210 Works

The value of increased spatial resolution of pesticide usage data for assessing risk to endangered species: Data, notebooks, and results

Erin Murphy, Steffen Eikenberry, Gwen Iacona, Greg Watson & Leah Gerber
Decision makers often cite data quality as a limitation in environmental management. Value of information approaches evaluates the benefit of new data collection for management outcomes. Pesticide exposure risk assessment for endangered species is one context where data limitations may affect decisions and a value of information type approach could be useful for identifying optimal data quality and resolution. Under the U.S. Federal Insecticide, Fungicide and Rodenticide Act, the U.S. Environmental Protection Agency (EPA) is...

Data from: Postglacial recolonisation in a cold climate specialist in Western Europe: patterns of genetic diversity in the adder (Vipera berus) support the central-marginal hypothesis

Sylvain Ursenbacher, Michaël Guillon, Hervé Cubizolle, Andréaz Dupoué, Gabriel Blouin-Demers & Olivier Lourdais
Understanding the impact of postglacial recolonization on genetic diversity is essential in explaining current patterns of genetic variation. The central–marginal hypothesis (CMH) predicts a reduction in genetic diversity from the core of the distribution to peripheral populations, as well as reduced connectivity between peripheral populations. While the CMH has received considerable empirical support, its broad applicability is still debated and alternative hypotheses predict different spatial patterns of genetic diversity. Using microsatellite markers, we analysed the...

Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

Arlin Stoltzfus, Brian O'Meara, Jamie Whitacre, Ross Mounce, Emily L. Gillespie, Sudhir Kumar, Dan F. Rosauer & Rutger A. Vos
BACKGROUND: Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote data sharing reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing phylogenetic trees and associated data in a way that promotes re-use. RESULTS: Here we summarize...

Data from: Linking a mutation to survival in wild mice

Rowan D. H. Barrett, Stefan Laurent, Ricardo Mallarino, Susanne P. Pfeifer, Charles C. Y. Xu, Matthieu Foll, Kazumasa Wakamatsu, Jonathan S. Duke-Cohan, Jeffrey D. Jensen & Hopi E. Hoekstra
Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underlying pigment locus, Agouti, by using experimental enclosures of mice on different soil colors. Next, we show how a mutation in Agouti associated with survival causes...

Data from: Regional paleoclimates and local consequences: Integrating GIS analysis of diachronic settlement patterns and process-based agroecosystem modeling of potential agricultural productivity in Provence (France)

Daniel Contreras, Eneko Hiriart, Alberte Bondeau, Alan Kirman, Joël Guiot, Loup Bernard, Romain Suarez, Sander Van Der Leeuw & Daniel A. Contreras
Holocene climate variability in the Mediterranean Basin is often cited as a potential driver of societal change, but the mechanisms of this putative influence are generally little explored. In this paper we integrate two tools - agro-ecosystem modeling of potential agricultural yields and spatial analysis of archaeological settlement pattern data - in order to examine the human consequences of past climatic changes. Focusing on a case study in Provence (France), we adapt an agro-ecosystem model...

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: Linking land use and the nutritional ecology of herbivores: a case study with the Senegalese locust

Marion Le Gall, Mira Word, Natalia Thompson, Balanding Manneh, Alioune Beye & Arianne Cease
1) Access to high-quality food is a main driver of population dynamics. For herbivores protein and carbohydrates are key nutrients that are notoriously variable in plants and are affected by land use. However, few studies have linked foraging decisions and performance in the laboratory to the nutritional landscape available in the field. 2) Oedaleus senegalensis is a nonmodel locust, a grass-feeder, and the main pest of millet, a subsistence crop in the Sahel. In this...

Data from: Age-based changes in kairomone response mediate task partitioning in stingless bee soldiers (Tetragonisca angustula)

Kaitlin Baudier, Meghan Bennett, Madeleine Ostwald, Sarah Hart, Theodore Pavlic & Jennifer Fewell
Collective defense is one of the most ubiquitous behaviors performed by social groups. Because of its importance, complex societies may engage a set of defensive specialists, with physical and/or neurological attributes tuned for defense against specific invaders. These strategies must be balanced, however, with the need to flexibly respond to different threat levels and sources. Insect societies rely heavily on olfaction for detecting and communicating in the context of defense. We therefore asked whether threat...

Data from: Foraging zebra finches (Taeniopygia guttata) are public information users rather than conformists

Edwin J. C. Van Leeuwen, Thomas Morgan & Katharina Riebel
Social learning enables adaptive information acquisition provided that it is not random but selective. To understand species typical decision-making and to trace the evolutionary origins of social learning, the heuristics social learners use need to be identified. Here, we experimentally tested the nature of majority influence in the zebra finch. Subjects simultaneously observed two demonstrator groups differing in relative and absolute numbers (ratios 1:2 / 2:4 / 3:3 / 1:5) foraging from two novel food...

