401 Works

Phototactic choices of Drosophila melanogaster

Indrikis Krams, Tatjana Krama, Ronalds Krams, Giedrius Trakimas, Sergejs Popovs, Priit Jõers, Maris Munkevics, Didzis Elferts, Markus Rantala, Janis Makna & Benjamin De Bivort
When organisms' environmental conditions vary unpredictably in time, it can be advantageous for individuals to hedge their phenotypic bets. It has been shown that a bet-hedging strategy underlies the high inter-individual diversity of phototactic choice in Drosophila melanogaster. This study shows that fruit flies from a population living in a boreal and relatively unpredictable climate had more variable phototactic choices than fruit flies from a more stable tropical climate, consistent with bet-hedging theory. We experimentally...

Supplementary data, code, and information for ‘Assessing Climate Change Impacts on Extreme Weather Events: The Case For an Alternative (Bayesian) Approach’ (Mann et al. 2017)

M.E. Mann, E.A. Lloyd & N. Oreskes
The conventional approach to detecting and attributing climate change impacts on extreme weather events is generally based on frequentist statistical inference wherein a null hypothesis of no influence is assumed, and the alternative hypothesis of an influence is accepted only when the null hypothesis can be rejected at a sufficiently high (e.g., 95% or p = 0.05) level of confidence. Using a simple conceptual model for the occurrence of extreme weather events, we show that...

Data from: Early origin of sweet perception in the songbird radiation

Yasuka Toda, Meng-Ching Ko, Qiaoyi Liang, Eliot Miller, Alejandro Rico-Guevara, Tomoya Nakagita, Ayano Sakakibara, Kana Uemura, Timothy Sackton, Takashi Hayakawa, Simon Yung Wa Sin, Yoshiro Ishimaru, Takumi Misaka, Pablo Oteiza, James Crall, Scott Edwards, Shuichi Matsumura & Maude Baldwin
Early events in the evolutionary history of a clade can shape the sensory systems of descendant lineages. Although the avian ancestor may not have had a sweet receptor, the widespread incidence of nectar-feeding birds suggests multiple acquisitions of sugar detection. In this study, we identify a single early sensory shift of the umami receptor (the T1R1-T1R3 heterodimer) that conferred sweet-sensing abilities in songbirds, a large radiation containing nearly half of all living birds. We demonstrate...

CMS-Flux NBE 2020

Junjie Liu, Lartha Baskarran, Kevin Bowman, David Schimel, A. Anthony Bloom, Nick Parazoo, Tomohiro Oda, Dustin Carrol, Dimitris Menemenlis, Joanna Joiner, Roisin Commane, Bruce Daube, Lucianna V. Gatti, Kathryn McKain, John Miller, Britton B. Stephens, Colm Sweeney & Steven Wofsy
Top-down Net biosphere exchange estimates between Jan 2010 and Dec 2018 constrained by column CO2 observations from Greenhouse gases Observing Satellite and Orbiting Carbon Observatory 2. This dataset is openly shared in accordance with NASA Data and Information Policy (https://earthdata.nasa.gov/collaborate/open-data-services-and-software/data-information-policy).

Cambrian comb jellies from Utah illuminate the early evolution of nervous and sensory systems in ctenophores - Phylogenetic dataset

Luke Parry, Rudy Lerosey Aubril, James Weaver & Javier Ortega-Hernández
Ctenophores are a group of predatory macroinvertebrates whose controversial phylogenetic position has prompted several competing hypotheses regarding the evolution of animal organ systems. Although ctenophores date back at least to the Cambrian, they have a poor fossil record due to their gelatinous bodies. Here, we describe two ctenophore species from the Cambrian of Utah, which illuminate the early evolution of nervous and sensory features in the phylum. Thalassostaphylos elegans has 16 comb rows, an oral...

Coping with impostor feelings: evidence-based recommendations from a mixed methods study

Jill Barr-Walker, Debra A. Werner, Liz Kellermeyer & Michelle B. Bass
The negative effects of impostor phenomenon, also called impostor syndrome, include burnout and decreased job satisfaction and have led to an increased interest in addressing this issue in libraries in recent years. While previous research has shown that many librarians experience impostor phenomenon, the experience of coping with these feelings has not been widely studied. Our study’s aim was to understand how health sciences librarians cope with impostor phenomenon in the workplace, using a quantitative...

Data from: Testing for phylogenetic conflict among molecular data sets in the Tribe Triticeae (Gramineae)

Roberta J. Mason-Gamer & Elizabeth A. Kellogg
Four molecular data sets are available for the diploid intersterile genera of the cereal grain tribe Triticeae, and there are numerous differences among the four published trees. All six pairwise combinations of data sets were examined using tree comparisons, the incongruence length difference test, the Wilcoxon signed ranks test, and a permutation test. We describe some advantages, disadvantages, and properties of the different comparison methods. Test results provide no evidence for significant differences in the...

