21 Works

Data from: Forensic genomics as a novel tool for identifying the causes of mass mortality events

Pierre De Wit, Laura Rogers-Bennett, Raphael M. Kudela & Stephen R. Palumbi
Toxic spills, hypoxia, disease outbreaks and toxin-producing algal blooms are all possible causes of mass mortality events, but in many cases it can be difficult to pinpoint the cause of death. Here we present a new approach that we name ‘forensic genomics’, combining field surveys, toxin testing and genomic scans. Forensic genomics queries allele frequencies of surviving animals for signatures of agents causing mass mortality and, where genetic diversity is high, is uniquely suited to...

Data from: Phylogenetic signal in extinction selectivity in Devonian terebratulide brachiopods

Paul G. Harnik, Paul C. Fitzgerald, Jonathan L. Payne & Sandra J. Carlson
Determining which biological traits affect taxonomic durations is critical for explaining macroevolutionary patterns. Two approaches are commonly used to investigate the associations between traits and durations and/or extinction and origination rates: analyses of taxonomic occurrence patterns in the fossil record and comparative phylogenetic analyses, predominantly of extant taxa. By capitalizing upon the empirical record of past extinctions, paleontological data avoid some of the limitations of existing methods for inferring extinction and origination rates from molecular...

Data from: Rapid evolution of adaptive niche construction in experimental microbial populations

Benjamin J. Callahan, Tadashi Fukami & Daniel S. Fisher
Many species engage in adaptive niche construction: modification of the local environment that increases the modifying organism's competitive fitness. Adaptive niche construction provides an alternative pathway to higher fitness, shaping the environment rather than conforming to it. Yet, experimental evidence for the evolutionary emergence of adaptive niche construction is lacking, leaving its role in evolution uncertain. Here we report a direct observation of the de novo evolution of adaptive niche construction in populations of the...

Data from: Novel interactions between non-native mammals and fungi facilitate establishment of invasive pines

Jamie R. Wood, Ian A. Dickie, Holly V. Moeller, Duane A. Peltzer, Karen I. Bonner, Gaye Rattray & Janet M. Wilmshurst
1. The role of novel ecological interactions between mammals, fungi and plants in invaded ecosystems remains unresolved, but may play a key role in the widespread successful invasion of pines and their ectomycorrhizal fungal associates, even where mammal faunas originate from different continents to trees and fungi as in New Zealand. 2. We examine the role of novel mammal associations in dispersal of ectomycorrhizal fungal inoculum of North American pines (Pinus contorta, Pseudotsuga menziesii), and...

Data from: Thermal stress and predation risk trigger distinct transcriptomic responses in the intertidal snail Nucella lapillus

Nathaniel D. Chu, Luke P. Miller, Stefan T. Kaluziak, Geoffrey C. Trussell & Steven V. Vollmer
Thermal stress and predation risk have profound effects on rocky shore organisms, triggering changes in their feeding behaviour, morphology and metabolism. Studies of thermal stress have shown that underpinning such changes in several intertidal species are specific shifts in gene and protein expression (e.g. upregulation of heat-shock proteins). But relatively few studies have examined genetic responses to predation risk. Here, we use next-generation RNA sequencing (RNA-seq) to examine the transcriptomic (mRNA) response of the snail...

Data from: Experimental defaunation of terrestrial mammalian herbivores alters tropical rain forest understory diversity

Angela A. Camargo-Sanabria, Eduardo Mendoza, Roger Guevara, Miguel Martínez-Ramos & Rodolfo Dirzo
It has been suggested that tropical defaunation may unleash community-wide cascading effects, leading to reductions in plant diversity. However, experimental evidence establishing cause–effect relationships thereof is poor. Through a 5 year exclosure experiment, we tested the hypothesis that mammalian defaunation affects tree seedling/sapling community dynamics leading to reductions in understorey plant diversity. We established plot triplets (n = 25) representing three defaunation contexts: terrestrial-mammal exclosure (TE), medium/large mammal exclosure (PE) and open access controls (C)....

