42 Works

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...

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...

Ecological opportunity and the rise and fall of crocodylomorph evolutionary innovation

Thomas Stubbs, Stephanie Pierce, Armin Elsler, Philip Anderson, Emily Rayfield & Michael Benton
Understanding the origin, expansion and loss of biodiversity is fundamental to evolutionary biology. The approximately 26 living species of crocodylomorphs (crocodiles, caimans, alligators and gharials) represent just a snapshot of the group’s rich 230-million-year history, whereas the fossil record reveals a hidden past of great diversity and innovation, including ocean and land-dwelling forms, herbivores, omnivores and apex predators. In this macroevolutionary study of skull and jaw shape disparity, we show that crocodylomorph ecomorphological variation peaked...

Habitat structure mediates vulnerability to climate change through its effects on thermoregulatory behavior

Lauren Neel, Michael Logan, Daniel Nicholson, Christina Miller, Albert Chung, Inbar Maayan, Zach Degon, Madeline DuBois, John David Curlis, Q Taylor, Kaitlin Keegan, Owen McMillan, Jonathan Losos & Christian Cox
Tropical ectotherms are thought to be especially vulnerable to climate change because they are thermal specialists, having evolved in aseasonal thermal environments. However, even within the tropics, habitat structure can influence opportunities for behavioral thermoregulation. Open (and edge) habitats likely promote more effective thermoregulation due to the high spatial heterogeneity of the thermal landscape, while forests are thermally homogenous and may constrain opportunities for behavioral buffering of environmental temperatures. Nevertheless, the ways in which behavior...

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...

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...

Dataset for: Conservation genomics of federally endangered Texella harvester species (Arachnida, Opiliones, Phalangodidae) from cave and karst habitats of central Texas

Marshal Hedin, Shahan Derkarabetian, James Reddell & Pierre Paquin
Genomic-scale data for non-model taxa are providing new insights into landscape genomic structuring and species limits, leading to more informed conservation decisions, particularly in taxa with extremely restricted microhabitat preferences and small geographic distributions. This study applied sequence capture of ultraconserved elements (UCEs) to gather genomic-scale data for two federally endangered Texella harvester species distributed in Edwards Formation cave and karst habitats of central Texas, near Austin. We gathered UCE data for 51 T. reyesi...

Multiple sequence alignments and phylogenetic trees from: Co-option of the limb patterning program in cephalopod eye development

Kristen Koenig
Background Across the Metazoa, similar genetic programs are found in the development of analogous, independently evolved, morphological features. The functional significance of this reuse and the underlying mechanisms of co-option remain unclear. Cephalopods have evolved a highly acute visual system with a cup shaped retina and a novel refractive lens in the anterior, important for a number of sophisticated behaviors including predation, mating and camouflage. Almost nothing is known about the molecular-genetics of lens development...

Data sets and analyses for genomics of cryptic speciation in Catharus thrushes

Scott Edwards, Flavia Termignoni-Garcia & Jeremy Kirchman
Cryptic speciation may occur when reproductive isolation is recent or the accumulation of morphological differences between sister lineages is slowed by stabilizing selection preventing phenotypic differentiation. In North America, Bicknell’s Thrush (Catharus bicknelli) and its sister species, the Gray-cheeked Thrush (Catharus minimus), are parapatrically breeding migratory songbirds, distinguishable in nature only by subtle differences in song and coloration, and were recognized as distinct species only in the 1990s. Previous molecular studies have estimated that the...

Data from: Functional innovation promotes diversification of form in the evolution of an ultrafast trap-jaw mechanism

Douglas Booher, Joshua Gibson, Cong Liu, John Longino, Brian Fisher, Milan Janda, Nitish Narula, Evropi Toulkeridou, Alexander Mikheyev, Andrew Suarez & Evan Economo
Evolutionary innovations underlie the rise of diversity and complexity—the two long-term trends in the history of life. How does natural selection redesign multiple interacting parts to achieve a new emergent function? We investigated the evolution of a biomechanical innovation, the latch-spring mechanism of trap-jaw ants, to address two outstanding evolutionary problems: how form and function change in a system during the evolution of new complex traits, and whether such innovations and the diversity they beget...

Supplemental Material for \"Biomechanical analyses of Cambrian euarthropod limbs reveal their effectiveness in mastication and durophagy\"

Russell Bicknell, James Holmes, Gregory Edgecombe, Sarah Losso, Javier Ortega-Hernández, Stephen Wroe & John Paterson
Durophagy arose in the Cambrian and greatly influenced the diversification of biomineralised defensive structures throughout the Phanerozoic. Spinose gnathobases on protopodites of Cambrian euarthropod limbs are considered key innovations for shell-crushing, yet few studies have demonstrated their effectiveness with biomechanical models. Here we present finite element analysis models of two Cambrian trilobites with prominent gnathobases—Redlichia rex and Olenoides serratus—and compare these to the protopodites of the Cambrian euarthropod Sidneyia inexpectans and the modern American horseshoe...

