74 Works

Revisiting the sedimentary record of the rise of diatoms

Sophie Westacott, Noah Planavsky, Ming-Yu Zhao & Pincelli Hull
Diatoms are a major primary producer in the modern oceans and play a critical role in the marine silica cycle. Their rise to dominance is recognized as one of the largest shifts in Cenozoic marine ecosystems, but the timing of this transition is debated. Here, we use a diagenetic model to examine the effect of sedimentation rate and temperature on the burial efficiency of biogenic silica over the past 66 million years (i.e., the Cenozoic)....

Data from: Phylogenomic subsampling and the search for phylogenetically reliable loci

Nicolás Mongiardino Koch
Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale datasets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods, or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their...

Dispersers and environment drive global variation in fruit color syndromes

Miranda Sinnott-Armstrong, Michael Donoghue & Walter Jetz
The colors of fleshy fruits play a critical role in plant dispersal by advertising ripe fruits to consumers. Fruit colors have long been classified into syndromes attributed to selection by animal dispersers, despite weak evidence for this hypothesis. Here, we test the relative importance of biotic (bird and mammal frugivory) and abiotic (wet season temperatures, growing season length, and UV-B radiation) factors in determining fruit color syndrome in 3,163 species of fleshy-fruited plants. We find...

Transect and plot data from: Fruit trees drive small-scale movement of elephants in Kibale National Park, Uganda

Lorena Benitez & Simon Queenborough
Understanding what motivates animal spatial behavior requires discerning the relationship between animals and the landscape in which they move. Many studies have focused on large scale trends that drive migrations and movement across broad landscapes, but few studies have focused on drivers of local movement within smaller areas based on fine–scale landscape heterogeneity. This is especially true for African elephants (Loxodonta africana), whose movements in relation to landscape variables have frequently been studied across vast...

Supplementary code for ‘Greenhouse Warming and Changes in the Seasonal Cycle of Temperature: Model Versus Observations’ (Mann and Park 1996)

M.E. Mann & J. Park
Thomson [1995] argues that an enhanced green-house effect may be altering the seasonal cycle in temperature. We compare trends in the amplitude and phase of the seasonal cycle in observational temperature data in the northern hemisphere with the response of two general circulation models to increased CO2 concentrations. Sizeable amplitude decreases are observed in both models and observations. Significant phase delays (ie, later seasonal transitions) are found in the simulations, opposite to the phase advances...

Supplementary data and code for ‘Robust estimation of background noise and signal detection in climatic time series’ (Mann and Lees 1996)

M.E. Mann & J.M. Lees
We present a new technique for isolating climate signals in time series with a characteristic ‘red’ noise background which arises from temporal persistence. This background is estimated by a ‘robust’ procedure that, unlike conventional techniques, is largely unbiased by the presence of signals immersed in the noise. Making use of multiple-taper spectral analysis methods, the technique further provides for a distinction between purely harmonic (periodic) signals, and broader-band (‘quasiperiodic’) signals. The effectiveness of our signal...

Population structure of giant clams (sub-family: Tridacninae) across Palau: implications for conservation

Lincoln Rehm, Lincy Marino, Randa Jonathan, Amanda Holt, Richard McCourt & Alison Sweeney
Giant clams (Sub-family: Tridacninae) are an important food and economic resource for the Republic of Palau. Previous surveys of giant clams conducted over 20 years ago found diverse, localized populations across Helen Reef and the Rock Islands Southern Lagoon. This study updates population structure data for Palauan giant clams and investigates the impacts of conservation on these important bivalves. We surveyed eleven sites within fringing, barrier, atoll, and oceanic reefs across the Palauan archipelago (total...

Ecosystem sulfur accumulation following woody encroachment drives a more open S-cycle in a subtropical savanna

Yong Zhou, Ayumi Hyodo & Thomas Boutton
Globally widespread woody encroachment into grass-dominated ecosystems has substantial consequences for carbon (C), nitrogen (N), and phosphorus (P) cycles. Despite its significance as an essential macronutrient, however, little is known regarding potential changes in the sulfur (S) cycle. We quantified S concentrations, stoichiometric relationships, and δ34S values in the plant-soil environment to investigate landscape-scale changes in the S cycle following grassland-to-woodland transitions in a subtropical savanna. Plant tissues of woody species had significantly higher S...

Raw images for: The narrowing of dendrite branches across nodes follows a well-defined scaling law

Maijia Liao, Xin Liang & Jonathon Howard
The systematic variation of diameters in branched networks has tantalized biologists since the discovery of da Vinci’s rule for trees. Da Vinci’s rule can be formulated as a power law with exponent two: the square of the mother branch’s diameter is equal to the sum of the squares of those of the daughters. Power laws, with different exponents, have been proposed for branching in circulatory systems (Murray’s law with exponent 3) and in neurons (Rall’s...