Data from: Identifying multiple coral reef regimes and their drivers across the Hawaiian archipelago

Jean-Baptiste Jouffray, Magnus Nyström, Albert V. Norström, Ivor D. Williams, Lisa M. Wedding, John N. Kittinger & Gareth J. Williams
Loss of coral reef resilience can lead to dramatic changes in benthic structure, often called regime shifts, which significantly alter ecosystem processes and functioning. In the face of global change and increasing direct human impacts, there is an urgent need to anticipate and prevent undesirable regime shifts and, conversely, to reverse shifts in already degraded reef systems. Such challenges require a better understanding of the human and natural drivers that support or undermine different reef...

Data from: Plant-derived differences in the composition of aphid honeydew and their effects on colonies of aphid-tending ants

Elizabeth G. Pringle, Alexandria Novo, Ian Ableson, Raymond V. Barbehenn & Rachel L. Vannette
In plant–ant–hemipteran interactions, ants visit plants to consume the honeydew produced by phloem-feeding hemipterans. If genetically based differences in plant phloem chemistry change the chemical composition of hemipteran honeydew, then the plant's genetic constitution could have indirect effects on ants via the hemipterans. If such effects change ant behavior, they could feed back to affect the plant itself. We compared the chemical composition of honeydews produced by Aphis nerii aphid clones on two milkweed congeners,...

Data from: Building the graph of medicine from millions of clinical narratives

Samuel G. Finlayson, Paea LePendu & Nigam H. Shah
Electronic health records (EHR) represent a rich and relatively untapped resource for characterizing the true nature of clinical practice and for quantifying the degree of inter-relatedness of medical entities such as drugs, diseases, procedures and devices. We provide a unique set of co-occurrence matrices, quantifying the pairwise mentions of 3 million terms mapped onto 1 million clinical concepts, calculated from the raw text of 20 million clinical notes spanning 19 years of data. Co-frequencies were...

Data from: Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila

Alan O. Bergland, Emily L. Behrman, Katherine R. O'Brien, Paul S. Schmidt & Dmitri A. Petrov
In many species, genomic data have revealed pervasive adaptive evolution indicated by the fixation of beneficial alleles. However, when selection pressures are highly variable along a species' range or through time adaptive alleles may persist at intermediate frequencies for long periods. So called “balanced polymorphisms” have long been understood to be an important component of standing genetic variation, yet direct evidence of the strength of balancing selection and the stability and prevalence of balanced polymorphisms...

Data from: Patterns of variation during adaptation in functionally linked loci

Diamantis Sellis & Mark D. Longo
An understanding of the distribution of natural patterns of genetic variation is relevant to such fundamental biological fields as evolution and development. One recent approach to understanding such patterns has been to focus on the constraints which may arise as a function of the network or pathway context in which genes are embedded. Despite theoretical expectations of higher evolutionary constraint for genes encoding upstream versus downstream enzymes in metabolic pathways, empirical results have varied. Here...

Data from: Pollination mitigates cucumber yield gaps more than pesticide and fertilizer use in tropical smallholder gardens

Iris Motzke, Teja Tscharntke, Thomas C. Wanger & Alexandra-Maria Klein
1. Pollination can be an essential but often neglected ecosystem service to mitigate crop yield gaps. Pollination services are usually studied in isolation and their relative role and possible interactions with other factors, such as major management practices, is little understood. 2. We tested how pollination (insect versus wind- and self-pollination) interacts with weed control, fertilization, and insect herbivore control and how these factors as well as flower-visiting bees influence fruit set and yield of...

Data from: Assortative social learning and its implications for human (and animal?) societies

Edith Katsnelson, Arnon Lotem & Marcus W. Feldman
Choosing from whom to learn is an important element of social learning. It affects learner success and the profile of behaviors in the population. Because individuals often differ in their traits and capabilities, their benefits from different behaviors may also vary. Homophily, or assortment, the tendency of individuals to interact with other individuals with similar traits, is known to affect the spread of behaviors in humans. We introduce models to study the evolution of assortative...

Data from: Pinus ponderosa alters nitrogen dynamics and diminishes the climate footprint in natural ecosystems of Patagonia

Laura J. T. Hess & Amy T. Austin
1. Evaluating climate effects on plant-soil interactions in terrestrial ecosystems remains challenging due to the fact that floristic composition co-varies with climate, particularly along rainfall gradients. It is difficult to separate effects of precipitation per se from those mediated indirectly through changes in species composition. As such, afforestation (the intentional planting of woody species) in terrestrial ecosystems provides an ecological opportunity to assess the relative importance of climate and vegetation controls on ecosystem processes. 2....