Estimating the Net Value of Treating Hepatitis C Virus Using Newly Available Direct-Acting Antivirals in India (Supporting Datasets)

David Bloom, Alex Khoury & V. Srinivasan
Recently developed direct-acting antiviral (DAA) treatments for hepatitis C virus (HCV) have been groundbreaking for their high efficacy across disease genotypes and lack of severe side effects. This study uses a cost-of-illness (COI) approach to estimate the net value conferred by this class of drugs using the cost and efficacy of one of these novel drug combinations, sofosbuvir and velpatasvir (SOF/VEL), recently licensed for generic manufacture in India. This study considers COI of lifetime earnings...

Phytogeographic history of the Tea family inferred through high-resolution phylogeny and fossils

Yujing Yan, Charles Davis, Dimitar Dimitrov, Zhiheng Wang, Carsten Rahbek & Michael Borregaard
The tea family (Theaceae) has a highly unusual amphi-Pacific disjunct distribution: most extant species in the family are restricted to subtropical evergreen broadleaf forests in East Asia, while a handful of species occur exclusively in the subtropical and tropical Americas. Here we used an approach that integrates the rich fossil evidence of this group with phylogenies in biogeographic analysis to study the processes behind this distribution pattern. We first combined genome-skimming sequencing with existing molecular...

Deletion of the sodium/hydrogen exchanger 6 causes low bone volume in adult mice

Fuster Daniel, Daniela Schnyder, Giuseppe Albano, Patrycja Kucharczyk, Silvia Dolder, Mark Siegrist, Manuel Anderegg, Ganesh Pathare, Willy Hofstetter, Roland Baron & Daniel G. Fuster
The sodium/hydrogen exchanger 6 (NHE6) localizes to recycling endosomes, where it mediates endosomal alkalinization through K+/H+ exchange. Mutations in the SLC9A6 gene encoding NHE6 cause severe X-linked mental retardation, epilepsy, autism and corticobasal degeneration in humans. Patients with SLC9A6 mutations exhibit skeletal malformations, and a previous study suggested a key role of NHE6 in osteoblast-mediated mineralization. The goal of this study was to explore the role of NHE6 in bone homeostasis. To this end, we...

Evolutionary tradeoffs between male secondary sexual traits revealed by a phylogeny of the hyperdiverse tribe Eumaeini (Lepidoptera: Lycaenidae)

Wendy A. Valencia-Montoya, Tiago B. Quental, João Filipe R. Tonini, Gerard Talavera, James D. Crall, Gerardo Lamas, Robert C. Busby, Ana Paula S. Carvalho, Ana B. Morais, Nicolás Oliveira Mega, Helena Piccoli Romanowski, Marjorie A. Liénard, Shayla Salzman, Melissa R. L. Whitaker, Akito Y. Kawahara, David J. Lohman, Robert K. Robbins & Naomi E. Pierce
Male butterflies in the hyperdiverse tribe Eumaeini possess an unusually complex and diverse repertoire of secondary sexual characteristics involved in pheromone production and dissemination. Maintaining multiple sexually selected traits is likely to be metabolically costly, potentially resulting in trade-offs in the evolution of male signals. However, a phylogenetic framework to test hypotheses regarding the evolution and maintenance of male sexual traits in Eumaeini has been lacking. Here, we infer a comprehensive, time-calibrated phylogeny from 379...

Dataset female gregariousness in bonobos and chimpanzees

Martin Surbeck
Spatial association between females often mirrors pattern and strength of social relationships and cooperation within groups. Here we test for proposed differences in female-female associations and the role of sexual signaling between the two species of the genus Pan that have been linked to difference in female cooperation. Unlike previous studies, we found only limited evidence for a higher female-female gregariousness in bonobos. While bonobo females exhibited a slightly higher average number of females in...

Vachellia drepanolobium nutrient translocation in response to smoke

Katherine Angier, Richard Rabideau-Childers, Brendan Dean, Meghan Blumstein, Walker Darling, Annina Kennedy-Yoon, Clayton Ziemke, Christian Perez-Martinez, Donghao Wu, Wenqing Ye, Inam Yekwayo, Duncan Kimuyu, Dino Martins & Naomi Pierce
1. Fire is a major selective force on arid grassland communities, favoring traits such as the smoke-induced seed germination response seen in a wide variety of plant species. However, little is known about the relevance of smoke as a cue for plants beyond the seedling stage. 2. We exposed a fire-adapted savanna tree, Vachellia (=Acacia) drepanolobium, to smoke and compared nutrient concentrations in leaf and root tissues to unexposed controls. Experiments were performed on three...

