45 Works

Data from: Divergent evolution and niche differentiation within the common peatmoss Sphagnum magellanicum

Narjes Yousefi, Kristian Hassel, Kjell Ivar Flatberg, Petri Kemppainen, Emiliano Trucchi, Arthur Jonathan Shaw, Magni Olsen Kyrkjeeide, Péter Szövényi & Hans Kristen Stenøien
PREMISE OF THE STUDY: Populations with phenotypic polymorphism in discrete characters may be good models for investigating genome evolution and speciation. Sphagnum magellanicum Brid. is found throughout the northern hemisphere, and despite considerable variation in morphological characters, it is considered one of the least taxonomically controversial peatmoss species. We have observed two main morphs of the species associated with different microhabitats. Here we investigated the genomic and environmental basis of this intraspecific morphological variation. METHODS:...

Data from: A genetic legacy of introgression confounds phylogeny and biogeography in oaks

John D. McVay, Andrew L. Hipp & Paul S. Manos
Oaks (Quercus L.) have long been suspected to hybridize in nature, and widespread genetic exchange between morphologically defined species is well documented in two- to six-species systems, but the phylogenetic consequences of hybridization in oaks have never been demonstrated in a phylogenetically diverse sample. Here, we present phylogenomic analyses of a ca 30 Myr clade that strongly support morphologically defined species and the resolution of novel clades of white oaks; however, historical hybridization across clade...

Data from: When sensing is gambling: an experimental system reveals how plasticity can generate tunable bet-hedging strategies

Colin S. Maxwell & Paul M. Magwene
Genotypes can persist in unpredictable environments by ‘hedging their bets’ and producing diverse phenotypes. Theoretical studies have shown that the phenotypic variability needed for a bet-hedging strategy can be generated by factors either inside or outside an organism. However, sensing the environment and bet hedging are frequently treated as distinct evolutionary strategies. Furthermore, nearly all empirical studies of the molecular underpinnings of bet-hedging strategies to date have focused on internal sources of variability. We took...

Data from: Oxidative stress-mediated NFκB phosphorylation upregulates p62/SQSTM1 and promotes retinal pigmented epithelial cell survival through increased autophagy

Chunjuan Song, Sayak K. Mitter, Xiaoping Qi, Eleni Beli, Haripriya V. Rao, Jindong Ding, Colin S. Ip, Hongmei Gu, Debra Akin, William A. Dunn, Catherine Bowes Rickman, Alfred S. Lewin, Maria B. Grant & Michael E. Boulton
p62 is a scaffolding adaptor implicated in the clearance of protein aggregates by autophagy. Reactive oxygen species (ROS) can either stimulate or inhibit NFκB-mediated gene expression influencing cellular fate. We studied the effect of hydrogen peroxide (H2O2)-mediated oxidative stress and NFκB signaling on p62 expression in the retinal pigment epithelium (RPE) and investigated its role in regulation of autophagy and RPE survival against oxidative damage. Cultured human RPE cell line ARPE-19 and primary human adult...

Data from: Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

Mark Ravinet, Rui Faria, Roger K. Butlin, Juan Galindo, Nicolas Bierne, Marina Rafajlović, Mohamed A. F. Noor, Bernhard Mehlig & Anja M. Westram
Speciation, the evolution of reproductive isolation amongst populations, is continuous, complex, and involves multiple, interacting barriers. Until it is complete, the effects of this process vary along the genome and can lead to a heterogeneous genomic landscape with peaks and troughs of differentiation and divergence. When gene flow occurs during speciation, barriers restricting migration locally in the genome lead to patterns of heterogeneity. However, genomic heterogeneity can also be produced or modified by variation in...

Data from: The distribution and numbers of cheetah (Acinonyx jubatus) in southern Africa

Florian J. Weise, Varsha Vijay, Andrew P. Jacobson, Rebecca F. Schoonover, Rosemary J. Groom, Jane Horgan, Derek Keeping, Rebecca Klein, Kelly Marnewick, Glyn Maude, Jorg Melzheimer, Gus Mills, Vincent Van Der Merwe, Esther Van Der Meer, Rudie J. Van Vuuren, Bettina Wacher, Stuart L. Pimm & Bettina Wachter
Assessing the numbers and distribution of threatened species is a central challenge in conservation, often made difficult because the species of concern are rare and elusive. For some predators, this may be compounded by their being sparsely distributed over large areas. Such is the case with the cheetah Acinonyx jubatus. The IUCN Red List process solicits comments, is democratic, transparent, widely-used, and has recently assessed the species. Here, we present additional methods to that process...