Data from: Loss of avian phylogenetic diversity in neotropical agricultural systems

Luke O. Frishkoff, Daniel S. Karp, Leithen K. M'Gonigle, Chase D. Mendenhall, Jim Zook, Claire Kremen, Elizabeth A. Hadly & Gretchen C. Daily
Habitat conversion is the primary driver of biodiversity loss, yet little is known about how it is restructuring the tree of life by favoring some lineages over others. We combined a complete avian phylogeny with 12 years of Costa Rican bird surveys (118,127 detections across 487 species) sampled in three land uses: forest reserves, diversified agricultural systems, and intensive monocultures. Diversified agricultural systems supported 600 million more years of evolutionary history than intensive monocultures but...

Data from: A highly pleiotropic amino acid polymorphism in the Drosophila insulin receptor contributes to life history adaptation

Annalise B. Paaby, Alan O. Bergland, Emily L. Behrman & Paul S. Schmidt
Finding the specific nucleotides that underlie adaptive variation is a major goal in evolutionary biology, but polygenic traits pose a challenge because the complex genotype-phenotype relationship can obscure the effects of individual alleles. However, natural selection working in large wild populations can shift allele frequencies and indicate functional regions of the genome. Previously, we showed that the two most common alleles of a complex amino acid insertion-deletion polymorphism in the Drosophila insulin receptor show independent,...

Data from: Gene duplication in an African cichlid adaptive radiation

Heather E. Machado, Ginger Jui, Domino A. Joyce, Christian R. L. Reilly, David H. Lunt & Suzy C. P. Renn
Background: Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; however, the relative importance of this process remains to be determined. The explosive divergence of the African cichlid adaptive radiations provides both a model for studying the general role of gene duplication in the divergence of lineages and also an exciting foray into the identification of genomic features that underlie the dramatic phenotypic and ecological diversification in this...

Data from: Strong coupling of plant and fungal community structure across western Amazonian rainforests

Kabir G. Peay, Christopher Baraloto & Paul V. A. Fine
The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across...

Data from: Fast and cost-effective genetic mapping in apple using next-generation sequencing

Kyle M. Gardner, Thomas F. Cooke, Patrick J. Brown, Scott Cann, Fabrizio Costa, Carlos D. Bustamante, Riccardo Velasco, Michela Troggio, Sean Myles, P. Brown & C. Bustamante
Next-generation DNA sequencing (NGS) produces vast amounts of DNA sequence data, but it is not specifically designed to generate data suitable for genetic mapping. Recently developed DNA library preparation methods for NGS have helped solve this problem, however, by combining the use of reduced representation libraries with DNA sample barcoding to generate genome-wide genotype data from a common set of genetic markers across a large number of samples. Here we use such a method, called...

Data from: Degree of glutathione deficiency and redox imbalance depend on subtype of mitochondrial disease and clinical status

Gregory M. Enns, Tereza Moore, Anthony Le, Kondala Atkuri, Monisha K. Shah, Kristina Cusmano-Ozog, Anna-Kaisa Niemi & Tina M. Cowan
Mitochondrial disorders are associated with decreased energy production and redox imbalance. Glutathione plays a central role in redox signaling and protecting cells from oxidative damage. In order to understand the consequences of mitochondrial dysfunction on in vivo redox status, and to determine how this varies by mitochondrial disease subtype and clinical severity, we used a sensitive tandem mass spectrometry assay to precisely quantify whole blood reduced (GSH) and oxidized (GSSG) glutathione levels in a large...

Data from: Context-dependent effects of large wildlife declines on small mammal communities in central Kenya

Hillary S. Young, Douglas J. McCauley, Rodolfo Dirzo, Jacob R. Goheen, Bernard Agwanda, Cara Brook, Erik O. Castillo, Adam W. Ferguson, Stephen N. Kinyua, Molly M. McDonough, Todd M. Palmer, Robert M. Pringle, Truman P. Young & Kristofer M. Helgen
Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife...

Registration Year

  • 2014

Resource Types

  • Dataset


  • Stanford University
  • University of Pennsylvania
  • University of California, Berkeley
  • University of California, Davis
  • University of Buenos Aires
  • Reed College
  • Lincoln University
  • Princeton University
  • Royal Swedish Academy of Sciences
  • University of Michigan-Ann Arbor