66 Works

Ecological opportunity from innnovation, not islands, drove the Anole lizard adaptive radiation

Edward Burress
Islands are thought to facilitate adaptive radiation by providing release from competition and predation. Anole lizards are considered a classic example of this phenomenon: different ecological specialists (‘ecomorphs’) evolved in the Caribbean Greater Antilles (Cuba, Hispaniola, Jamaica, and Puerto Rico), resulting in convergent assemblages that are not observed in mainland Latin America. Yet, the role of islands in facilitating adaptive radiation is more often implied than directly tested, leaving uncertain the role of biogeography in...

Supplementary data and code for ‘Oscillatory Spatiotemporal Signal Detection in Climate Studies: A Multiple-Taper Spectral Domain Approach’ (Mann and Park 1999)

M.E. Mann & J. Park
This chapter introduces a methodology for signal detection and reconstruction of irregular spatiotemporal oscillatory signals—the multiple-taper spectrum estimation method (MTM)–singular-value decomposition (SVD) methodology. This methodology is offered as an alternative technique which avoids most of the problems encountered in traditional techniques and provides an efficient exploratory method for climate signal detection. The associated signal-detection parameter—the local fractional variance spectrum (LFV) spectrum—yields the correct null distribution for a very general class of spatiotemporal climate noise processes...

Ocean and ice spin-up 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...

Varying impacts of logging frequency on tree communities and carbon storage across evergreen and deciduous tropical forests in the Andaman Islands, India

Akshay Surendra, Anand Osuri & Jayashree Ratnam
The majority of Earth’s tropical forests have been selectively logged; some on repeated occasions. Selective logging is known to affect forest structure, composition and function in various ways, but how such effects vary with logging frequency and across forest types remains unclear. In the Andaman Archipelago in India, we examined adult and pole-sized trees in baseline (unlogged since 1990s), once-logged (logged between 2007 and 2014) and twice-logged (logged in early 1990s and between 2007 and...

Ultraconserved elements data for Amarsipus and Pelagiaria

Richard Harrington, Matt Friedman, Masaki Miya, Thomas Near & Matthew Campbell
Amarsipus carlsbergi is a rare mesopelagic fish distributed in the Indian and Pacific Oceans, and is the only species classified in the family Amarsipidae. Since its description in 1969, phylogenetic hypotheses have varied regarding its relationship with other percomorph lineages, but most have indicated a close relationship with the traditional suborder Stromateoidei. Molecular phylogenies place families previously classified in Stromateoidei within a diverse clade– Pelagiaria– that includes fishes such as tunas, cutlassfishes, and pomfrets. A...

Structure Here, Bias There: Hierarchical Generalization by Jointly Learning Syntactic Transformations

Karl Mulligan, Robert Frank & Tal Linzen

Comparing methods of tree-construction across mildly context-sensitive formalisms

Tim Hunter & Robert Frank

An unanticipated role for sphingosine kinase-2 in bone and in the anabolic effect of parathyroid hormone: Supplementary figures

Joanne Walker, Gang-Qing Yao, Edwin Siu, Meiling Zhu, Christine Simpson & Karl Insogna
Sphingosine-1-phosphate (S1P) is an anabolic clastokine. SPHK is the rate-limiting enzyme in S1P production and has two isoforms. To evaluate the roles of SPHK1 and SPHK2 in bone, we examined the skeletal phenotype of mice with selective deletion of SPHK1 in osteoclasts (SPHK1-Oc-/-) and mice in which the SPHK2 gene was deleted in all tissues (SPHK2-/-). SPHK1-Oc-/- had normal bone mass. By contrast, SPHK2-/- female mice had a 14% lower spinal BMD (p<0.01) and males...

Compartmentalization of cerebrospinal fluid inflammation across the spectrum of HIV infection

Richard Price, Magnus Gisslen, Sheila Keating, Serena Spudich, Victor Arechiga, Sophie Stephenson, Henrik Zetterberg, Clara Di Germanio, Kaj Blennow, Lars Hagberg, Philip Norris, Julia Peterson, Barbara Shacklett & Constantin Yiannoutsos
Objective: To characterize the evolution of central nervous system (CNS) inflammation in HIV-1 infection applying a panel of cerebrospinal fluid (CSF) inflammatory biomarkers to grouped subjects representing a broad spectrum of systemic HIV-1 immune suppression, CNS injury and viral control. Methods: This is a cross-sectional analysis of archived CSF and blood samples, assessing concentrations of 10 functionally diverse soluble inflammatory biomarkers by immunoassays in 143 HIV-1-infected subjects divided into 8 groups: untreated primary HIV-1 infection...

Data from: Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments

Sylvie Estrela, Alicia Sanchez-Gorostiaga, Jean Vila & Alvaro Sanchez
A major open question in microbial community ecology is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by this challenge, we investigate whether communities assembled in pairs of nutrients can be predicted from those assembled in every single nutrient alone. We first find that although the null, naturally additive model generally predicts well the family-level community composition, there exist systematic deviations from the additive...