Data from: Punctuated changes in the morphology of an endemic diatom from Lake Titicaca

Trisha L. Spanbauer, Sherilyn C. Fritz & Paul A. Baker
High levels of biodiversity and endemism in ancient lakes have motivated research on evolutionary processes in these systems. Drill core records from Lake Titicaca (Bolivia, Peru), an ancient lake in the high-elevation Altiplano, record the history of climate, landscape dynamics, and diatom evolution. That record was used to examine the patterns and drivers of morphological evolution of an endemic species complex of diatoms in the lake, the Cyclostephanos andinus complex. In an attempt to delineate...

Data from: Foraging impacts of Asian megafauna on tropical rainforest structure and biodiversity

John Terborgh, Lisa C. Davenport, Lisa Ong & Ahimsa Campos-Arceiz
Megaherbivores are known to influence the structure, composition, and diversity of vegetation. In Central Africa, forest elephants act as ecological filters by breaking tree saplings and stripping them of foliage. Much less is known about impacts of megafauna on Southeast Asian rain forests. Here, we ask whether herbivory by Asian megafauna has impacts analogous to those of African forest elephants. To answer this, we studied forest (1) structure, (2) composition, (3) diversity, and (4) tree...

Data from: Transcriptomics in the wild: hibernation physiology in free‐ranging dwarf lemurs

Sheena L. Faherty, José Luis Villanueva‐Cañas, Marina B. Blanco, M. Mar Albà & Anne D. Yoder
Hibernation is an adaptive strategy some mammals use to survive highly seasonal or unpredictable environments. We present the first investigation on the transcriptomics of hibernation in a natural population of primate hibernators: Crossley's dwarf lemurs (Cheirogaleus crossleyi). Using capture–mark–recapture techniques to track the same animals over a period of 7 months in Madagascar, we used RNA‐seq to compare gene expression profiles in white adipose tissue (WAT) during three distinct physiological states. We focus on pathway...

Data from: Defaunation increases the spatial clustering of lowland Western Amazonian tree communities

Robert Bagchi, Varun Swamy, Jean-Paul Latorre Farfan, John Terborgh, César I. A. Vela, Nigel C. A. Pitman & Washington Galiano Sanchez
1.Declines of large vertebrates in tropical forests may reduce dispersal of tree species that rely on them, and the resulting undispersed seedlings might suffer increased distance- and density- dependent mortality. Consequently, extirpation of large vertebrates may alter the composition and spatial structure of plant communities and impair ecosystem functions like carbon storage. 2.We analysed spatial patterns of tree recruitment within six forest plots along a defaunation gradient in western Amazonia. We divided recruits into two...

Data from: Testing the optimal defense hypothesis in nature: variation for glucosinolate profiles within plants

Rose A. Keith & Thomas Mitchell-Olds
Plants employ highly variable chemical defenses against a broad community of herbivores, which vary in their susceptibilities to specific compounds. Variation in chemical defenses within the plant has been found in many species; the ecological and evolutionary influences on this variation, however, are less well-understood. One central theory describing the allocation of defenses in the plant is the Optimal Defense Hypothesis (ODH), which predicts that defenses will be concentrated in tissues that are of high...

Data from: Chronotype variation drives night-time sentinel-like behaviour in hunter–gatherers

David Samson, Alyssa Crittenden, Ibrahim Mabulla, Audax Mabulla, Charles Nunn, Charles L. Nunn, David R. Samson, Audax Z. P. Mabulla, Ibrahim A. Mabulla & Alyssa N. Crittenden
Sleep is essential for survival, yet it also represents a time of extreme vulnerability to predation, hostile conspecifics, and environmental dangers. To reduce the risks of sleeping, the sentinel hypothesis proposes that group-living animals share the task of vigilance during sleep, with some individuals sleeping while others are awake. To investigate sentinel-like behaviour in sleeping humans, we investigated activity patterns at night among Hadza hunter-gatherers of Tanzania. Using actigraphy, we discovered that all subjects were...