The Anatomy of Sentiment-Driven Fluctuations

Sushant Acharya, Jess Benhabib & Zhen Huo
We show that changes in sentiment that aren’t related to fundamentals can drive persistent macroeconomic fluctuations even when all economic agents are rational. Changes in sentiment can also affect how fundamental shocks affect macroeconomic outcomes.

Evidence of hippocampal learning in human infants

Cameron Ellis, Lena Skalaban, Tristan Yates, Vikranth Bejjanki, Natalia Córdova & Nicholas Turk-Browne
The hippocampus is essential for human memory. The protracted maturation of memory capacities from infancy through early childhood is thus often attributed to hippocampal immaturity. The hippocampus of human infants has been characterized in terms of anatomy, but its function has never been tested directly because of technical challenges. Here we use recently developed methods for task-based fMRI in awake human infants to test whether the infant hippocampus supports statistical learning. Hippocampal activity increased with...

Data from: Rapid microgeographic evolution in response to climate change

A. Z. Andis Arietta & David Skelly
Environmental change is predicted to accelerate into the future and will exert strong selection pressure on biota. While many species may be fated to extinction, others may survive through their capacity to evolve rapidly at highly localized (i.e. microgeographic) scales. Yet, even as new examples have been discovered, the limits to such evolutionary responses have not often been evaluated. One of the first examples of microgeographic variation involved pond populations of wood frogs (Rana sylvatica)....

Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers

Kai He, Michael Berenbrink, Kevin Campbell, Triston Eastman, Hannah Czolacz, Shuhao Li, Akio Shinohara, Shin-Ichiro Kawada & Mark Springer
Identifying the phylogenomic underpinnings of specialized phenotypes that fueled evolutionary transitions into new adaptive zones is central to evolutionary biology. The order Eulipotyphla (e.g., moles, shrews, and hedgehogs) is ideally suited to address this question as semi-fossorial, fossorial, and semi-aquatic forms have repeatedly arisen from terrestrial forbearers. However, our understanding of the ecomorphological pathways leading to these diverse lifestyles has been confounded by a fragmentary fossil record and potential morphological convergence. The net surface charge...

Data from: Accelerated diversification explains the exceptional species richness of tropical characoid fishes

Bruno Melo, Brian Sidlauskas, Thomas Near, Fabio Roxo, Ava Ghezelayagh, Luz Ochoa, Melanie Stiassny, Jairo Arroyave, Jonathan Chang, Brant Faircloth, Daniel MacGuigan, Richard Harrington, Ricardo Benine, Michael Burns, Kendra Hoekzema, Natalia Sanches, Javier Maldonado-Ocampo, Ricardo Castro, Fausto Foresti, Michael Alfaro & Claudio Oliveira
The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1288 ultraconserved element loci spanning 293 species, 211...

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...

Genomic and phenotypic divergence informs translocation strategies for an endangered freshwater fish

Liam Taylor, Edgar Benavides, Jeffrey Simmons & Thomas Near
Translocation, the movement of organisms for conservation purposes, can result in unintended introgression if genetic material flows between populations in new ways. The Bluemask Darter Etheostoma akatulo is a federally endangered species of freshwater fish inhabiting the Caney Fork River system and three of its tributaries (Collins River, Rocky River, and Cane Creek) in Tennessee. The current conservation strategy for Bluemas­k Darters involves translocating the progeny of broodstock from the Collins River, in the west,...

DNS results (Nusselt number) for: The effect of rotation on double diffusive convection: Perspectives from linear stability analysis

Yu Liang, Jeffrey Carpenter & Mary-Louise Timmermans
Diffusive convection can occur when two constituents of a stratified fluid have opposing effects on its stratification and different molecular diffusivities. This form of convection arises for the particular temperature and salinity stratification in the Arctic Ocean and is relevant to heat fluxes. Previous studies have suggested that planetary rotation may influence diffusive-convective heat fluxes, although the precise physical mechanisms and regime of rotational influence are not well understood. A linear stability analysis of a...

Noctuid and geometrid moth assemblages show divergent elevational gradients in body size and color lightness

Lea Heidrich, Stefan Pinkert, Roland Brandl, Claus Bässler, Hermann Hacker, Nicolas Roth, Annika Busse & Jörg Müller
Previous macroecological studies have suggested that larger and darker insects are favored in cold environments and that the importance of body size and color for the absorption of solar radiation is not limited to diurnal insects. However, whether these effects hold true for local communities and are consistent across taxonomic groups and sampling years remains unexplored. This study examined the variations in body size and color lightness of the two major families of nocturnal moths,...

