54 Works

Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

Carl J. Rothfels, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Anders Larsson, Dylan O. Burge, Markus Ruhsam, Michael Deyholos, Douglas E. Soltis, , Shane W. Shaw, Lisa Pokorny, Tao Chen, Claude DePamphilis, Lisa DeGironimo, Li Chen, Xiaofeng Wei, Xiao Sun, Petra Korall, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer, C. Neal Stewart, Gane K-S. Wong … & Claude De Pamphilis
Premise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. Methods: Here we take a curated phylogenomics approach to infer the...

Data from: Genome-wide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus)

Kristina M. Cammen, Thomas F. Schultz, Patricia E. Rosel, Randall S. Wells & Andrew J. Read
Harmful algal blooms (HABs), which can be lethal in marine species and cause illness in humans, are increasing worldwide. In the Gulf of Mexico, HABs of Karenia brevis produce neurotoxic brevetoxins that cause large-scale marine mortality events. The long history of such blooms, combined with the potentially severe effects of exposure, may have produced a strong selective pressure for evolved resistance. Advances in next-generation sequencing, in particular genotyping-by-sequencing, greatly enable the genomic study of such...

Data from: Biogeographic consequences of nutrient enrichment for plant-herbivore interactions in coastal wetlands

Qiang He & Brian R. Silliman
A major challenge in ecology is to understand broadscale trends in the impact of environmental change. We provide the first integrative analysis of the effects of eutrophication on plants, herbivores, and their interactions in coastal wetlands across latitudes. We show that fertilisation strongly increases herbivory in salt marshes, but not in mangroves, and that this effect increases with increasing latitude in salt marshes. We further show that stronger nutrient effects on plant nitrogen concentration at...

Data from: Newspaper coverage of maternal health in Bangladesh, Rwanda, and South Africa: a quantitative and qualitative content analysis

Frey Gugsa, Ellora Karmarkar, Andrew Cheyne & Gavin Yamey
Objective: To examine newspaper coverage of maternal health in three countries that have made varying progress towards Millennium Development Goal 5 (MDG 5): Bangladesh (on track), Rwanda (making progress, but not on track) and South Africa (no progress). Design: We analysed each country's leading national English-language newspaper: Bangladesh's The Daily Star, Rwanda's The New Times/The Sunday Times, and South Africa's Sunday Times/The Times. We quantified the number of maternal health articles published from 1 January...

Data from: Hosts of avian brood parasites have evolved egg signatures with elevated information content

Eleanor M. Caves, Martin Stevens, Edwin S. Iversen & Claire N. Spottiswoode
Hosts of brood-parasitic birds must distinguish their own eggs from parasitic mimics, or pay the cost of mistakenly raising a foreign chick. Egg discrimination is easier when different host females of the same species each lay visually distinctive eggs (egg ‘signatures’), which helps to foil mimicry by parasites. Here, we ask whether brood parasitism is associated with lower levels of correlation between different egg traits in hosts, making individual host signatures more distinctive and informative....

Data from: Social networks predict gut microbiome composition in wild baboons

Jenny Tung, Luis B. Barriero, Michael B. Burns, J. C. Grenier, Josh Lynch, L. E. Grieneisen, J. Altmann, S. C. Alberts, R. Blekhman, E. A. Archie, Laura E Grieneisen, Elizabeth A Archie, Susan C Alberts, Jeanne Altmann, Luis B Barreiro, Jean-Christophe Grenier, Michael B Burns & Ran Blekhman
Social relationships have profound effects on health in humans and other primates, but the mechanisms that explain this relationship are not well understood. Using shotgun metagenomic data from wild baboons, we found that social group membership and social network relationships predicted both the taxonomic structure of the gut microbiome and the structure of genes encoded by gut microbial species. Rates of interaction directly explained variation in the gut microbiome, even after controlling for diet, kinship,...

