505 Works

Data from: Mice infected with low-virulence strains of Toxoplasma gondii lose their innate aversion to cat urine, even after extensive parasite clearance

Wendy Marie Ingram, Leeanne M. Goodrich, Ellen A. Robey & Michael B. Eisen
Toxoplasma gondii chronic infection in rodent secondary hosts has been reported to lead to a loss of innate, hard-wired fear toward cats, its primary host. However the generality of this response across T. gondii strains and the underlying mechanism for this pathogen-mediated behavioral change remain unknown. To begin exploring these questions, we evaluated the effects of infection with two previously uninvestigated isolates from the three major North American clonal lineages of T. gondii, Type III...

Data from: Pollinator interactions with yellow starthistle (Centaurea solstitialis) across urban, agricultural, and natural landscapes

Misha Leong, Claire Kremen & George K. Roderick
Pollinator-plant relationships are found to be particularly vulnerable to land use change. Yet despite extensive research in agricultural and natural systems, less attention has focused on these interactions in neighboring urban areas and its impact on pollination services. We investigated pollinator-plant interactions in a peri-urban landscape on the outskirts of the San Francisco Bay Area, California, where urban, agricultural, and natural land use types interface. We made standardized observations of floral visitation and measured seed...

Data from: The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Angelique D'Hont, France Denoeud, Jean-Marc Aury, Franc-Christophe Baurens, Françoise Carreel, Olivier Garsmeur, Benjamin Noel, Stéphanie Bocs, Gaëtan Droc, Mathieu Rouard, Corinne Da Silva, Jabbari Kamel, Céline Cardi, Julie Poulain, Marlène Souquet, Karine Labadie, Cyril Jourda, Juliette Lengellé, Marguerite Rodier-Goud, Adriana Alberti, Maria Bernard, Margot Correa, Saravanaraj Ayyampalayam, Michael R. McKain, Jim Leebens-Mack … & Patrick Wincker
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid...

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...

Data from: Deep genetic structure and ecological divergence in a widespread human commensal toad

Guinevere O. U. Wogan, Bryan L. Stuart, Djoko T. Iskandar & Jimmy A. McGuire
The Asian common toad (Duttaphrynus melanostictus) is a human commensal species that occupies a wide variety of habitats across tropical Southeast Asia. We test the hypothesis that genetic variation in D. melanostictus is weakly associated with geography owing to natural and human-mediated dispersal facilitated by its commensal nature. Phylogenetic and population genetic analyses of mitochondrial and nuclear DNA sequence variation, and predictive species distribution modelling, unexpectedly recovered three distinct evolutionary lineages that differ genetically and...

Data from: Total-evidence dating under the fossilized birth-death process

Chi Zhang, Tanja Stadler, Seraina Klopfstein, Tracy A. Heath & Fredrik Ronquist
Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is...

Data from: Landscape diversity and crop vigor influence biological control of the western grape leafhopper (E. elegantula Osborn) in vineyards

Houston Wilson, Albie F. Miles, Kent M. Daane & Miguel A. Altieri
This study evaluated how the proportional area of natural habitat surrounding a vineyard (i.e. landscape diversity) worked in conjunction with crop vigor, cultivar and rootstock selection to influence biological control of the western grape leafhopper (Erythroneura elegantula Osborn). The key natural enemies of E. elegantula are Anagrus erythroneurae S. Trjapitzin & Chiappini and A. daanei Triapitsyn, both of which are likely impacted by changes in landscape diversity due to their reliance on non-crop habitat to...

Data from: Stronger effect of gastropods than rodents on seedling establishment, irrespective of exotic or native plant species origin

Lotte Korell, Claudia Stein, Isabell Hensen, Helge Bruelheide, Katharine N. Suding & Harald Auge
Experimental evidence about how generalist consumers affect exotic plant invasions is equivocal, but most tests have been limited to few plant species, single herbivore guilds, and single locations. Using a seed-addition experiment, we studied effects of gastropods and rodents on recruitment success of 37 exotic and 37 native plant species affiliated to three different functional groups (i.e. grasses, legumes and non-legume herbs). We replicated our seed addition x herbivore exclusion experiment at multiple grassland sites,...

Data from: Orchid phylogenomics and multiple drivers of their extraordinary diversification

Thomas J. Givnish, Daniel Spalink, Mercedes Ames, Stephanie P. Lyon, Steven J. Hunter, Alejandro Zuluaga, William J. D. Iles, Mark A. Clements, Mary T. K. Arroyo, James Leebens-Mack, Lorena Endara, Ricardo Kriebel, Kurt M. Neubig, W. Mark Whitten, Norris H. Williams & Kenneth M. Cameron
Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144...

Data from: The origin and evolution of phototropins

Fay-Wei Li, Kathleen M. Pryer, Gane K.-S. Wong, Carl J. Rothfels, Michael Melkonian, Sarah Mathews, Juan C. Villarreal & Sean W. Graham
Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent...