Data for: Ecology and behavior predict an evolutionary trade-off between song complexity and elaborate plumages in antwrens (Aves, Thamnophilidae)

Renata Beco, Luís Fábio Silveira, Elizabeth Derryberry & Gustavo Bravo
The environment can impose constraints on signal transmission properties such that signals should evolve in predictable directions (Sensory Drive Hypothesis). However, behavioral and ecological factors can limit investment in more than one sensory modality leading to a trade-off in use of different signals (Transfer Hypothesis). In birds, there is mixed evidence for both sensory drive and transfer hypothesis. Few studies have tested sensory drive while also evaluating the transfer hypothesis, limiting understanding of the relative...

Dataset S1 - Noelaerhabdaceae organic carbon isotope culture data compilation

Samuel Phelps, Gwenn Hennon, Sonya Dyhrman, María Hernández-Limón, Olivia Williamson & Pratigya Polissar
The carbon isotope fractionation in algal organic matter (Ep), including the long-chain alkenones produced by the coccolithophorid family Noelaerhabdaceae, is used to reconstruct past atmospheric CO2 levels. The conventional proxy linearly relates Ep to changes in cellular carbon demand relative to diffusive CO2 supply, with larger Ep values occurring at lower carbon demand relative to supply (i.e. abundant CO2). However, the response of Gephyrocapsa oceanica, one of the dominant alkenone producers of the last few...

Genomic and transcriptomic data for the frog Platyplectrum ornatum

Scott Edwards, Sangeet Lamichhaney, Renee Catullo, Scott Keogh, Simon Clulow & Tariq Ezaz
The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms that drive or constrain genome size are poorly understood. Here we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog (Platyplectrum ornatum)...

Beneficial worm allies warn plants of parasite attack belowground and reduce aboveground herbivore preference and performance

Shokoofeh Kamali, Ali Javadmanesh, Lukasz Stelinski, Tina Kydnt, Alireza Seifi, Mojtaba Hosseini, Mehyar Heydarpour, Javad Asili & Javad Karimi
We investigated responses of tomato (Solanum lycopersicum) to two functional guilds of nematodes - plant parasite (Meloidogyne javanica) and entomopathogens (Heterorhabditis bacteriophora, Steinernema feltiae belowground, and S. carpocapsae) - as well as a leaf mining insect (Tuta absoluta) aboveground. Our results indicate that entomopathogenic nematodes (EPNs): 1) induced plant defense responses, 2) reduced root knot nematode (RKN) infestation belowground and 3) reduced herbivore (T. absoluta) host preference and performance aboveground. Concurrently, we investigated the plant...

The AI Economist: Taxation policy design via two-level deep reinforcement learning

Stephan Zheng, Alexander Trott, Sunil Srinivasa, David Parkes & Richard Socher
This dataset contains all raw experimental data for the paper "The AI Economist: Taxation Policy Design via Two-level Deep Multi-Agent Reinforcement Learning". The accompanying simulation, reinforcement learning, and data visualization code can be found at https://github.com/salesforce/ai-economist. For the one-step economy experiments, we provide: training histories, configuration files (these experiments do not use phases), and final agent and planner models. For the Gather-Trade-Build scenario, the data covers 6 spatial layouts: two Open-Quadrant (with 4 and 10...

Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog

Ricardo Medina, Ella Vázquez-Domínguez, Guinevere O.U. Wogan, Ke Bi, Flavia Termignoni-García, Manuel Hernando Bernal, Juan P. Jaramillo-Correa & Ian J. Wang
Understanding how geographic and environmental heterogeneity drive local patterns of genetic variation is a major goal of ecological genomics and a key question in evolutionary biology. The tropical Andes and inter-Andean valleys are shaped by markedly heterogeneous landscapes, where species experience strong selective processes. We examined genome-wide SNP data together with behavioral and ecological traits (mating calls and body size) known to contribute to genetic isolation in anurans in the emerald-eyed treefrog, Boana platanera, distributed...

The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)

Keaka Farleigh, Sarah A. Vladimirova, Christopher Blair, Jason T. Bracken, Nazila Koochekian, Drew R. Schield, Daren C. Card, Nicholas Finger, Jonathan Henault, Adam D. Leaché, Todd A. Castoe & Tereza Jezkova
Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here we explore...

Shorter distal forelimbs benefit bipedal walking and running mechanics: implications for hominin forelimb evolution

Andrew Yegian, Yanish Tucker, Stephen Gillinov & Daniel Lieberman
This file provides the data from the manuscript "Shorter distal forelimbs benefit bipedal walking and running mechanics: implications for hominin forelimb evolution" sin the American Journal of Physical Anthropology. Objectives: Brachial index is a skeletal ratio that describes the relative length of the distal forelimb. Over the course of hominin evolution, a shift towards smaller brachial indices occurred. First, Pleistocene australopiths yield values between extant chimpanzees and humans, with further evolution in Pliocene Homo to...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Harvard University
  • University of Florida
  • Smithsonian Tropical Research Institute
  • Yale University
  • Zhejiang University
  • University of Washington
  • Stanford University
  • Botanical Institute of Barcelona
  • University of California, San Diego
  • University of Nevada Reno