Data from: Charting the complete elastic properties of inorganic crystalline compounds

Maarten De Jong, Wei Chen, Thomas Angsten, Anubhav Jain, Randy Notestine, Anthony Gamst, Marcel Sluiter, Chaitanya Krishna Ande, Sybrand Van Der Zwaag, Jose J. Plata, Cormac Toher, Stefano Curtarolo, Gerbrand Ceder, Kristin A. Persson & Mark Asta
The elastic constant tensor of an inorganic compound provides a complete description of the response of the material to external stresses in the elastic limit. It thus provides fundamental insight into the nature of the bonding in the material, and it is known to correlate with many mechanical properties. Despite the importance of the elastic constant tensor, it has been measured for a very small fraction of all known inorganic compounds, a situation that limits...

Data from: The importance of spinner dolphin (Stenella longirostris) resting habitat: implications for management

Julian A. Tyne, David W. Johnston, Robert Rankin, Neil R. Loneragan & Lars Bejder
Linking key ecological characteristics with animal behaviour is essential for identifying and protecting important habitats that support life functions. Spinner dolphins display a predictable diurnal behavioural pattern where they forage offshore at night and return to sheltered bays during daytime to rest. These bays, which are also subject to considerable use by humans, have long been recognized as key habitats for this species although the extent to which dolphins rely on specific characteristics of these...

Data from: Assessing the utility of whole genome amplified DNA for next-generation molecular ecology

Christopher Blair, C. Ryan Campbell, Anne D Yoder & Anne D. Yoder
DNA quantity can be a hindrance in ecological and evolutionary research programmes due to a range of factors including endangered status of target organisms, available tissue type, and the impact of field conditions on preservation methods. A potential solution to low-quantity DNA lies in whole genome amplification (WGA) techniques that can substantially increase DNA yield. To date, few studies have rigorously examined sequence bias that might result from WGA and next-generation sequencing of nonmodel taxa....

Data from: Bonobos and chimpanzees exhibit human-like framing effects

Christopher Krupenye, Alexandra G. Rosati, Brian Hare, B. Hare, C. Krupenye & A. G. Rosati
Humans exhibit framing effects when making choices, appraising decisions involving losses differently from those involving gains. To directly test for the evolutionary origin of this bias, we examined decision-making in humans' closest living relatives: bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). We presented the largest sample of non-humans to date (n = 40) with a simple task requiring minimal experience. Apes made choices between a ‘framed’ option that provided preferred food, and an alternative option...

Data from: Baby on board: olfactory cues indicate pregnancy and fetal sex in a non-human primate

Jeremy Chase Crawford, Christine M. Drea, J. C. Crawford & C. M. Drea
Olfactory cues play an integral, albeit underappreciated, role in mediating vertebrate social and reproductive behaviour. These cues fluctuate with the signaller's hormonal condition, coincident with and informative about relevant aspects of its reproductive state, such as pubertal onset, change in season and, in females, timing of ovulation. Although pregnancy dramatically alters a female's endocrine profiles, which can be further influenced by fetal sex, the relationship between gestation and olfactory cues is poorly understood. We therefore...

Data from: Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii

Jonathan M. Flowers, Khaled M. Hazzouri, Gina M. Pham, Ulises Rosas, Tayebeh Bahmani, Basel Khraiwesh, David R. Nelson, Kenan Jijakli, Rasha Abdrabu, Elizabeth H. Harris, Paul A. Lefebvre, Erik F. Y. Hom, Kourosh Salehi-Ashtiani & Michael D. Purugganan
We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ∼3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates...

Data from: Self-organizing dominance hierarchies in a wild primate population

Mathias Franz, Emily McLean, Jenny Tung, Jeanne Altmann & Susan C. Alberts
Linear dominance hierarchies, which are common in social animals, can profoundly influence access to limited resources, reproductive opportunities and health. In spite of their importance, the mechanisms that govern the dynamics of such hierarchies remain unclear. Two hypotheses explain how linear hierarchies might emerge and change over time. The ‘prior attributes hypothesis’ posits that individual differences in fighting ability directly determine dominance ranks. By contrast, the ‘social dynamics hypothesis’ posits that dominance ranks emerge from...