Data from: Fog as a source of nitrogen for redwood trees: evidence from fluxes and stable isotopes

Pamela H. Templer, Kathleen C. Weathers, Holly A. Ewing, Todd E. Dawson, Stefania Mambelli, Amanda M. Lindsey, Jeramy Webb, Vanessa K. Boukili & Mary K. Firestone
A defining feature of the redwood forest in coastal California is the presence of fog in the summer months, a time when there is typically little rainfall. Our goal was to determine the role of summer fog in canopy transformation of nitrogen, nitrogen uptake by trees and photosynthesis within a coastal redwood forest ecosystem. We measured horizontal and vertical inputs of nitrogen, the isotopic composition of nitrogen in a variety of atmospheric sources (summer fog,...

Data from: Exon capture phylogenomics: efficacy across scales of divergence

Jason G. Bragg, Sally Potter, Ke Bi & Craig Moritz
The evolutionary histories of species are not measured directly, but estimated using genealogies inferred for particular loci. Individual loci can have discordant histories, but in general we expect to infer evolutionary histories more accurately as more of the genome is sampled. High Throughput Sequencing (HTS) is now providing opportunities to incorporate thousands of loci in ‘phylogenomic’ studies. Here, we used target enrichment to sequence c.3000 protein-coding exons in a group of Australian skink lizards (crown...

Data from: An extracellular biochemical screen reveals that FLRTs and Unc5s mediate neuronal subtype recognition in the retina

Jasper J. Visser, Yolanda Cheng, Steven C. Perry, Andrew Benjamin Chastain, Bayan Parsa, Shatha S. Masri, Ray Thomas A., Jeremy N. Kay, Woj M. Wojtowicz, Thomas A Ray, Jeremy N Kay, Jasper J Visser, Steven C Perry, Shatha S Masri & Woj M Wojtowicz
In the inner plexiform layer of the mouse retina, ~70 neuronal subtypes form a stereotyped circuit that underlies visual processing. During development, subtypes organize into an intricate laminar structure. This organization is choreographed by extracellular interactions that mediate cell recognition events. To identify recognition proteins involved in lamination, we utilized microarray data from 13 subtypes to identify differentially-expressed cell surface and secreted proteins. Using these candidates, we performed a biochemical screen and identified ~50 previously-unknown...

Data from: Does wildlife resource selection accurately inform corridor conservation?

Briana Abrahms, Sarah C. Sawyer, Neil R. Jordan, J. Weldon McNutt, Alan M. Wilson & Justin S. Brashares
Evaluating landscape connectivity and identifying and protecting corridors for animal movement have become central challenges in applied ecology and conservation. Currently, resource selection analyses are widely used to focus corridor planning where animal movement is predicted to occur. An animal's behavioural state (e.g. foraging, dispersing) is a significant determinant of resource selection patterns, yet has largely been ignored in connectivity assessments. We review 16 years of connectivity studies employing resource selection analysis to evaluate how...

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 & Hannah M. Wood
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: Small-scale restoration in intensive agricultural landscapes supports more specialized and less mobile pollinator species

Claire Kremen & Leithen K. M'Gonigle
1. Agriculture now constitutes 40–50% of terrestrial land use globally. By enhancing habitat suitability and connectivity, restoration within agricultural landscapes could have a major influence on biodiversity conservation. However, habitat management within intensive agricultural landscapes may primarily boost abundances of common, highly mobile generalists, rather than vulnerable or endangered species. We studied pollinator community response to small-scale habitat restoration in the intensively farmed Central Valley of California to determine whether restoration could also promote more...

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, R. Damasceno, J. VanDerWal, D. Rosauer, M. T. Rodrigues & C. 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: 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: Ontogeny of aerial righting and wing flapping in juvenile birds

Dennis Evangelista, Sharlene Cam, Tony Huynh, Igor Krivitskiy, Robert Dudley, S. Cam, R. Dudley, D. Evangelista, T. Huynh & I. Krivitskiy
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: 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: 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...

Data from: Quantifying past and present connectivity illuminates a rapidly changing landscape for the African elephant

Clinton W. Epps, Samuel K. Wasser, Jonah L. Keim, Benezeth M. Mutayoba & Justin S. Brashares
There is widespread concern about impacts of land-use change on connectivity among animal and plant populations, but those impacts are difficult to quantify. Moreover, lack of knowledge regarding ecosystems before fragmentation may obscure appropriate conservation targets. We use occurrence and population genetic data to contrast connectivity for a long-lived mega-herbivore over historical and contemporary time frames. We test whether (i) historical gene flow is predicted by persistent landscape features rather than human settlement, (ii) contemporary...

Data from: No early warning signals for stochastic transitions: insights from large deviation theory

Carl Boettiger, Alan Hastings, C. Boettiger & A. Hastings
Code to replicate the analysis and generate Figure 1A dynamic document for running the analysis and generating the data and graphs shown in Figure 1. After installing the packages indicated, this code can be run by copy-pasting the code blocks into any R terminal, or compiled at once by running `knit("Figure1.Rmd")` in the R terminal using the knitr package.Figure1.RmdData from: No early warning signals for stochastic transitions: insights from large deviation theoryA csv file containing...

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  • University of California, Berkeley
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