Data from: Computed tomography shows high fracture prevalence among physically active forager-horticulturalists with high fertility

Jonathan Stieglitz, Benjamin C. Trumble, Study Team HORUS, Caleb Finch, Dong Li, Matthew J. Budoff, Hillard Kaplan & Michael Gurven
Modern humans have more fragile skeletons than other hominins, which may result from physical inactivity. Here we test whether reproductive effort also compromises bone strength, by measuring using computed tomography thoracic vertebral bone mineral density (BMD) and fracture prevalence among physically active Tsimane forager-horticulturalists. Earlier onset of reproduction and shorter interbirth intervals are associated with reduced BMD for women. Tsimane BMD is lower versus Americans, but only for women, contrary to simple predictions relying on...

Data from: Nitrogen fertilizer decreases survival and reproduction of female locusts by increasing plant protein to carbohydrate ratio

Marion Le Gall, Mira Word, Natalia Thompson, Alioune Beye & Arianne Cease
1. Nitrogen limitation theory predicts that terrestrial plants should benefit from nitrogen inputs and that herbivores should benefit from subsequent higher plant protein contents. While this pattern has generally been supported, some herbivorous insects have shown preference and higher performance on low protein (p), high carbohydrate (c) diets as juveniles. 2. However, little is known about the effects on reproduction in adults. Using nitrogen fertilizer, we demonstrate that high plant p:c has negative effects on...

Data for: Landscape scale variation in the hydrologic niche of California coast redwood

Emily J. Francis, Gregory P. Asner, Katharine J. Mach & Christopher B. Field
Topoclimatic diversity within forest landscapes can underlie variation in water availability, which may correspond to patterns in habitat suitability of tree species with differing hydrologic niches. However, the trade-off between the collection of data at a fine grain size over large spatial extents has limited comprehensive analyses of landscape scale variation in habitat suitability. We present a fine scale analysis of the roles of topographic gradients in moisture availability, soil water storage, and fog frequency...

Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution

Ana Y. Morales-Arce, Rebecca Harris, Anne Stone & Jeffrey Jensen
The within-host evolutionary dynamics of TB remain unclear, and underlying biological characteristics render standard population genetic approaches based upon the Wright-Fisher model largely inappropriate. In addition, the compact genome combined with an absence of recombination is expected to result in strong purifying selection effects. Thus, it is imperative to establish a biologically-relevant evolutionary framework incorporating these factors in order to enable an accurate study of this important human pathogen. Further, such a model is critical...

Phylogenomic species delimitation in the ants of the Temnothorax salvini Group (Hymenoptera: Formicidae): An integrative approach

Matthew Prebus
The members of the Temnothorax salvini species group are rarely collected, arboreally nesting ants of Central American forests. Previously thought to consist of two broadly dispersed species, recent collections have revealed a diversity of specimens that defy the two-species salvini group concept, but these are difficult to distinguish from each other based solely on morphology. I contrast several model-based approaches to species delimitation based on target-enriched genomic data. With molecular data from thousands of ultraconserved...

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...

Data from: Adaptive multi-degree of freedom Brain Computer Interface using online feedback: Towards novel methods and metrics of mutual adaptation between humans and machines for BCI.

Chuong H Nguyen, George K Karavas & Panagiotis Artemiadis
This paper proposes a novel adaptive online-feedback methodology for Brain Computer Interfaces (BCI). The method uses ElectroEncephaloGraphic (EEG) signals and combines motor with speech imagery to allow for tasks that involve multiple degrees of freedom (DoF). The main approach utilizes the covariance matrix descriptor as feature, and the Relevance Vector Machines (RVM) classifier. The novel contributions include, (1) a new method to select representative data to update the RVM model, and (2) an online classifier...

Data from: Social learning and the replication process: an experimental investigation

Maxime Derex, Romain Feron, Bernard Godelle & Michel Raymond
Human cultural traits typically result from a gradual process that has been described as analogous to biological evolution. This observation has led pioneering scholars to draw inspiration from population genetics to develop a rigorous and successful theoretical framework of cultural evolution. Social learning, the mechanism allowing information to be transmitted between individuals, has thus been described as a simple replication mechanism. Although useful, the extent to which this idealization appropriately describes the actual social learning...

