170 Works

Data from: Relative importance of competition and plant-soil feedback, their synergy, context dependency and implications for coexistence

Ylva Lekberg, James D. Bever, Rebecca A. Bunn, Ray M. Callaway, Miranda M. Hart, Stephanie N. Kivlin, John Klironomos, Beau G. Larkin, John L. Maron, Kurt O. Reinhart, Michael Remke, Wim H. Van Der Putten & Ragan M. Callaway
Plants interact simultaneously with each other and with soil biota, yet the relative importance of competition versus plant soil feedback (PSF) on plant performance is poorly understood. Using a meta-analysis of 38 published studies and 150 plant species, we show that effects of interspecific competition (either growing plants with a competitor or singly, or comparing inter- vs. intraspecific competition) and PSF (comparing home vs. away soil, live vs. sterile soil, or control vs. fungicide-treated soil)...

Data from: Substantial differences in bias between single-digest and double-digest RAD-seq libraries: a case study

Sarah P. Flanagan & Adam G. Jones
The trade‐offs of using single‐digest vs. double‐digest restriction site‐associated DNA sequencing (RAD‐seq) protocols have been widely discussed. However, no direct empirical comparisons of the two methods have been conducted. Here, we sampled a single population of Gulf pipefish (Syngnathus scovelli) and genotyped 444 individuals using RAD‐seq. Sixty individuals were subjected to single‐digest RAD‐seq (sdRAD‐seq), and the remaining 384 individuals were genotyped using a double‐digest RAD‐seq (ddRAD‐seq) protocol. We analysed the resulting Illumina sequencing data and...

Data from: Weather-driven dynamics in a dual-migrant system: moths and bats

Jennifer J. Krauel, John K. Westbrook & Gary F. McCracken
Animal migrations generate large spatial and temporal fluctuations in biomass that provide a resource base for many predator-prey interactions. These interactions are often driven by continent-scale weather patterns and are difficult to study. Few studies have included migratory animals on more than a single trophic level or for periods spanning multiple entire seasons. We tracked migrations of three species of agricultural pest noctuid moths over the 2010-2012 autumn seasons as the moths traveled past a...

Data from: Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave

Hengfu Yin, Hao-Bo Guo, David J. Weston, Anne M. Borland, Priya Ranjan, Paul E. Abraham, Sara S. Jawdy, James Wachira, Gerald A. Tuskan, Timothy J. Tschaplinski, Stan D. Wullschleger, Hong Guo, Robert L. Hettich, Stephen Gross, Zhong Wang, Axel Visel & Xiaohan Yang
Background: Crassulacean acid metabolism (CAM) enhances plant water-use efficiency through an inverse day/night pattern of stomatal closure/opening that facilitates nocturnal CO2 uptake. CAM has evolved independently in over 35 plant lineages, accounting for ~ 6% of all higher plants. Agave species are highly heat- and drought-tolerant, and have been domesticated as model CAM crops for beverage, fiber, and biofuel production in semi-arid and arid regions. However, the genomic basis of evolutionary innovation of CAM in...

Data from: Overall seed dispersal effectiveness is lower in endemic Trillium species than in their widespread congeners

Chelsea Nicole Miller & Charles Kwit
PREMISE OF THE STUDY: Comparing ecological attributes of endemic species with related, widespread species can reveal differences accounting for rarity. Forests of the southeastern US are home to many range-restricted endemic and widespread species of Trillium, a genus of ant-dispersed herbs. Evidence suggests that aspects of seed-related life history stages are often correlated with plant rarity, but few studies have tested whether the process of seed dispersal differs for endemic and widespread species. To address...

Data from: Acoustic adaptation to city noise through vocal learning by a songbird

Dana Lynn Moseley, Graham Earnest Derryberry, Jennifer Nicole Phillips, Julie Elizabeth Danner, Raymond Michael Danner, David Andrew Luther & Elizabeth Perrault Derryberry
Anthropogenic noise imposes novel selection pressures, especially on species that communicate acoustically. Many animals – including insects, frogs, whales, and birds – produce sounds at higher frequencies in areas with low-frequency noise pollution. Although there is support for animals changing their vocalizations in real time in response to noise (i.e., immediate flexibility), other evolutionary mechanisms for animals that learn their vocalizations remain largely unexplored. We hypothesize that cultural selection for signal structures less masked by...

