32 Works

Data from: Diversification practices reduce organic to conventional yield gap

Lauren C. Ponisio, Leithen K. M'Gonigle, Kevi C. Mace, Jenny Palomino, Perry De Valpine, Claire Kremen, P. De Valpine, C. Kremen, L. K. M'Gonigle, K. C. Mace, J. Palomino & L. C. Ponisio
Agriculture today places great strains on biodiversity, soils, water and the atmosphere, and these strains will be exacerbated if current trends in population growth, meat and energy consumption, and food waste continue. Thus, farming systems that are both highly productive and minimize environmental harms are critically needed. How organic agriculture may contribute to world food production has been subject to vigorous debate over the past decade. Here, we revisit this topic comparing organic and conventional...

Data from: Sequence Capture using PCR-generated Probes (SCPP): a cost-effective method of targeted high-throughput sequencing for non-model organisms

Joshua V. Peñalba, Lydia L. Smith, Maria A. Tonione, Chodon Sass, Sarah M. Hykin, Phillip L. Skipwith, James A. McGuire, Rauri C. K. Bowie, Craig Moritz & Jimmy A. McGuire
Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of non-model organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes (SCPP) protocol requires no specialized...

Data from: Monocyte recruitment to the dermis and differentiation to dendritic cells increases the targets for Dengue virus replication

Michael A. Schmid & Eva Harris
Dengue virus (DENV) causes the most prevalent arthropod-borne viral disease in humans. Although Aedes mosquitoes transmit DENV when probing for blood in the skin, no information exists on DENV infection and immune response in the dermis, where the blood vessels are found. DENV suppresses the interferon response, replicates, and causes disease in humans but not wild-type mice. Here, we used mice lacking the interferon-α/β receptor (Ifnar–/–), which had normal cell populations in the skin and...

Data from: The trouble with triplets in biodiversity informatics: a data-driven case against current identifier practices

Robert Guralnick, Tom Conlin, John Deck, Brian Stucky, Nico Cellinese & Brian J. Stucky
The biodiversity informatics community has discussed aspirations and approaches for assigning globally unique identifiers (GUIDs) to biocollections for nearly a decade. During that time, and despite misgivings, the de facto standard identifier has become the “Darwin Core Triplet”, which is a concatenation of values for institution code, collection code, and catalog number associated with biocollections material. Our aim is not to rehash the challenging discussions regarding which GUID system in theory best supports the biodiversity...

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: 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: Assembly of root-associated bacteria communities: interactions between abiotic and biotic factors

Sarah L. Dean, Emily C. Farrer, Andrea Porras-Alfaro, Katharine N. Suding, Robert L. Sinsabaugh, Sarah L Dean, Robert L Sinsabaugh, Emily C Farrer & Katharine N Suding
Nitrogen (N) deposition in many areas of the world is over an order of magnitude greater than it would be in absence of human activity. We ask how abiotic (N) and biotic (plant host and neighborhood) effects interact to influence root-associated bacterial (RAB) community assembly. Using 454 pyrosequencing, we examined RAB communities from two dominant alpine tundra plants, Geum rossii and Deschampsia cespitosa, under control, N addition and D. cespitosa removal treatments, implemented in a...

Data from: Rapid diversification of sexual signals in Hawaiian Nesosydne planthoppers (Hemiptera: Delphacidae): the relative role of neutral and selective forces

Kari Roesch Goodman, J. Patrick Kelley, Stephen Welter, George K. Roderick, Damian O. Elias, S. C. Welter, J. P. Kelley, K. R. Goodman, G. K. Roderick & D. O. Elias
Changes in sexual signals have the potential to promote rapid divergence and reproductive isolation among populations of animals. Thus, identifying processes contributing to variation in signals is key to understanding the drivers of speciation. However, it is difficult to identify the processes initiating changes in signals in empirical systems because (1) the demographic history of populations under study is usually unclear, and (2) there is no unified hypothesis-testing framework for evaluating the simultaneous contribution of...

