31 Works

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

Paul M. Oliver, Phillip Skipwith & Michael S. Y. Lee
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: 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
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: 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: 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: 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: 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
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: 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: 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: 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: 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: 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
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: 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: 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
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: 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: Parasite-mediated selection drives an immunogenetic tradeoff in plains zebras (Equus quagga)

Pauline L. Kamath, Wendy C. Turner, Martina Küsters & Wayne M. Getz
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: 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...

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: Prediction of phylogeographic endemism in an environmentally complex biome.

Ana Carolina Carnaval, Eric Waltari, Miguel T. Rodrigues, Dan Rosauer, Jeremy VanDerWal, Roberta Damasceno, Ivan Prates, Maria Strangas, Zoe Spanos, Danielle Rivera, Marcio R. Pie, Carina R. Firkowski, Marcos R. Bornschein, Luiz F. Ribeiro & Craig Moritz
Phylogeographic endemism, the degree to which the history of recently evolved lineages is spatially restricted, reflects fundamental evolutionary processes such as cryptic divergence, adaptation and biological responses to environmental heterogeneity. Attempts to explain the extraordinary diversity of the tropics, which often includes deep phylogeographic structure, frequently invoke interactions of climate variability across space, time and topography. To evaluate historical versus contemporary drivers of phylogeographic endemism in a tropical system, we analyse the effects of current...

Data from: Delimiting species in the genus Otospermophilus (Rodentia: Sciuridae) using genetics, ecology, and morphology

Mark A. Phuong, Marisa C. W. Lim, Daniel R. Wait, Kevin C. Rowe & Craig Moritz
We apply an integrative taxonomy approach to delimit species of ground squirrels in the genus Otospermophilus because the diverse evolutionary histories of organisms shape the existence of taxonomic characters. Previous studies of mitochondrial DNA from this group recovered three divergent lineages within Otospermophilus beecheyi separated into northern, central, and southern geographical populations, with Otospermophilus atricapillus nested within the southern lineage of O. beecheyi. To further evaluate species boundaries within this complex, we collected additional genetic...

Data from: Ontogeny of aerial righting and wing flapping in juvenile birds

Dennis Evangelista, Sharlene Cam, Tony Huynh, Igor Krivitskiy & Robert Dudley
Mechanisms of aerial righting in juvenile chukar partridge (Alectoris chukar) were studied from hatching to 14 days-post-hatching (dph). Asymmetric movements of the wings were used from 1 to 8 dph to effect progressively more successful righting behaviour via body roll. Following 8 dph, wing motions transitioned to bilaterally symmetric flapping that yielded aerial righting via nose-down pitch, along with substantial increases in vertical force production during descent. Ontogenetically, the use of such wing motions to...

Data from: Why is Madagascar special? The extraordinarily slow evolution of pelican spiders (Araneae, Archaeidae)

Hannah Marie Wood, Rosemary G. Gillespie, Charles E. Griswold & Peter C. Wainwright
Although Madagascar is an ancient fragment of Gondwana, the majority of taxa studied thus far appear to have reached the island through dispersal from Cenozoic times. Ancient lineages may have experienced a different history compared to more recent Cenozoic arrivals, as such lineages would have encountered geoclimatic shifts over an extended time period. The motivation for this study was to unravel the signature of diversification in an ancient lineage by comparing an area known for...

Data from: Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades

Nicholas J. Matzke
Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models against data using standard statistical model choice procedures, as long as multiple models are available. I re-implement the Dispersal-Extinction-Cladogenesis (DEC) model of LAGRANGE in the R package BioGeoBEARS, and...

Data from: Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus

Matthew MacManes & Michael Eisen
As a direct result of intense heat and aridity, deserts are thought to be among the most harsh of environments, particularly for their mammalian inhabitants. Given that osmoregulation can be challenging for these animals, with failure resulting in death, strong selection should be observed on genes related to the maintenance of water and solute balance. One such animal, Peromyscus eremicus, is native to the desert regions of the southwest United States and may live its...

Data from: Positive selection of deleterious alleles through interaction with a sex-ratio suppressor gene in African buffalo: a plausible new mechanism for a high frequency anomaly

Pim Van Hooft, Ben J. Greyling, Wayne M. Getz, Paul D. Van Helden, Bas J. Zwaan & Armanda D. S. Bastos
Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high frequencies of deleterious alleles in the African buffalo (Syncerus caffer) population of Kruger National Park, through positive selection of these alleles that is ultimately driven by a sex-ratio suppressor. We have previously shown that one in four Kruger buffalo has a Y-chromosome profile that, despite...

Registration Year

  • 2014
    31

Resource Types

  • Dataset
    31

Affiliations

  • University of California, Berkeley
    31
  • University of California System
    6
  • Australian National University
    4
  • University of Oslo
    3
  • University of California, Davis
    3
  • Stanford University
    2
  • University of KwaZulu-Natal
    2
  • California Polytechnic State University
    1
  • University of Pretoria
    1
  • The University of Texas at Austin
    1