Data from: Step matrices and the interpretation of homoplasy

Richard H. Ree & Michael J. Donoghue
Assumptions about the costs of character change, coded in the form of a step matrix, determine most-parsimonious inferences of character evolution on phylogenies. We present a graphical approach to exploring the relationship between cost assumptions and evolutionary inferences from character data. The number of gains and losses of a binary trait on a phylogeny can be plotted over a range of cost assumptions, to reveal the inflection point at which there is a switch from...

Data from: Resolving the evolutionary relationships of molluscs with phylogenomic tools

Stephen A. Smith, Casey W. Dunn, Nerida G. Wilson, Freya E. Goetz, Caitlin Feehery, Sónia C. S. Andrade, Greg W. Rouse & Gonzalo Giribet
Molluscs (snails, octopuses, clams, and relatives) have great body plan disparity, and among animals only arthropods surpass them in species number. This diversity has made Mollusca one of the best-studied groups of animals, yet their evolutionary relationships remain poorly resolved. Open questions have important implications for the origin of Mollusca and morphological evolution within the group. These include whether the shell-less vermiform aplacophoran molluscs diverged prior to the origin of the shelled molluscs (Conchifera), or...

Data from: Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange, and distinct demographic histories

Mark J. Statham, Zhenghuan Wang, Carl D. Soulsbury, Jan Janecka, Benjamin N. Sacks, Keith B. Aubry, Oliver Berry, Ceiridwen J. Edwards & James Murdoch
Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin...

Data from: Context-dependent effects of large wildlife declines on small mammal communities in central Kenya

Hillary S. Young, Douglas J. McCauley, Rodolfo Dirzo, Jacob R. Goheen, Bernard Agwanda, Cara Brook, Erik O. Castillo, Adam W. Ferguson, Stephen N. Kinyua, Molly M. McDonough, Todd M. Palmer, Robert M. Pringle, Truman P. Young & Kristofer M. Helgen
Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife...

Data from: Pathogen burden, co-infection and major histocompatibility complex variability in the European badger (Meles meles)

Yung Wa Sin, Geetha Annavi, Hannah L. Dugdale, Chris Newman, Terry Burke & David W. Macdonald
Pathogen-mediated selection is thought to maintain the extreme diversity in the major histocompatibility complex (MHC) genes, operating through the heterozygote advantage, rare-allele advantage and fluctuating selection mechanisms. Heterozygote advantage (i.e., recognizing and binding a wider range of antigens than homozygotes) is expected to be more detectable when multiple pathogens are considered simultaneously. Here, we test if MHC diversity in a wild population of European badgers (Meles meles) is driven by pathogen-mediated selection. We examined individual...

Data from: Examining the full effects of landscape heterogeneity on spatial genetic variation: a multiple matrix regression approach for quantifying geographic and ecological isolation

Ian J. Wang
Understanding the effects of landscape heterogeneity on spatial genetic variation is a primary goal of landscape genetics. Ecological and geographic variables can contribute to genetic structure through geographic isolation, in which geographic barriers and distances restrict gene flow, and ecological isolation, in which gene flow among populations inhabiting different environments is limited by selection against dispersers moving between them. Although methods have been developed to study geographic isolation in detail, ecological isolation has received much...

Data from: A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages

Alicia R. Pérez-Porro, Daniel Navarro-Gómez, Maria J. Uriz & Gonzalo Giribet
Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available,...

Data from: A Palaeozoic stem-group to mite harvestmen revealed through integration of phylogenetics and development

Russell J. Garwood, Prashant P. Sharma, Jason A. Dunlop & Gonzalo Giribet
Successfully placing fossils in phylogenies is integral to understanding the tree of life. Crown-group Paleozoic members of the arachnid order Opiliones are indicative of ancient origins and one of the earliest arthropod terrestrialization events. Opiliones epitomize morphological stasis, and all known fossils have been placed within the four extant suborders. Here we report a Carboniferous harvestman species, Hastocularis argusgen. nov., sp. nov., reconstructed with microtomography (microCT). Phylogenetic analysis recovers this species, and the Devonian Eophalangium...

Data from: Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli

Nicholas Leiby & Christopher J. Marx
Evolutionary adaptation to a constant environment is often accompanied by specialization and a reduction of fitness in other environments. We assayed the ability of the Lenski Escherichia coli populations to grow on a range of carbon sources after 50,000 generations of adaptation on glucose. Using direct measurements of growth rates, we demonstrated that declines in performance were much less widespread than suggested by previous results from Biolog assays of cellular respiration. Surprisingly, there were many...

Data from: DOG1 expression is predicted by the seed-maturation environment and contributes to geographic variation in germination in Arabidopsis thaliana.

George C K Chiang, Melanie Bartsch, Deepak Barua, Kazumi Nakabayashi, Marilyne Debieu, Ilkka Kronholm, Maarten Koornneef, Wim J J Soppe, Kathleen Donohue & Juliette De Meaux
Seasonal germination timing of Arabidopsis thaliana strongly influences overall life history expression and is the target of intense natural selection. This seasonal germination timing depends strongly on the interaction between genetics and seasonal environments both before and after seed dispersal. DELAY OF GERMINATION 1 (DOG1) is the first gene that has been identified to be associated with natural variation in primary dormancy in Arabidopsis thaliana. Here, we report inter-accession variation in DOG1 expression and document...