Data from: Crossing the line: increasing body size in a trans-Wallacean lizard radiation (Cyrtodactylus, Gekkota)

Paul M. Oliver, Phillip Skipwith, Michael S. Y. Lee, M. S. Y. Lee, P. M. Oliver & P. Skipwith
The region between the Asian and Australian continental plates (Wallacea) demarcates the transition between two differentiated regional biotas. Despite this striking pattern, some terrestrial lineages have successfully traversed the marine barriers of Wallacea and subsequently diversified in newly colonized regions. The hypothesis that these dispersals between biogeographic realms are correlated with detectable shifts in evolutionary trajectory has however rarely been tested. Here, we analyse the evolution of body size in a widespread and exceptionally diverse...

Data from: Spatially heterogeneous impact of climate change on small mammals of montane California

Kevin C. Rowe, Karen M. C. Rowe, Morgan W. Tingley, Michelle S. Koo, James L. Patton, Christopher J. Conroy, John D. Perrine, Steven R. Beissinger, Craig Moritz, S. R. Beissinger, C. J. Conroy, M. S. Koo, J. L. Patton, M. W. Tingley, C. Moritz, J. D. Perrine, K. C. Rowe & K. M. C. Rowe
Resurveys of historical collecting localities have revealed range shifts, primarily leading edge expansions, which have been attributed to global warming. However, there have been few spatially replicated community-scale resurveys testing whether species' responses are spatially consistent. Here we repeated early twentieth century surveys of small mammals along elevational gradients in northern, central and southern regions of montane California. Of the 34 species we analysed, 25 shifted their ranges upslope or downslope in at least one...

Data from: Phosphoprotein SAK1 is a regulator of acclimation to singlet oxygen in Chlamydomonas reinhardtii

Setsuko Wakao, Brian L. Chin, Krishna K. Niyogi, Heidi K. Ledford, David Casero, Matteo Pellegrini, Rachel M. Dent, Sabeeha S. Merchant, Krishna K Niyogi, Sabeeha S Merchant, Brian L Chin, Heidi K Ledford & Rachel M Dent
Singlet oxygen is a highly toxic and inevitable byproduct of oxygenic photosynthesis. The unicellular green alga Chlamydomonas reinhardtii is capable of acclimating specifically to singlet oxygen stress, but the retrograde signaling pathway from the chloroplast to the nucleus mediating this response is unknown. Here we describe a mutant, singlet oxygen acclimation knocked-out 1 (sak1), that lacks the acclimation response to singlet oxygen. Analysis of genome-wide changes in RNA abundance during acclimation to singlet oxygen revealed...

Data from: The utility of normalized difference vegetation index for predicting African buffalo forage quality

Sadie J. Ryan, Paul C. Cross, John Winnie, Craig Hay, Justin Bowers & Wayne M. Getz
Many studies of mammalian herbivores have employed remotely sensed vegetation greenness, in the form of Normalized Difference Vegetation Index (NDVI) as a proxy for forage quality. The assumption that reflected greenness represents forage quality often goes untested, and limited data exist on the relationships between remotely sensed and traditional forage nutrient indicators. We provide the first study connecting NDVI and forage nutrient indicators within a free-ranging African herbivore ecosystem. We examined the relationships between fecal...

Data from: Nonlinear thermal gradients shape broad-scale patterns in geographic range size and can reverse Rapoport’s rule

Adam Tomasovych, David Jablonski, Sarah K. Berke, Andrew Z. Krug & James W. Valentine
Aim: Species living at latitudes that have greater annual temperature variations are expected to achieve broader geographic ranges than species living at latitudes that have smaller annual temperature variations, generating a positive relationship between range size and latitude (Rapoport's rule). However, this prediction fails to take into account the greater latitudinal extent of tropical temperatures relative to those at higher latitudes. Here we model the contributions of the broader latitudinal extent of equal-temperature habitats at...

