Kelli Birdsall & Greg Gibson
One objective of quantitative genetics is to identify the nucleotide variants within genes that contribute to phenotypic variation and susceptibility [1]. In an evolutionary context, this means characterizing the molecular polymorphisms that modify the penetrance and expressivity of perturbed traits. A survey of association between 267 SNPs in almost 11 kb of the D. melanogaster Egfr and the degree of eye roughening due to a gain-of-function EgfrE1 allele crossed into 210 isogenic wild-type lines provides...

Data from: Wing patterning gene redefines the mimetic history of Heliconius butterflies

Heather M. Hines, Brian A. Counterman, Riccardo Papa, Priscila Albuquerque De Moura, Marcio Z. Cardoso, Mauricio Linares, James Mallet, Robert D. Reed, Chris D. Jiggins, Marcus R. Kronforst & W. Owen McMillan
The mimetic butterflies Heliconius erato and H. melpomene have undergone parallel radiations to form a near-identical patchwork of over 20 different wing pattern races across the Neotropics. Previous molecular phylogenetic work on these radiations has suggested that similar but geographically disjunct color patterns arose multiple times independently in each species. The neutral markers used in these studies, however, can move freely across color pattern boundaries and therefore might not represent the history of the adaptive...

Data from: Fossil grebes from the Truckee Formation (Miocene) of Nevada and a new phylogenetic analysis of Podicipediformes (Aves)

Daniel T. Ksepka, Amy M. Balanoff, Michael A. Bell & Michel D. Houseman
Podicipediformes is a cosmopolitan clade of foot-propelled diving birds that, despite inhabiting marine and lacustrine environments, have a poor fossil record. In this contribution, we describe three new grebe fossils from the diatomite beds of the Late Miocene Truckee Formation (10.2 ± 0.2 Ma) of Nevada (USA). Two postcranial skeletons and an associated set of wing elements indicate that at least two distinct grebe species occupied the large, shallow Lake Truckee during the Miocene. Phylogenetic...

Data from: Are shy individuals less behaviorally variable? Insights from a captive population of mouse lemurs

Jennifer L. Verdolin & John Harper
Increasingly, individual variation in personality has become a focus of behavioral research in animal systems. Boldness and shyness, often quantified as the tendency to explore novel situations, are seen as personality traits important to the fitness landscape of individuals. Here we tested for individual differences within and across contexts in behavioral responses of captive mouse lemurs (Microcebus murinus) to novel objects, novel foods, and handling. We report consistent differences in behavioral responses for objects and...

Data from: Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies

Sagar M. Utturkar, Dawn M. Klingeman, José M. Bruno-Barcena, Mari S. Chinn, Amy M. Grunden, Michael Köpke & Steven D. Brown
During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig...

Data from: Diet specialization in an extreme omnivore: nutritional regulation in glucose-averse German cockroaches

Jonathan Z. Shik, Coby Schal & Jules Silverman
Organisms have diverse adaptations for balancing dietary nutrients, but often face trade-offs between ingesting nutrients and toxins in food. While extremely omnivorous cockroaches would seem excluded from such dietary trade-offs, German cockroaches (Blattella germanica) in multiple populations have rapidly evolved a unique dietary specialization – an aversion to glucose, the phagostimulant in toxic baits used for pest control. We used factorial feeding experiments within the geometric framework to test whether glucose-averse (GA) cockroaches with limited...

Data from: Size, sex, and individual-level behavior drive intra-population variation in cross-ecosystem foraging of a top-predator

James C. Nifong, Craig A. Layman & Brian R. Silliman
1. Large-bodied, top-predators are often highly mobile, with the potential to provide important linkages between spatially distinct food webs. What biological factors contribute to variation in cross-ecosystem movements, however, have rarely been examined. 2. Here, we investigated how ontogeny (body size), sex, and individual-level behavior impacts intra-population variation in cross-ecosystem foraging (i.e., between freshwater and marine systems), by the top-predator Alligator mississippiensis. 3. Field surveys revealed A. mississippiensis uses marine ecosystems regularly and are abundant...

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: Host association drives significant genetic divergence in the bed bug, Cimex lectularius

Warren Booth, Ondřej Balvín, Edward L. Vargo, Jitka Vilímová & Coby Schal
Genetic differentiation may exist among sympatric populations of a species due to long-term associations with alternative hosts (i.e., host-associated differentiation). While host-associated differentiation has been documented in several phytophagus insects, there are far fewer cases known in animal parasites. The bed bug, Cimex lectularius, a wingless insect, represents a potential model organism for elucidating the processes involved in host-associated differentiation in animal parasites with relatively limited mobility. In conjunction with the expansion of modern humans...

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: Global genetic analysis reveals the putative native source of the invasive termite, Reticulitermes flavipes, in France

Elfie Perdereau, Anne-Geneviève Bagnères-Urbany, Stephanie Bankhead-Dronnet, Simon Dupont, Marie Zimmermann, Edward L. Vargo & Franck Dedeine
Biological invasions are recognized as a major threat to both natural and managed ecosystems. Phylogeographic and population genetic analyses can provide information about the geographical origins and patterns of introduction and explain the causes and mechanisms by which introduced species have become successful invaders. Reticulitermes flavipes is a North American subterranean termite that has been introduced into several areas, including France where introduced populations have become invasive. To identify likely source populations in the USA...