Data from: Hybridization promotes color polymorphism in the aposematic harlequin poison frog, Oophaga histrionica

Iliana Medina, Ian J. Wang, Camilo Salazar & Adolfo Amezquita
Whether hybridization can be a mechanism that drives phenotypic diversity is a widely debated topic in evolutionary biology. In poison frogs (Dendrobatidae), assortative mating has been invoked to explain how new color morphs persist despite the expected homogenizing effects of natural selection. Here, we tested the complementary hypothesis that new morphs arise through hybridization between different color morphs. Specifically, we (1) reconstructed the phylogenetic relationships among the studied populations of a dart-poison frog to provide...

Data from: Early bursts of body size and shape evolution are rare in comparative data

Luke J. Harmon, Jonathan B. Losos, T. Jonathan Davies, Rosemary G. Gillespie, John L. Gittleman, W. Bryan Jennings, Kenneth H. Kozak, Mark A. McPeek, Franck Moreno-Roark, Thomas J. Near, Andy Purvis, Robert E. Ricklefs, Dolph Schluter, , Ole Seehausen, Brian L. Sidlauskas, Omar Torres-Carvajal, Jason T. Weir & Arne Ø. Mooers
George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed...

Data from: Identification of a transporter complex responsible for the cytosolic entry of nitrogen-containing-bisphosphonates

Zhou Yu, Lauren E. Surface, Chong Yon Park, Max A Horlbeck, Gregory A Wyant, Monther Abu-Remaileh, Timothy R. Peterson, David M. Sabatini, Jonathan S. Weissman & Erin K. O'Shea
Nitrogen-containing-bisphosphonates (N-BPs) are widely prescribed to treat osteoporosis and other bone-related diseases. Although previous studies established that N-BPs function by inhibiting the mevalonate pathway in osteoclasts, the mechanism by which N-BPs enter the cytosol from the extracellular space to reach their molecular target is not understood. Here we implemented a CRISPRi-mediated genome-wide screen and identified SLC37A3 (solute carrier family 37 member A3) as a gene required for the action of N-BPs in mammalian cells. We...

Data from: Herbarium specimens reveal increasing herbivory over the past century

Emily K. Meineke, Aimee T. Classen, Nathan J. Sanders & T. Jonathan Davies
Predicting how ecological interactions will respond to global change is a major challenge. Plants and their associated insect herbivores compose much of macroscopic diversity, yet how their interactions have been altered by recent environmental change remains underexplored. To address this gap, we quantified herbivory on herbarium specimens of four plant species with records extending back 112 years. Our study focused on the northeastern US, where temperatures have increased rapidly over the last few decades. This...

Data from: Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

Benjamin E. R. Rubin, Jon G. Sanders, Kyle M. Turner, Naomi E. Pierce & Sarah D. Kocher
Social interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviors and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both eusocial and solitary bee species within the behaviorally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between...

Data from: Locality or habitat? Exploring predictors of biodiversity in Amazonia

Camila D. Ritter, Alexander Zizka, Christopher Barnes, R. Henrik Nilsson, Fabian Roger & Alexandre Antonelli
Amazonia is an environmentally heterogeneous and biologically megadiverse region, and its biodiversity varies considerably over space. However, existing knowledge on Amazonian biodiversity and its environmental determinants stems almost exclusively from studies of macroscopic above‐ground organisms, notably vertebrates and trees. In contrast, diversity patterns of most other organisms remain elusive, although some of them, for instance microorganisms, constitute the overwhelming majority of taxa in any given location, both in terms of diversity and abundance. Here, we...

Data from: The spectre of too many species

Adam D. Leache, Tianqi Zhu, Bruce Rannala & Ziheng Yang
Recent simulation studies examining the performance of Bayesian species delimitation as implemented in the BPP program have suggested that BPP may detect population splits but not species divergences and that it tends to over-split when data of many loci are analyzed. Here we confirm these results and provide the mathematical justifications. We point out that the distinction between population and species splits made in the protracted speciation model has no influence on the generation of...

Data from: Structural complexity of hunting habitat and territoriality increase the reversed sexual size dimorphism in diurnal raptors

Lorenzo Pérez-Camacho, Sara Martínez-Hesterkamp, Salvador Rebollo, Gonzalo García-Salgado & Ignacio Morales-Castilla
Despite numerous efforts and many hypotheses to explain the selective pressures that may have favoured reversed sexual dimorphism (RSD) in raptors ‐ i.e. that the female is larger than the male ‐ some drivers of RSD are still unknown. Here we analyse how much variation in RSD is explained by hunting habitat structure, territoriality or territory size. We do so using data on diurnal raptors from the New World and the Western Palearctic – i.e....

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