Clinical Trial Transparency and Data-Sharing Among Bio-Pharmaceutical Companies and the Role of Company Size, Location, and Product Type: A Cross-Sectional Descriptive Analysis

Sydney Axson, Michelle Mello, Deborah Lincow, Catherine Yang, Cary Gross, Joseph Ross & Jennifer Miller
Objective: To examine company characteristics associated with better transparency and to apply a tool used to measure and improve clinical trial transparency among large companies and drugs, to smaller companies and biologics. Design: Cross-sectional descriptive analysis. Setting and participants. Novel drugs and biologics FDA approved in 2016 and 2017, and their company sponsors. Using established Good Pharma Scorecard (GPS) measures, companies and products were evaluated on their clinical trial registration, results dissemination, and FDA Amendments...

An objective-based prioritization approach to support trophic complexity through ecological restoration

Emma Ladouceur, Jennifer McGowan, Patrick Huber, Hugh Possingham, Davide Scridel, Roel Van Klink, Peter Poschlod, Hans Cornelissen, Costantino Bonomi & Borja Jiménez-Alfaro
1. Reassembling ecological communities and rebuilding habitats through active restoration treatments requires curating the selection of plant species to use in seeding and planting mixes. Ideally, these mixes should be assembled based on attributes that support ecosystem function and services, promote plant and animal species interactions and ecological networks in restoration while balancing project constraints. Despite these critical considerations, it is common for species mixes to be selected opportunistically. Reframing the selection of seed mixes...

Retinotopic organization of visual cortex in human infants

Cameron Ellis, Tristan Yates, Lena Skalaban, Vikranth Bejjanki, Michael Arcaro & Nicholas Turk-Browne
Vision develops rapidly during infancy, yet how visual cortex is organized during this period is unclear. In particular, it is unknown whether functional maps that organize the mature adult visual cortex are present in the infant striate and extrastriate cortex. Here we test the functional maturity of infant visual cortex by performing retinotopic mapping with fMRI. Infants aged 5–23 months had retinotopic maps, with alternating preferences for vertical and horizontal meridians indicative of area boundaries...

Cnidocyte discharge analysis

Natasha Picciani
Complex biological traits often originate by integrating previously separate parts, but the organismal functions of these precursors are challenging to infer. If we can understand the ancestral functions of these precursors, it could help explain how they persisted and how they facilitated the origins of complex traits. Animal eyes are some of the best studied complex traits, and they include many parts, such as opsin-based photoreceptor cells, pigment cells, and lens cells. Eye evolution is...

High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria

Kaitlyn Kortright, Benjamin Chan & Paul Turner
As the most abundant microbes on earth, novel bacteriophage (phage; bacteria-specific viruses) are readily isolated from environmental samples. However, it remains challenging to characterize phage-bacteria interactions, such as the host receptor(s) phage bind to initiate infection. Here, we tested whether transposon insertion sequencing, INSeq, could be used to identify bacterial genes involved in phage binding. As proof of concept, results showed that INSeq screens successfully identified genes encoding known receptors for previously characterized viruses of...

Biodiversity data from: The mass extinction debt of the Anthropocene

Christopher Spalding & Pincelli Hull
To make sense of our present biodiversity crises, the modern rate of species extinctions is commonly compared to a benchmark, or “background,” rate derived from the fossil record. These estimates are critical for bounding the scale of modern diversity loss, but have yet to account for the fundamental structure of extinction rates through time. Namely, a substantial fraction of extinctions within the fossil record occur within relatively short-lived extinction pulses, and not during intervals characterized...

Fatty acid composition data for producers and consumers

Cornelia Twining, Joey Bernhardt & Blake Matthews
The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth, and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In the paper associated with this dataset, we document the extensive diversity in...

Resolving the consequences of gradual phenotypic plasticity for populations in variable environments

Samuel Fey, Colin Kremer, Tamara Layden & David Vasseur
Phenotypic adjustments following environmental change are ubiquitous and trait changes arising through phenotypic plasticity often lag behind their environmental stimuli. Evolutionary biologists seeking to understand how adaptive plasticity can evolve have extensively studied this phenomenon. However, the ecological consequences of common features of plastic responses to environmental variability, including gradual phenotypic change (i.e., slower than the pace of environmental change), are underappreciated. We present a framework based on the unifying concept of phenotype x environment...

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...

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...

LAM output for: The excitation of the Madden-Julian Oscillation as part of atmospheric adjustment to equatorial heating

Yu Liang, Alexey Fedorov, Patrick Haertel & Vladimir Zeitlin
We study the adjustment of the tropical atmosphere to localized surface heating using a Lagrangian atmospheric model(LAM) that simulates a realistic Madden-Julian Oscillation (MJO) – the dominant, eastward-propagating mode of tropical intraseasonal variability modulating atmospheric convection. Idealized warm sea surface temperature (SST) anomalies of different aspect ratios and magnitudes are imposed in the equatorial Indian Ocean during MJO-neutral conditions and then maintained for 15 days. Throughout these experiments, we observe a robust generation of an...

Data from: A Silurian ophiuroid with soft tissue preservation

Reece Carter, Mark Sutton, Derek Briggs, David Siveter & Derek Siveter
Palaeozoic brittle stars are not equipped with the fused arm ossicles (vertebrae) that facilitate the remarkable mode of walking that characterizes living forms. Here we describe a stem ophiuroid from the Herefordshire Lagerstätte (Silurian, Wenlock Series) which is remarkable in preserving the body cavity uncompacted and long tube feet which lack suckers. We tentatively assign the specimen to Protaster. The morphology of the arms and attitude of the specimen suggest that locomotion was achieved by...

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)....

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Affiliations

  • Yale University
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