379 Works

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...

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: 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: Preference for conspecifics evolves earlier in males than females in a sexually dimorphic radiation of fishes

Tamra C. Mendelson, Jennifer M. Gumm, Michael D. Martin & Patrick J. Ciccotto
Speciation by sexual selection is generally modeled as the co-evolution of female preferences and elaborate male ornaments leading to behavioral (sexual) reproductive isolation. One prediction of these models is that female preference for conspecific males should evolve earlier than male preference for conspecific females in sexually dimorphic species with male ornaments. We tested that prediction in darters, a diverse group of freshwater fishes with sexually dimorphic ornamentation. Focusing on the earliest stages of divergence, we...

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: Rare frost events reinforce tropical savanna-forest boundaries

William A. Hoffmann, Samuel W. Flake, Rodolfo C.R. Abreu, Natashi A.L. Pilon, Davi R. Rossatto, Giselda Durigan & Rodolfo C. R. Abreu
1) The ability of vegetation to ameliorate or exacerbate environmental extremes can generate feedbacks that mediate the distribution of biomes. It has been suggested that feedbacks between vegetation and frost damage may be important for maintaining savanna, particularly at the edge of the tropics. 2) We quantified frost damage and air temperature across a network of 30 permanent plots distributed across tropical savanna-forest boundaries in Brazil during an uncommonly hard frost. 3) Tree cover strongly...

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: Natural selection and repeated patterns of molecular evolution following allopatric divergence

Yibo Dong, Shichao Chen, Shifeng Cheng, Wenbin Zhou, Qing Ma, Zhiduan Chen, Cheng-Xin Fu, Xin Liu, Yun-Peng Zhao, Pamela S. Soltis, Gane Ka-Shu Wong, Douglas E. Soltis & Jenny Xiang
Background: Geographic speciation is a major force in generating biodiversity. However, how genomes diverge over time after geographic isolation has halted gene flow has remained unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) from transcriptomes in 20 allopatric species/variety pairs from diverse angiosperm clades. Sixteen of these pairs reflect the well-known eastern Asia – eastern North America floristic disjunction; these species have been isolated for different lengths of time, from the Miocene...

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: 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: 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: Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change.

Kaitlin C. Maguire, Douglas J. Shinneman, Kevin M. Potter & Valerie D. Hipkins
Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of...

Data from: Efficacy of Aedes aegypti control by indoor Ultra Low Volume (ULV) insecticide spraying in Iquitos, Peru

Christian E. Gunning, Kenichi Okamoto, Helvio Astete, Gissella M. Vasquez, Erik B. Erhardt, Clara Del Aguila, Raul Pinedo, Roldan Cardenas, Carlos Pacheco, Enrique Chalco, Hugo Rodriguez-Ferruci, Thomas W. Scott, Alun L. Lloyd, Fred Gould, Amy C. Morrison, Kenichi W. Okamoto & Erik Erhardt
Background: Aedes aegypti is a primary vector of dengue, chikungunya, Zika, and urban yellow fever viruses. Indoor, ultra low volume (ULV) space spraying with pyrethroid insecticides is the main approach used for Ae. aegypti emergency control in many countries. Given the widespread use of this method, the lack of large-scale experiments or detailed evaluations of municipal spray programs is problematic. Methodology/Principal Findings: Two experimental evaluations of non-residual, indoor ULV pyrethroid spraying were conducted in Iquitos,...

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: 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: 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...

Data from: Taxonomic resolution is a determinant of biodiversity effects in arbuscular mycorrhizal fungal communities

Haishui Yang, Qian Zhang, Roger T. Koide, Jason D. Hoeksema, Jianjun Tang, Xinmin Bian, Shuijin Hu & Xin Chen
Arbuscular mycorrhizal fungi (AMF) are key regulators of ecosystem processes, yet how their biodiversity works in ecosystems remains poorly understood. We documented the extent to which taxonomic resolution influenced the effect of biodiversity of AMF taxa on plant performance (growth, nutrient uptake and stress tolerance) in a meta-analysis of 902 articles. We found that the effect of biodiversity of AMF taxa depended on taxonomic resolution. Plant performance was positively promoted by AMF family richness, while...

Data from: Pre-infection effects of nectar secondary compounds on a bumble bee gut pathogen

Kristen Michaud, Rebecca Irwin, Nicholas Barber & Lynn Adler
Bumble bee pollinators can be exposed to pathogens when foraging on flowers previously visited by infected individuals. Infectious cells may be deposited in floral nectar, providing a site for pathogens to interact with nectar secondary compounds prior to infecting bees. Some nectar secondary compounds can reduce pathogen counts in infected bumble bees, but we know less about how exposure to these compounds directly affects pathogens prior to being ingested by their host. We exposed the...

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: Experimental evidence does not support the Habitat Amount Hypothesis

Nick M. Haddad, Andrew Gonzalez, Lars A. Brudvig, Melissa A. Burt, Douglas J. Levey & Ellen I. Damschen
For a half century, habitat configuration – the arrangement of habitat patches within a landscape – has been central to theories of landscape ecology, population dynamics, and community assembly, in addition to conservation strategies. A recent hypothesis advanced by Fahrig (2013) would, if supported, greatly diminish the relevance of habitat configuration as a predictor of diversity. The Habitat Amount Hypothesis posits that the sample area effect overrides patch size and patch isolation effects of habitat...

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: 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: 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: 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...

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