Data from: Do constructional constraints influence cyprinid (Cyprinidae: Leuciscinae) craniofacial coevolution?

C Darrin Hulsey & Phillip R Hollingsworth
Constraints on form may determine how organisms diversify. As a result of competition for the limited space within the body, investment in adjacent structures could represent an evolutionary compromise. For example, evolutionary trade-offs resulting from limited space in the head could have influenced how the sizes of the jaw muscle, as well as the eyes, evolved in North American cyprinid fishes. To test the evolutionary independence of the size of these structures, we measured the...

Data from: Ancestral polyploidy in seed plants and angiosperms

Yuannian Jiao, Norman J. Wickett, Ayyampalayam Saravanaraj, André S. Chanderbali, Lena Landherr, Paula E. Ralph, Lynn P. Tomsho, Yi Hu, Haiying Liang, Pamela S. Sotis, Douglas E. Soltis, Sandra W. Clifton, Scott E. Schlarbaum, Stephan C. Schuster, Hong Ma, Jim Leebens-Mack & Claude W. DePamphilis
Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms1, 2, 3, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications4, 5, 6, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive...

Data from: Mitochondrial genome primers for Lake Malawi cichlids

C. Darrin Hulsey, Hugo Alamillo, Benjamin P. Keck & Brian C. O'Meara
Resolving the evolutionary history of rapidly diversifying lineages like the Lake Malawi Cichlid Flock demands powerful phylogenetic tools. Although this clade of over 500 species of fish likely diversified in less than two million years, the availability of extensive sequence data sets, such as complete mitochondrial genomes, could help resolve evolutionary patterns in this group. Using a large number of newly developed primers, we generated whole mitochondrial genome sequences for 14 Lake Malawi cichlids. We...

Data from: Morphometric investigation of the Pentremites fauna from the Glen Dean Formation, Kentucky

James W. Atwood & Colin D. Sumrall
New techniques involving three-dimensional (3D) data collection and landmark analysis provide an opportunity to make breakthroughs in understanding blastoid morphology. This pilot study examines four species (Pentremites pyriformis, P. tulipiformis, P. fredericki n. sp., and P. meganae n. sp.), using 3D morphological variation and geometric morphometrics to discriminate between species. All specimens were collected from a single shale unit within the Upper Mississippian Glen Dean Formation near Hopkinsville, Kentucky. A 3D laser scanner was used...

Data from: Water stress strengthens mutualism among ants, trees, and scale insects

Elizabeth G. Pringle, Erol Akçay, Ted K. Raab, Rodolfo Dirzo & Deborah M. Gordon
Abiotic environmental variables strongly affect the outcomes of species interactions. For example, mutualistic interactions between species are often stronger when resources are limited. The effect might be indirect: water stress on plants can lead to carbon stress, which could alter carbon-mediated plant mutualisms. In mutualistic ant–plant symbioses, plants host ant colonies that defend them against herbivores. Here we show that the partners' investments in a widespread ant–plant symbiosis increase with water stress across 26 sites...

Data from: More than meets the eye? the role of annual ornamental flowers in supporting pollinators

Emily Erickson, S Adam, L Russo, V Wojcik, H M Patch & C M Grozinger
Ornamental flowers are commonly planted in urban and suburban areas to provide foraging resources for pollinator populations. However, their role in supporting broad pollinator biodiversity is not well established as previous studies have been conducted in urban landscapes with pollinator communities that are distinct from those in natural systems. We observed pollinator visitation patterns to five ornamental annual plant genera and their cultivars over multiple years at two semi-natural sites in Pennsylvania to understand their...