Data from: Genetic diversity does not explain variation in extra-pair paternity in multiple populations of a songbird

Irene A. Liu, James E. Johndrow, James Abe, Stefan Lüpold, Ken Yasukawa, David F. Westneat & Stephen Nowicki
Many songbirds are socially monogamous but genetically polyandrous, mating with individuals outside their pair bonds. Extra-pair paternity (EPP) varies within and across species, but reasons for this variation remain unclear. One possible source of variation is population genetic diversity, which has been shown in interspecific meta-analyses to correlate with EPP but which has limited support from intraspecific tests. Using eight populations of the genetically polyandrous red-winged blackbird (Agelaius phoeniceus), including an island population, we investigated...

Data from: Mainland size variation informs predictive models of exceptional insular body size change in rodents

Paul A. P. Durst & V. Louise Roth
The tendency for island populations of mammalian taxa to diverge in body size from their mainland counterparts consistently in particular directions is both impressive for its regularity and, especially among rodents, troublesome for its exceptions. However, previous studies have largely ignored mainland body size variation, treating size differences of any magnitude as equally noteworthy. Here, we use distributions of mainland population body sizes to identify island populations as ‘extremely’ big or small, and we compare...

Data from: An archive of longitudinal recordings of the vocalizations of adult Gombe chimpanzees

Frans X. Plooij, Hetty Van De Rijt-Plooij, Martha Fischer & Anne Pusey
Studies of chimpanzee vocal communication provide valuable insights into the evolution of communication in complex societies, and also comparative data for understanding the evolution of human language. One particularly valuable dataset of recordings from free-living chimpanzees was collected by Frans X. Plooij and the late Hetty van de Rijt-Plooij at Gombe National Park, Tanzania (1971–73). These audio specimens, which have not yet been analysed, total over 10 h on 28 tapes, including 7 tapes focusing...

Data from: From a line in the sand to a landscape of decisions: a Hierarchical Diversity Decision Framework (HiDDeF) for estimating and communicating biodiversity loss along anthropogenic gradients

Kristofor A. Voss, Ryan S. King & Emily S. Bernhardt
1. In setting water quality criteria, managers must choose thresholds for stressors that are protective of aquatic biodiversity. Setting such thresholds requires making implicit judgments about the degree of biodiversity loss that managers are willing to accept. 2. We present a new modeling approach, the Hierarchical Diversity Decision Framework model (HiDDeF) that explicitly communicates the sensitivity of water quality benchmarks to these implicit judgements. We apply HiDDeF to a dataset of stream macroinvertebrate abundances across...

Data from: Genetic isolation between two recently diverged populations of a symbiotic fungus

Sara Branco, Pierre Gladieux, Christopher E. Ellison, Alan Kuo, Kurt LaButii, Anna Lipzen, Igor V. Grigoriev, Hui-Ling Liao, Rytas Vilgalys, Kabir G. Peay, John W. Taylor, Thomas D. Bruns & Kurt LaButti
Fungi are an omnipresent and highly diverse group of organisms, making up a significant part of eukaryotic diversity. Little is currently known about the drivers of fungal population differentiation and subsequent divergence of species, particularly in symbiotic, mycorrhizal fungi. Here, we investigate the population structure and environmental adaptation in Suillus brevipes (Peck) Kuntze, a wind-dispersed soil fungus that is symbiotic with pine trees. We assembled and annotated the reference genome for Su. brevipes and resequenced...

Data from: Resource base influences genome-wide DNA methylation levels in wild baboons (Papio cynocephalus)

Amanda J. Lea, Jeanne Altmann, Susan C. Alberts & Jenny Tung
Variation in resource availability commonly exerts strong effects on fitness-related traits in wild animals. However, we know little about the molecular mechanisms that mediate these effects, or about their persistence over time. To address these questions, we profiled genome-wide whole blood DNA methylation levels in two sets of wild baboons: (i) ‘wild-feeding’ baboons that foraged naturally in a savanna environment and (ii) ‘Lodge’ baboons that had ready access to spatially concentrated human food scraps, resulting...