Data from: Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation

Elyse Parker, Alex Dornburg, Carl Struthers, Christopher Jones & Thomas Near
Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are...

Ocean and ice without waves data for role of surface gravity waves in aquaplanet ocean climates

Joshua Studholme, Margarita Markina & Sergey Gulev
This data corresponds to the runs analysed in the manscript: Role of Surface Gravity Waves in Aquaplanet Ocean Climates (JAMES, 2021). In this work, we present a set of idealised numerical experiments that demonstrate the thermodynamic and dynamic implications of surface gravity waves for the oceanic climate of an aquaplanet. We study the impact of accounting for modulations by such waves upon air-sea momentum fluxes, Langmuir circulation and the Stokes-Coriolis force. This dataset is made...

Plasmodium infection induces cross-reactive antibodies to carbohydrate epitopes on the SARS-CoV-2 Spike protein

Sarah Lapidus, Feimei Liu, Arnau Casanovas-Massana, Yile Dai, John D. Huck, Carolina Lucas, Jon Klein, Renata B. Filler, Madison S. Strine, Mouhamad Sy, Awa B. Deme, Aida S. Badiane, Baba Dieye, Ibrahima Mbaye Ndiaye, Younous Diedhiou, Amadou Moctar Mbaye, Cheikh Tidiane Diagne, Inés Vigan-Womas, Alassane Mbengue, Bacary D. Sadio, Moussa M. Diagne, Adam J. Moore, Khadidiatou Mangou, Fatoumata Diallo, Seynabou D. Sene … & Amy K. Bei
Individuals with acute malaria infection generated high levels of antibodies that cross-react with the SARS-CoV-2 Spike protein. Cross-reactive antibodies specifically recognized the sialic acid moiety on N-linked glycans of the Spike protein and do not neutralize in vitro SARS-CoV-2. Sero-surveillance is critical for monitoring and projecting disease burden and risk during the pandemic; however, routine use of Spike protein-based assays may overestimate SARS-CoV-2 exposure and population-level immunity in malaria-endemic countries.

Trends and geographic variation in population thriving, struggling, and suffering across the US, 2008-2017: A retrospective repeated cross-sectional study

Jeph Herrin
Objectives: Wellbeing is a holistic, positively framed conception of health, integrating physical, emotional, social, financial, community, and spiritual aspects of life. High wellbeing is an intrinsically worthy goal for individuals, communities, and nations. Multiple measures of wellbeing exist, yet we lack information to identify benchmarks, geographical disparities, and targets for intervention to improve population life evaluation. Design: Using data from the Gallup National Health and Well-Being Index, we conducted retrospective analyses of a series of...

Data from: Belowground community turnover accelerates the decomposition of standing dead wood

Mark Bradford
Standing dead trees (snags) decompose more slowly than downed dead wood and provide critical habitat for many species. The rate at which snags fall therefore influences forest carbon dynamics and biodiversity. Fall rates correlate strongly with mean annual temperature, presumably because warmer climates facilitate faster wood decomposition and hence degradation of the structural stability of standing wood. These faster decomposition rates coincide with turnover from fungal-dominated wood decomposer communities in cooler forests to co-domination by...

Data for: Africa’s oldest dinosaurs reveal early climatic suppression of dinosaurian distribution

Christopher Griffin, Brenen Wynd, Darlington Munyikwa, Timothy Broderick, Michel Zondo, Stephen Tolan, Max Langer, Sterling Nesbitt & Hazel Taruvinga
The vertebrate lineages that would shape Mesozoic and Cenozoic terrestrial ecosystems originated within faunas across Triassic Pangaea1-11. By the Late Triassic (Carnian Stage, ~235 Ma), cosmopolitan ‘disaster faunas’12-14 had given way to highly endemic assemblages12,13 on the supercontinent. Testing the tempo and mode of the establishment of this endemism is challenging—paradoxically, there were few geographic barriers to dispersal across Pangaea during the Late Triassic. Instead, palaeolatitudinal climate belts, and not continental boundaries, are hypothesized to...

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  • 2021

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  • Yale University
  • University of Oxford
  • Institute of Oceanology. PP Shirshov Russian Academy of Sciences
  • Pennsylvania State University
  • University of Pennsylvania
  • Stanford University
  • Princeton University
  • University of Michigan-Ann Arbor
  • National Autonomous University of Mexico
  • University of Sao Paulo