Data from: Automated assembly of a reference taxonomy for phylogenetic data synthesis

Jonathan A. Rees, Karen Ann Cranston, Jonathan Rees & Karen Cranston
Taxonomy and nomenclature data are critical for any project that synthesizes biodiversity data, as most biodiversity data sets use taxonomic names to identify taxa. Open Tree of Life is one such project, synthesizing sets of published phylogenetic trees into comprehensive summary trees. No single published taxonomy met the taxonomic and nomenclatural needs of the project. Here we describe a system for reproducibly combining several source taxonomies into a synthetic taxonomy, and we discuss the challenges...

Data from: Unmapped sequencing reads identify additional candidate genes linked to magnetoreception in rainbow trout

Monica B. Arniella, Robert R. Fitak & Sönke Johnsen
A recent study identified candidate genes linked to magnetoreception in rainbow trout (Oncorhynchus mykiss) by sequencing transcriptomes from the brains of fish exposed to a magnetic pulse. However, the discovery of these candidate genes was limited to sequences that aligned to the reference genome. The unaligned, or unmapped, sequences may yet contain valuable information resulting from regions missing, misassembled, or divergent from the reference. Using the available sequencing data from the trout brain transcriptomes, we...

Data from: Quantifying how short-term environmental variation leads to long-term demographic responses to climate change

Robert K. Shriver
1. Climate change is expected to alter not only year-to-year variation in climate but also aspects of within-year variation, such as the length of the intervals between rainfall events and the duration of heat waves. Yet we still have a poor understanding of how intra-annual climate variability and individual weather events alter key vital rates (e.g. individual growth, reproduction and survival) that in part determine population dynamics. 2. Traditionally, ecologists have accounted for this variability...

Data from: Resource partitioning facilitates coexistence in sympatric cetaceans in the California Current

Sabrina Fossette, Briana Abrahms, Elliott L. Hazen, Steven J. Bograd, Kelly M. Newton, John Calambokidis, Julia A. Burrows, Jeremy A. Goldbogen, James T. Harvey, Baldo Marinovic, Bernie Tershy, Donald A. Croll & Kelly M. Zilliacus
1. Resource partitioning is an important process driving habitat use and foraging strategies in sympatric species that potentially compete. Differences in foraging behavior are hypothesized to contribute to species coexistence by facilitating resource partitioning, but little is known on the multiple mechanisms for partitioning that may occur simultaneously. Studies are further limited in the marine environment, where the spatial and temporal distribution of resources is highly dynamic and subsequently difficult to quantify. 2. We investigated...

Data from: Functional preservation and variation in the cone opsin genes of nocturnal tarsiers

Gillian L. Moritz, Perry S. Ong, George H. Perry & Nathaniel J. Dominy
The short-wavelength sensitive (S-) opsin gene OPN1SW is pseudogenized in some nocturnal primates and retained in others, enabling dichromatic colour vision. Debate on the functional significance of this variation has focused on dark conditions, yet many nocturnal species initiate activity under dim (mesopic) light levels that can support colour vision. Tarsiers are nocturnal, twilight-active primates and exemplary visual predators; they also express different colour vision phenotypes, raising the possibility of discrete adaptations to mesopic conditions....

Data from: Expression and function of ATP-dependent potassium channels in zebrafish islet β-cells

Christopher H. Emfinger, Alecia Welscher, Zihan Yan, Yixi Wang, Hannah Conway, Jennifer B. Moss, Larry G. Moss, Maria S. Remedi & Colin G. Nichols
ATP-sensitive potassium channels (KATP channels) are critical nutrient sensors in many mammalian tissues. In the pancreas, KATP channels are essential for coupling glucose metabolism to insulin secretion. While orthologous genes for many components of metabolism–secretion coupling in mammals are present in lower vertebrates, their expression, functionality and ultimate impact on body glucose homeostasis are unclear. In this paper, we demonstrate that zebrafish islet β-cells express functional KATP channels of similar subunit composition, structure and metabolic...