Data from: Ancient, but not recent, population declines have had a genetic impact on alpine yellow-bellied toad populations, suggesting potential for complete recovery

Luca Cornetti, Andrea Benazzo, Sean M. Hoban, Cristiano Vernesi, Giorgio Bertorelle & Sean Hoban
Reduction in population size and local extinctions have been reported for the yellow-bellied toad, Bombina variegata, but the genetic impact of this is not yet known. In this study, we genotyped 200 individuals, using mtDNA cytochrome b and 11 nuclear microsatellites. We investigated fine-scale population structure and tested for genetic signatures of historical and recent population decline, using several statistical approaches, including likelihood methods and approximate Bayesian computation. Five major genetically divergent groups were found,...

Intraspecific variation in symbiont density in an insect-microbe symbiosis

Benjamin Parker, Jan Hrcek, Ailsa McLean, Charles Godfray & Jennifer Brisson
Many insects host vertically-transmitted microbes, which can confer benefits to their hosts but are costly to maintain and regulate. A key feature of these symbioses is variation: for example, symbiont density can vary among host and symbiont genotypes. However, the evolutionary forces maintaining this variation remain unclear. We studied variation in symbiont density using the pea aphid (Acyrthosiphon pisum) and the bacterium Regiella insecticola, a symbiont that can protect its host against fungal pathogens. We...

Putative resistance and tolerance mechanisms have little impact on disease progression for an emerging salamander pathogen

Mark Wilber, Edward Carter, Matthew Gray & Cheryl Briggs
1. Resistance and tolerance are unique host defense strategies that can limit the impacts of a pathogen on a host. However, for most wildlife-pathogen systems there are still fundamental uncertainties regarding 1) how changes in resistance and tolerance can affect disease outcomes and 2) the mechanisms underlying resistance and tolerance in host populations. 2. Here, we first compared observed patterns of resistance and tolerance and their effects on disease outcomes among salamander species that are...

Data from: A parametric method for assessing diversification rate variation in phylogenetic trees

Premal Shah, Benjamin Minault Fitzpatrick & James Andrew Fordyce
Phylogenetic hypotheses are frequently used to examine variation in rates of diversification across the history of a group. Patterns of diversification-rate variation can be used to infer underlying ecological and evolutionary processes responsible for patterns of cladogenesis. Most existing methods examine rate variation through time. Methods for examining differences in diversification among groups are more limited. Here we present a new method, parametric rate comparison (PRC), that explicitly compares diversification rates among lineages in a...

Data from: The adaptive value of gluttony: predators mediate the life history trade-offs of satiation threshold

Jonathan N Pruitt & Jennifer J Krauel
Animals vary greatly in their tendency to consume large meals. Yet, whether or how meal size influences fitness in wild populations is infrequently considered. Using a predator exclusion, marked-recapture experiment, we estimated selection on the amount of food accepted during an ad libitum feeding bout (hereafter termed "satiation threshold") in the wolf spider Schizocosa ocreata. Individually marked, size-matched females of known satiation threshold were assigned to predator exclusion and predator inclusions treatments and tracked for...

Data from: Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

Thomas J. Near, Alex Dornburg, Ron I. Eytan, Benjamin P. Keck, W. Leo Smith, Kristen L. Kuhn, Jon A. Moore, Samantha A. Price, Frank T. Burbrink, Matt Friedman & Peter C. Wainwright
Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the “bush at...

Data from: Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

Matt Friedman, Benjamin P. Keck, Alex Dornburg, Ron I. Eytan, Christopher H. Martin, C. Darrin Hulsey, Peter C. Wainwright & Thomas J. Near
Cichlid fishes are a key model system in the study of adaptive radiation, speciation and evolutionary developmental biology. More than 1600 cichlid species inhabit freshwater and marginal marine environments across several southern landmasses. This distributional pattern, combined with parallels between cichlid phylogeny and sequences of Mesozoic continental rifting, has led to the widely accepted hypothesis that cichlids are an ancient group whose major biogeographic patterns arose from Gondwanan vicariance. Although the Early Cretaceous (ca 135...