Data from: Assessing gene-environment interactions for common and rare variants with binary traits using gene-trait similarity regression

Guolin Zhao, Rachel Marceau, Daowen Zhang, Jung-Ying Tzeng & J.-Y. Tzeng
Accounting for gene-environment (GxE) interactions in complex trait association studies can facilitate our understanding of genetic heterogeneity under different environmental exposures, improve the ability to discover susceptible genes that exhibit little marginal effect, provide insight into the biological mechanisms of complex diseases, help to identify high-risk subgroups in the population, and uncover hidden heritability. However, significant GxE interactions can be difficult to find. The sample sizes required for sufficient power to detect association are much...

Data from: Assessment of coyote-wolf-dog admixture using ancestry-informative diagnostic SNPs

Javier Monzón, Roland Kays & Daniel E. Dykhuizen
The evolutionary importance of hybridization as a source of new adaptive genetic variation is rapidly gaining recognition. Hybridization between coyotes and wolves may have introduced adaptive alleles into the coyote gene pool that facilitated an expansion in their geographic range and dietary niche. Furthermore, hybridization between coyotes and domestic dogs may facilitate adaptation to human-dominated environments. We genotyped 63 ancestry-informative single nucleotide polymorphisms in 427 canids in order to examine the prevalence, spatial distribution, and...

Data from: Importance of deep water uptake in tropical eucalypt forest

Mathias Christina, Yann Nouvellon, Jean-Paul Laclau, Jose L. Stape, Jean-Pierre Bouillet, George R. Lambais & Guerric Le Maire
Climate models predict that the frequency, intensity and duration of drought events will increase in tropical regions. Although water withdrawal from deep soil layers is generally considered to be an efficient adaptation to drought, there is little information on the role played by deep roots in tropical forests. Tropical Eucalyptus plantations managed in short rotation cycles are simple forest ecosystems that may provide an insight into the water use by trees in tropical forests. The...

Data from: Extremophile Poeciliidae: multivariate insights into the complexity of speciation along replicated ecological gradients

Rüdiger Riesch, Michael Tobler, Hannes Lerp, Jonas Jourdan, Tess Doumas, Patrik Nosil, R. Brian Langerhans & Martin Plath
Background: Replicate population pairs that diverge in response to similar selective regimes allow for an investigation of (a) whether phenotypic traits diverge in a similar and predictable fashion, (b) whether there is gradual variation in phenotypic divergence reflecting variation in the strength of natural selection among populations, (c) whether the extent of this divergence is correlated between multiple character suites (i.e., concerted evolution), and (d) whether gradual variation in phenotypic divergence predicts the degree of...

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: Little evidence for morphological change in a resilient endemic species following the introduction of a novel predator

Diana M. T. Sharpe, R. Brian Langerhans, Etienne Low-Décarie & Lauren J Chapman
Human activities, such as species introductions, are dramatically and rapidly altering natural ecological processes, and often result in novel selection regimes. To date, we still have a limited understanding of the extent to which such anthropogenic selection may be driving contemporary phenotypic change in natural populations. Here we test whether the introduction of the piscivorous Nile perch, Lates niloticus, into East Africa's Lake Victoria and nearby lakes coincided with morphological change in one resilient native...

Data from: Disruption of endosperm development is a major cause of hybrid seed inviability between Mimulus guttatus and Mimulus nudatus

Elen Oneal, John H. Willis & Robert G. Franks
Divergence of developmental mechanisms within populations could lead to hybrid developmental failure, and might be a factor driving speciation in angiosperms. We investigate patterns of endosperm and embryo development in Mimulus guttatus and the closely related, serpentine endemic Mimulus nudatus, and compare them to those of reciprocal hybrid seed. We address whether disruption in hybrid seed development is the primary source of reproductive isolation between these sympatric taxa. M. guttatus and M. nudatus differ in...

Data from: Reduced cellular immune response in social insect lineages

Margarita M. López-Uribe, Warren B. Sconiers, Steven D. Frank, Robert R. Dunn & David R. Tarpy
Social living poses challenges for individual fitness because of the increased risk of disease transmission among conspecifics. Despite this challenge, sociality is an evolutionarily successful lifestyle, occurring in the most abundant and diverse group of organisms on earth—the social insects. Two contrasting hypotheses predict the evolutionary consequences of sociality on immune systems. The social group hypothesis posits that sociality leads to stronger individual immune systems because of the higher risk of disease transmission in social...

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: 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: Grouping substitution types into different relaxed molecular clocks

Hui-Jie Lee, Hirohisa Kishino, Nicolas Rodrigue & Jeffrey L. Thorne
Different types of nucleotide substitutions experience different patterns of rate change over time. We propose clustering context-dependent (or context-independent) nucleotide substitution types according to how their rates change and then using the grouping for divergence time estimation. With our models, relative rates among types that are in the same group are fixed, whereas absolute rates of the types within a group change over time according to a shared relaxed molecular clock. We illustrate our procedure...

Data from: Does hunting or hiking affect wildlife communities in protected areas?

Roland Kays, Arielle W. Parsons, Megan C. Baker, Ellizabeth L. Kalies, Tavis Forrester, Robert Costello, Christopher T. Rota, Joshua J. Millspaugh & William J. McShea
Managed public wild areas have dual mandates to protect biodiversity and provide recreational opportunities for people. These goals could be at odds if recreation, ranging from hiking to legal hunting, disrupts wildlife enough to alter their space use or community structure. We evaluated the effect of managed hunting and recreation on 12 terrestrial wildlife species by employing a large citizen science camera trapping survey at 1947 sites stratified across different levels of human activities in...

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