Data from: Recurrent sublethal warming reduces embryonic survival, inhibits juvenile growth, and alters species distribution projections under climate change

Michael A. Carlo, Eric A. Riddell, Ofir Levy & Michael W. Sears
The capacity to tolerate climate change often varies across ontogeny in organisms with complex life cycles. Recently developed species distribution models incorporate traits across life stages; however, these life-cycle models primarily evaluate effects of lethal change. Here, we examine impacts of recurrent sublethal warming on development and survival in ecological projections of climate change. We reared lizard embryos in the laboratory under temperature cycles that simulated contemporary conditions and warming scenarios. We also artificially warmed...

Data from: Strategic use of affiliative vocalizations by wild female baboons

Joan B. Silk, Robert M. Seyfarth & Dorothy L. Cheney
Although vocal production in non-human primates is highly constrained, individuals appear to have some control over whether to call or remain silent. We investigated how contextual factors affect the production of grunts given by wild female chacma baboons, Papio ursinus, during social interactions. Females grunted as they approached other adult females 28% of the time. Supporting previous research, females were much more likely to grunt to mothers with young infants than to females without infants....

Data from: Refinement of a theoretical trait space for North American trees via environmental filtering

Michael Fell & Kiona Ogle
We refer to a theoretical trait space (TTS) as an n-dimensional hypervolume (“hypercube”) characterizing the range of values and covariations among multiple functional traits, in the absence of explicit filtering mechanisms. We previously constructed a 32-dimensional TTS for North American trees by fitting the Allometrically Constrained Growth and Carbon Allocation (ACGCA) model to USFS Forest Inventory and Analysis (FIA) data. Here, we sampled traits from this TTS, representing different individual “trees,” and subjected these trees...

Data from: Colony personality and plant health in the Azteca-Cecropia mutualism

Peter R. Marting, William T. Wcislo & Stephen C. Pratt
For interspecific mutualisms, the behavior of one partner can influence the fitness of the other, especially in the case of symbiotic mutualisms where partners live in close physical association for much of their lives. Behavioral effects on fitness may be particularly important if either species in these long-term relationships displays personality. We conducted a field study on collective personality in Azteca constructor colonies that live in Cecropia trees, one of the most successful and prominent...

Data from: The distribution of plants and seed dispersers in response to habitat fragmentation in an artificial island archipelago

Jiajia Liu, Ferry Slik, David Coomes, Richard T. Corlett, Yanping Wang, Maxwell Wilson, Guang Hu, Ping Ding & Mingjian Yu
Aim: Small, old-growth forest fragments generally have more small-seeded plants than large patches, due to the disappearance of large seed dispersing vertebrates. This pattern may differ for secondary forest fragments where differential migration ability rather than persistence of seed dispersers may be driving plant community assembly. In this paper, we investigated the effect of habitat fragmentation on seed dispersers and plant community structure in regenerating forests. Location: The Thousand Island Lake, China. Taxon: Plants, birds...

Data from: The role of continental shelf width in determining freshwater phylogeographic patterns in southeastern Australian pygmy perches (Teleostei: Percichthyidae)

Peter J. Unmack, Michael P. Hammer, Mark Adams, Jerald B. Johnson & Thomas E. Dowling
Biogeographic patterns displayed by obligate freshwater organisms are intimately related to the nature and extent of connectivity between suitable habitats. Two of the more significant barriers to freshwater connections are seawater and major drainage divides. South-eastern Australia provides a contrast between these barriers as it has discrete areas that are likely influenced to a greater or lesser extent by each barrier type. We use continental shelf width as a proxy for the potential degree of...

Data from: Social costs enforce honesty of a dynamic signal of motivation

Russell A. Ligon & Kevin J. McGraw
Understanding the processes that promote signal reliability may provide important insights into the evolution of diverse signaling strategies among species. The signals that animals use to communicate must comprise mechanisms that prohibit or punish dishonesty, and social costs of dishonesty have been demonstrated for several fixed morphological signals (e.g. color badges of birds and wasps). The costs maintaining the honesty of dynamic signals, which are more flexible and potentially cheatable, are unknown. Using an experimental...

Data from: Long-term effect of yolk carotenoid levels on testis size in a precocial bird

Mathieu Giraudeau, Ann-Kathrin Ziegler & Barbara Tschirren
Conditions experienced during prenatal development can have long-lasting organizational effects on offspring. Maternal carotenoids deposited in the eggs of birds and other oviparous species play an important role during fast embryonic growth and chick development through their antioxidant properties. However, the long-term consequences of variation in maternal carotenoid transfer for the offspring have seldom been considered. Since plasma carotenoid levels at adulthood are known to influence testis size and yolk carotenoid levels influence the ability...

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