Data from: Evidence for ecological divergence across a mosaic of soil types in an Amazonian tropical tree: Protium subserratum (Burseraceae)

Tracy M. Misiewicz & Paul V. A. Fine
Soil gradients are known to be an important driver of divergent natural selection in plant populations. Neotropical trees have the highest diversity on earth and it is not uncommon to find soil specialist congeners distributed parapatrically. Nevertheless very little is known about the role that edaphic heterogeneity plays in the origin and maintenance of tropical tree diversity. We predict that the mosaic of different soils in the lowland Amazon rainforest play a major role in...

Data from: Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria

Alexandra Calteau, David P. Fewer, Amel Latifi, Thérèse Coursin, Thierry Laurent, Jouni Jokela, Cheryl A. Kerfeld, Kaarina Sivonen, Jörn Piel & Muriel Gugger
Background: Cyanobacteria are an ancient lineage of photosynthetic bacteria from which hundreds of natural products have been described, including many notorious toxins but also potent natural products of interest to the pharmaceutical and biotechnological industries. Many of these compounds are the products of non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways. However, current understanding of the diversification of these pathways is largely based on the chemical structure of the bioactive compounds, while the evolutionary...

Data from: Parasite-mediated selection drives an immunogenetic tradeoff in plains zebras (Equus quagga)

Pauline L. Kamath, Wendy C. Turner, Martina Küsters, Wayne M. Getz, W. M. Getz & W. C. Turner
Pathogen evasion of the host immune system is a key force driving extreme polymorphism in genes of the major histocompatibility complex (MHC). Although this gene family is well characterized in structure and function, there is still much debate surrounding the mechanisms by which MHC diversity is selectively maintained. Many studies have investigated relationships between MHC variation and specific pathogens, and have found mixed support for and against the hypotheses of heterozygote advantage, frequency-dependent or fluctuating...

Data from: Novel trophic niches drive variable progress toward ecological speciation within an adaptive radiation of pupfishes

Christopher H. Martin & Laura C. Feinstein
Adaptive radiation is recognized by a rapid burst of phenotypic, ecological, and species diversification. However, it is unknown whether different species within an adaptive radiation evolve reproductive isolation at different rates. We compared patterns of genetic differentiation among nascent species within an adaptive radiation of Cyprinodon pupfishes using genotyping by sequencing. Similar to classic adaptive radiations, this clade exhibits rapid morphological diversification rates and two species are novel trophic specialists, a scale-eater and hard-shelled prey...

Data from: Drosophila embryogenesis scales uniformly across temperature in developmentally diverse species

Steven Gregory Kuntz, Michael B. Eisen & Steven G. Kuntz
Temperature affects both the timing and outcome of animal development, but the detailed effects of temperature on the progress of early development have been poorly characterized. To determine the impact of temperature on the order and timing of events during Drosophila melanogaster embryogenesis, we used time-lapse imaging to track the progress of embryos from shortly after egg laying through hatching at seven precisely maintained temperatures between 17.5°C and 32.5°C. We employed a combination of automated...

Data from: Species distribution models of an endangered rodent offer conflicting measures of habitat quality at multiple scales

William T. Bean, R. Stafford, H. Scott Butterfield, Laura R. Prugh, Michael Westphal & Justin S. Brashares
1. The high cost of directly measuring habitat quality has led ecologists to test alternate methods for estimating and predicting this critically important ecological variable. In particular, it is frequently assumed but rarely tested that models of habitat suitability (“species distribution models”, SDMs) may provide useful indices of habitat quality, either from an individual animal or manager’s perspective. Critically, SDMs are increasingly used to estimate species’ ranges, with an implicit assumption that areas of high...