Data from: Optimal group size in a highly social mammal

A. Catherine Markham, Laurence R. Gesquiere, Susan C. Alberts & Jeanne Altmann
What are the costs and benefits for animals living in groups of different sizes? Balancing the trade-offs between within-group competition (which favors smaller groups) and between-group competition (which favors larger groups) suggests that intermediate-sized groups may be best, yet empirical support for this prediction has largely been lacking. Using long-term data on wild baboons, we provide novel evidence that individuals living in intermediate-sized groups have energetically optimal space-use strategies and lower glucocorticoid (stress hormone) concentrations...

Data from: Natural variation, differentiation and genetic tradeoffs of ecophysiological traits in response to water limitation in Brachypodium distachyon and its descendent allotetraploid B. hybridum (Poaceae)

Antonio J. Manzaneda, Pedro José Rey, Jill Theresa Anderson, Evan Raskin, Christopher Weiss-Lehman, Thomas Mitchell-Olds & Jill T. Anderson
Differences in tolerance to water stress may underlie ecological divergence of closely-related ploidy lineages. However, the mechanistic basis of physiological variation governing eco-geographical cytotype segregation is not well understood. Here, using Brachypodium distachyon and its derived allotetraploid B. hybridum as model, we test the hypothesis that, for heteroploid annuals, ecological divergence of polyploids in drier environments is based on trait differentiation enabling drought-escape. We demonstrate that under water limitation allotetraploids maintain higher photosynthesis and stomatal...

Data from: Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach

Jeannine Cavender-Bares, Antonio González-Rodríguez, Deren A. R. Eaton, Andrew A. L. Hipp, Anne Beulke & Paul S. Manos
The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spans the unglaciated temperate and tropical regions of North America and Mesoamerica, provides an instructive system in which to examine speciation and niche evolution. We generated a fossil-calibrated phylogeny of Virentes using RADseq data to estimate divergence times and used nuclear microsatellites, chloroplast sequences and an intron...

Data from: Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, , Emily Jane McTavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams & Karen Ann Cranston
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly...

Data from: Exaggerated sexual swellings and male mate choice in primates: testing the reliable indicator hypothesis in the Amboseli baboons

Courtney L. Fitzpatrick, Jeanne Altmann & Susan C. Alberts
The paradigm of competitive males vying to influence female mate choice has been repeatedly upheld, but, increasingly, studies also report competitive females and choosy males. One female trait that is commonly proposed to influence male mate choice is the exaggerated sexual swelling displayed by females of many Old World primate species. The reliable indicator hypothesis posits that females use the exaggerated swellings to compete for access to mates, and that the swellings advertise variation in...

Data from: Variation in the impact of non-native seaweeds along gradients of habitat degradation: a meta-analysis and an experimental test

Laura Tamburello, Elena Maggi, Lisandro Benedetti-Cecchi, Giuseppe Bellistri, Alex James Rattray, Chiara Ravaglioli, Luca Rindi, Jason Roberts & Fabio Bulleri
Biological invasions are acknowledged among the main drivers of global changes in biodiversity. Despite compelling evidence of species interactions being strongly regulated by environmental conditions, there is a dearth of studies investigating how the effects of non-native species vary among areas exposed to different anthropogenic pressures. Focusing on marine macroalgae, we performed a meta-analysis to test whether and how the direction and magnitude of their effects on resident communities and species varies in relation to...

Registration Year

  • 2015
    54

Resource Types

  • Dataset
    54

Affiliations

  • Duke University
    54
  • Princeton University
    6
  • University of California, Berkeley
    6
  • National Evolutionary Synthesis Center
    3
  • University of Alberta
    3
  • University of Minnesota
    3
  • Institute of Primate Research
    3
  • Smithsonian Institution
    3
  • Yale University
    3
  • The Bronx Defenders
    2