Data from: Pharmacological inactivation does not support a unique causal role for intraparietal sulcus in the discrimination of visual number

Nicholas K. DeWind, Jiyun Peng, Andrew Luo, Elizabeth M. Brannon & Michael L. Platt
The “number sense” describes the intuitive ability to quantify without counting. Single neuron recordings in non-human primates and functional imaging in humans suggest the intraparietal sulcus is an important neuroanatomical locus of numerical estimation. Other lines of inquiry implicate the IPS in numerous other functions, including attention and decision making. Here we provide a direct test of whether IPS has functional specificity for numerosity judgments. We used muscimol to reversibly and independently inactivate the ventral...

Data from: Mechanism matters: the cause of fluctuations in boom-bust populations governs optimal habitat restoration strategy

Gina K. Himes Boor, Cheryl B. Schultz, Elizabeth E. Crone & William F. Morris
Many populations exhibit boom-bust dynamics in which abundance fluctuates dramatically over time. Past research has focused on identifying whether the cause of fluctuations is primarily exogenous, e.g., environmental stochasticity coupled with weak density dependence, or endogenous, e.g., over-compensatory density dependence. Far fewer studies have addressed whether the mechanism responsible for boom-bust dynamics matters with respect to at-risk species management. Here, we ask whether the best strategy for restoring habitat across a landscape differs under exogenously...

Data from: Young inversion with multiple linked QTLs under selection in a hybrid zone

Thomas Mitchell-Olds
Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose...

Data from: From the track to the ocean: using flow control to improve marine bio-logging tags for cetaceans

Giovani Fiore, Erik Anderson, C. Spencer Garborg, Mark Murray, Mark Johnson, Michael J. Moore, Laurens Howle & K. Alex Shorter
Bio-logging tags are an important tool for the study of cetaceans, but superficial tags inevitably increase hydrodynamic loading. Substantial forces can be generated by tags on fast-swimming animals, potentially affecting behavior and energetics or promoting early tag removal. Streamlined forms have been used to reduce loading, but these designs can accelerate flow over the top of the tag. This non-axisymmetric flow results in large lift forces (normal to the animal) that become the dominant force...

Data from: A classification system for zebrafish adipose tissues

James E. N. Minchin & John F. Rawls
The zebrafish model system offers significant utility for in vivo imaging of adipose tissue (AT) dynamics and for screening to identify chemical and genetic modifiers of adiposity. In particular, AT can be quantified accurately in live zebrafish using fluorescent lipophilic dyes. Although this methodology offers considerable promise, the comprehensive identification and classification of zebrafish ATs has not been performed. Here, we use fluorescent lipophilic dyes and in vivo imaging systematically to identify, classify and quantify...

Data from: Candidate genes mediating magnetoreception in rainbow trout (Oncorhynchus mykiss)

Robert R. Fitak, Benjamin R. Wheeler, David A. Ernst, Kenneth J. Lohmann & Sonke Johnsen
Diverse animals use Earth's magnetic field in orientation and navigation, but little is known about the molecular mechanisms that underlie magnetoreception. Recent studies have focused on two possibilities: (i) magnetite-based receptors; and (ii) biochemical reactions involving radical pairs. We used RNA sequencing to examine gene expression in the brain of rainbow trout (Oncorhynchus mykiss) after exposure to a magnetic pulse known to disrupt magnetic orientation behaviour. We identified 181 differentially expressed genes, including increased expression...

Data from: Known mutator alleles do not markedly increase mutation rate in clinical Saccharomyces cerevisiae strains

Daniel A. Skelly, Paul M. Magwene, Brianna Meeks & Helen A. Murphy
Natural selection has the potential to act on all phenotypes, including genomic mutation rate. Classic evolutionary theory predicts that in asexual populations, mutator alleles, which cause high mutation rates, can fix due to linkage with beneficial mutations. This phenomenon has been demonstrated experimentally and may explain the frequency of mutators found in bacterial pathogens. By contrast, in sexual populations, recombination decouples mutator alleles from beneficial mutations, preventing mutator fixation. In the facultatively sexual yeast Saccharomyces...

Registration Year

  • 2017

Resource Types

  • Dataset
  • Text


  • Duke University
  • University of Toronto
  • University of Connecticut
  • Field Museum of Natural History
  • University of Oslo
  • Indiana University Bloomington
  • University of Florida
  • Pompeu Fabra University
  • University of Kansas
  • Fred Hutchinson Cancer Research Center