Data from: Fatal attraction: vegetation responses to nutrient inputs attract herbivores to infectious anthrax carcass sites

Wendy C. Turner, Kyrre L. Kausrud, Yathin S. Krishnappa, Joris P. G. M. Cromsigt, Holly H. Ganz, Isaac Mapaure, Claudine C. Cloete, Zepee Havarua, Martina Küsters, Wayne M. Getz, Nils Chr. Stenseth, K. L. Kausrud, Y. S. Krishnappa, W. C. Turner, J. P. G. M. Cromsigt, H. H. Ganz, W. M. Getz, C. C. Cloete, Z. Havarua & I. Mapaure
Parasites can shape the foraging behaviour of their hosts through cues indicating risk of infection. When cues for risk co-occur with desired traits such as forage quality, individuals face a trade-off between nutrient acquisition and parasite exposure. We evaluated how this trade-off may influence disease transmission in a 3-year experimental study of anthrax in a guild of mammalian herbivores in Etosha National Park, Namibia. At plains zebra (Equus quagga) carcass sites we assessed (i) carcass...

Data from: Shifting habitats, morphology and selective pressures: developmental polyphenism in an adaptive radiation of Hawaiian spiders

Michael S. Brewer, Rebecca Alice Carter, Peter J. P. Croucher, Rosemary G. Gillespie & Rebecca A. Carter
Particularly intriguing examples of adaptive radiation are those in which lineages show parallel or convergent evolution, suggesting utilization of similar genetic or developmental pathways. The current study focuses on an adaptive radiation of Hawaiian “spiny-leg” spiders in which diversification is associated with repeated convergent evolution leading to similar sets of ecomorphs on each island. However, two species on the oldest islands in the archipelago exhibit variability, occurring as two different ecomorphs. More derived species on...

Data from: Community assembly and functional diversity along succession post-management

Radika Bhaskar, Todd E. Dawson & Patricia Balvanera
1. Despite extensive development of successional theory, few empirical studies have evaluated whether existing models are applicable to human-modified landscapes. Seasonally dry tropical forests are experiencing widespread transformation, and represent a critical system to assess in a successional framework to infer the mechanisms that shape assembly of secondary forests post-management. 2. We used a functional trait-based approach to assess changes in community assembly mechanisms along succession in secondary dry forests of varying stages following abandonment...

Data from: Muscle tradeoffs in a power-amplified prey capture system

S. N. Patek, M. Mendoza Blanco & M. Mendoza Blanco
Should animals operating at great speeds and accelerations use fast or slow muscles? The answer hinges on a fundamental tradeoff: muscles can be maximally fast or forceful, but not both. Direct lever systems offer a straightforward manifestation of this tradeoff, yet the fastest organisms use power amplification, not direct lever action. Power-amplified systems typically use slow, forceful muscles to pre-load springs which then rapidly release elastic potential energy to generate high speeds and accelerations. However,...

Data from: Genetic and ecotypic differentiation in a Californian plant polyploid complex (Grindelia, Asteraceae)

Abigail J. Moore, William L. Moore & Bruce G. Baldwin
Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations in different ecological settings....

Data from: Frequent and seasonally variable sublethal anthrax infections are accompanied by short-lived immunity in an endemic system

Carrie A. Cizauskas, Steven E. Bellan, Wendy C. Turner, Russell E. Vance & Wayne M. Getz
1. Few studies have examined host-pathogen interactions in wildlife from an immunological perspective, particularly in the context of seasonal and longitudinal dynamics. In addition, though most ecological immunology studies employ serological antibody assays, endpoint titer determination is usually based on subjective criteria and needs to be made more objective. 2. Despite the fact that anthrax is an ancient and emerging zoonotic infectious disease found worldwide, its natural ecology is not well understood. In particular, little...

Registration Year

  • 2014

Resource Types

  • Dataset


  • University of California, Berkeley
  • University of California System
  • Australian National University
  • University of Oslo
  • University of California, Davis
  • Stanford University
  • Museum of Vertebrate Zoology
  • University of KwaZulu-Natal
  • California Polytechnic State University
  • University of Pretoria