Data from: Male mealworm beetles increase resting metabolic rate under terminal investment

Indrikis A. Krams, Tatjana Krama, Fhionna R. Moore, Inese Kivleniece, Aare Kuusik, Todd M. Freeberg, Raivo Mänd, M. J. Rantala, Janina Daukšte & Marika Mänd
Harmful parasite infestation can cause energetically costly behavioural and immunological responses, with the potential to reduce host fitness and survival. It has been hypothesized that the energetic costs of infection cause resting metabolic rate (RMR) to increase. Furthermore, under terminal investment theory, individuals exposed to pathogens should allocate resources to current reproduction when life expectancy is reduced, instead of concentrating resources on an immune defence. In this study, we activated the immune system of Tenebrio...

Data from: Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome

Nathan P. McNulty, Wu Meng, Alison R. Erickson, Chongle Pan, Brian K. Erickson, Eric C. Martens, Nicholas A. Pudlo, Brian D. Muegge, Bernard Henrissat, Robert L. Hettich, Jeffrey I. Gordon & Meng Wu
The human gut microbiota is an important metabolic organ. However, little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In the current study, gnotobiotic mice colonized with a simplified model microbiota composed of 12 sequenced human gut bacterial species were fed oscillating diets of disparate composition. Rapid, reproducible and reversible changes in community structure were observed. Time series microbial RNA-Seq analyses revealed...

Data from: Effects of climatic and geological processes during the Pleistocene on the evolutionary history of the northern cavefish, Amblyopsis spelaea (Teleostei: Amblyopsidae)

Matthew Lance Niemiller, James R. McCandless, Robert Graham Reynolds, James Caddle, Thomas J. Near, Christopher R. Tillquist, William D. Pearson & Benjamin Minault Fitzpatrick
Climatic and geological processes associated with glaciation cycles during the Pleistocene have been implicated in influencing patterns of genetic variation and promoting speciation of temperate flora and fauna. However, determining the factors promoting divergence and speciation is often difficult in many groups because of our limited understanding of potential vicariant barriers and connectivity between populations. Pleistocene glacial cycles are thought to have significantly influenced the distribution and diversity of subterranean invertebrates; however, impacts on subterranean...

Data from: Unraveling the determinants of insular body size shifts

Craig R. McClain, Paul A. P. Durst, Alison G. Boyer & Clinton D. Francis
The island rule, a pattern of size shifts on islands, is an oft-cited but little understood phenomenon of evolutionary biology. Here we explore the evolutionary mechanisms behind the rule in 184 mammal species, testing climatic, ecological, and phylogenetic hypotheses in a robust quantitative framework. Our findings confirm the importance of species’ ecological traits in determining both the strength and the direction of body size changes on islands. Although the island rule pattern appears relatively weak...

Data from: A combined morphometric and phylogenetic revision of the late Ordovician brachiopod genera Eochonetes and Thaerodonta

Jennifer E. Bauer & Alycia L. Stigall
Systematic revision of the Late Ordovician brachiopod genera Eochonetes Reed, 1917 and Thaerodonta Wang, 1949 was conducted utilizing specimen-based morphometric and species-level phylogenetic analyses. Previous studies had recognized Thaerodonta and Eochonetes as either distinct taxonomic entities or synonyms. New multivariate and phylogenetic analyses confirm the synonymy of Thaerodonta with Eochonetes and provide a framework to assess evolutionary and ecological patterns within the clade. Multivariate analyses were employed to delineate species in morphospace and provided information...

Data from: Landscape and environmental influences on Mycobacterium ulcerans distribution among aquatic sites in Ghana

Shannon M. Pileggi, Heather Jordan, Julie A. Clennon, Ellen Whitney, M. Eric Benbow, Richard Merritt, Mollie McIntosh, Ryan Kimbirauskas, Pamela Small, Daniel Boayke, Charles Quaye, Jiaguo Qi, Lindsay Campbell, Jenni Gronseth, Edwin Ampadu, William Opare, Lance Waller, Lance A. Waller & Daniel Boakye
Buruli ulcer, caused by Mycobacterium ulcerans, is highly endemic in West Africa. While the mode of transmission is unknown, many studies associate Buruli ulcer with different types of water exposure. We present results from the largest study to date to test for M. ulcerans in aquatic sites and identify environmental attributes associated with its presence. Environmental samples from 98 aquatic sites in the Greater Accra, Ashanti, and Volta regions of Ghana were tested for the...

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