220 Works

Hair phenotype diversity across Indriidae lemurs

Elizabeth Tapanes, Rachel Jacobs, Ian Harryman, , Mitchell Irwin, Jason Kamilar & Brenda Bradley
Objectives: Hair (i.e., pelage/fur) is a salient feature of primate (including human) diversity and evolution—serving functions tied to thermoregulation, protection, camouflage, and signaling—but wild primate pelage evolution remains relatively understudied. Specifically, assessing multiple hypotheses across distinct phylogenetic scales is essential but is rarely conducted. We examine whole body hair color and density variation across Indriidae (Avahi, Indri, Propithecus)—a lineage that, like humans, exhibits vertical posture (i.e., their whole bodies are vertical to the sun). Materials...

Behavioral context affects social signal representations within single primate prefrontal cortex neurons

Adam Fishbein, Vladimir Jovanovic, Lisa De La Mothe, Kuo-Fen Lee & Cory Miller
We tested whether social signal processing in more traditional, head-restrained contexts is representative of the putative natural analog – social communication – by comparing responses to vocalizations within individual neurons in marmoset prefrontal cortex (PFC) across a series of behavioral contexts ranging from traditional to naturalistic. Although vocalization responsive neurons were evident in all contexts, cross-context consistency was notably limited. A response to these social signals when subjects were head-restrained was not predictive of a...

Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing

Animesh Gupta
Viruses and their hosts can undergo coevolutionary arms races where hosts evolve increased resistance and viruses evolve counter-resistance. Given these arms race dynamics (ARD), both players are predicted to evolve along a single trajectory as more recently evolved genotypes replace their predecessors. By coupling phenotypic and genomic analyses of coevolving populations of bacteriophage lambda and Escherichia coli, we find conflicting evidence for ARD. Virus-host infection phenotypes fit the ARD model, yet genomic analyses revealed fluctuating...

Data from: Phytoplankton functional composition determines limitation by nutrients and grazers across a lake productivity gradient

Marika Schulhof, Dedmer Van De Waal, Steven Declerck & Jonathan Shurin
Functional tradeoffs among ecologically important traits govern the diversity of communities and changes in species composition along environmental gradients. A tradeoff between predator defense and resource competitive ability has been invoked as a mechanism that may maintain diversity in lake phytoplankton. Tradeoffs may promote diversity in communities where grazing- and resource-limited taxa coexist, which determines the extent to which communities are resource- or consumer-controlled. In addition, changes in temperature may alter nutrient demands and grazing...

Traits and depth: what do hydroids tell us about morphology and life-history strategies in the deep sea?

Marina Oliveira Fernandez, Allen Collins, Arjan Gittenberger, Roy Kaustuv & Antonio Carlos Marques
Aim: Traits affect the survival and reproduction of individuals in different habitat conditions, ultimately altering their distributions. In the oceans, changes in environmental conditions with bathymetry may influence the occurrence of specific traits. Therefore, characterizing trait variation with depth can illuminate drivers related to the distribution of diversity of forms, functions, and life histories. We aimed to investigate patterns of variation in the diversified life histories and morphologies of hydroids with depth, integrating these patterns...

Large mitochondrial DNA deletions in HIV sensory neuropathy

Ricardo Roda, David Bargiela, Weiran Chen, Ken Perry, Ronald J. Ellis, David B. Clifford, Ajay Bharti, Asha Kallianpur, Michelli F Oliveira, Monica M. Diaz, Leah H. Rubin, Christina Gavegnano, Justin C. McArthur, Ahmet Hoke & Michael Polydefkis
Objective: The primary objective of this study was to evaluate the correlation of large mitochondrial DNA deletions in skin samples of people with HIV with measure of neuropathy and prior exposure to therapy. We hypothesized that deletions would be associated with the presence of neuropathy. As secondary objectives we determined the correlation of deletion burden with demographic data and neuropathy measures. Methods: In this retrospective cohort study we measured the accumulation of large mtDNA deletions...

Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities

Thiago Lima, Ricardo Pereira, Ronald Burton, Tessa Pierce & Lin Chao
Reproductive isolation is often achieved when genes that are neutral or beneficial in their genomic background become functionally incompatible in a foreign genome, causing inviability, sterility or low fitness in hybrids. Recent studies suggest that mitonuclear interactions are among the initial incompatibilities to evolve at early stages of population divergence across taxa. Yet, the genomic architecture of mitonuclear incompatibilities has rarely been elucidated. We employ an experimental evolution approach starting with low-fitness F2 interpopulation hybrids...

Accuracy in near-perfect virus phylogenies

Joel Wertheim
Phylogenetic trees from real-world data often include short edges with very few substitutions per site, which can lead to partially resolved trees and poor accuracy. Theory indicates that the number of sites needed to accurately reconstruct a fully resolved tree grows at a rate proportional to the inverse square of the length of the shortest edge. However, when inferred trees are partially resolved due to short edges, "accuracy" should be defined as the rate of...

Test data from SPCAM for machine learning in moist physics

Guang Zhang, Yilun Han, Xiaomeng Huang & Yong Wang
Current moist physics parameterization schemes in general circulation models (GCMs) are the main source of biases in simulated precipitation and atmospheric circulation. Recent advances in machine learning make it possible to explore data-driven approaches to developing parameterization for moist physics processes such as convection and clouds. This study aims to develop a new moist physics parameterization scheme based on deep learning. We use a residual convolutional neural network (ResNet) for this purpose. It is trained...

Data from: Sugar content of diet does not buffer against chronic oral imidacloprid exposure in the alfalfa leafcutting bee, Megachile rotundata (Hymenoptera: Megachilidae)

Jacob Cecala, Danelle Angeline Baronia & Erin Wilson Rankin
Bees are economically critical pollinators, but are declining broadly due to several stressors, including non-target exposure to insecticides and deficiencies in nutrition. Understanding the simultaneous impact of stressors, particularly interactions between them, are critical to effectively conserving bees. While behavioral effects of pesticides like neonicotinoids have received some attention in solitary bees, our understanding of how they are modulated by diet quality is limited. Furthermore, scarce data exist on what concentrations of orally ingested neonicotinoids...

Closed-loop control of k-space sampling via physiologic feedback for cine MRI

Francisco Contijoch
This dataset accompanies the manuscript outlining a method for closed-loop sampling of k-space in response to physiologic changes. The closed-loop approach enables near-uniform radial sampling in a segmented acquisition approach which was higher than predetermined golden-angle radial sampling. This can be utilized to increase the sampling or decrease the temporal footprint of an acquisition and the closed-loop framework has the potential to be applied to patients with complex heart rhythms. Briefly, Segmented cine cardiac MRI...

Hawkmoths use wingstroke-to-wingstroke frequency modulation for aerial recovery to vortex ring perturbations

Jeff Gau, Ryan Gemilere, FM Subteam LDS-VIP, James Lynch, Nick Gravish & Simon Sponberg
Centimetre-scale fliers must contend with the high power requirements of flapping flight. Insects have elastic elements in their thoraxes which may reduce the inertial costs of their flapping wings. Matching wingbeat frequency to a mechanical resonance can be energetically favourable, but also poses control challenges. Many insects use frequency modulation on long timescales, but wingstroke-to-wingstroke modulation of wingbeat frequencies in a resonant spring-wing system is potentially costly because muscles must work against the elastic flight...

Utilizing next-generation sequencing to identify prey DNA in western North Atlantic grey seal (Halichoerus grypus) diet

Kelly Flanders, Zachary Olson & Kathryn Ono
Increasing grey seal (Halichoerus grypus) abundance in coastal New England is leading to social, political, economic, and ecological controversies. We studied grey seal feeding habits through next-generation sequencing of prey DNA using 16S amplicons from seal scat (N = 74) collected from a breeding colony on Monomoy Island in Massachusetts, U.S. and report frequency of occurrence and relative read abundance. We also assigned seal sex to scat samples using a revised PCR assay. In contrast...

Supplemental material for: NINDS consensus diagnostic criteria for Traumatic Encephalopathy Syndrome

Douglas Katz, Charles Bernick, David Dodick, Jesse Mez, Megan Mariani, Charles Adler, Michael Alosco, Laura Balcer, Sarah Banks, William Barr, David Brody, Robert Cantu, Kristen Dams-O'Connor, Yonas Geda, Barry Jordan, Thomas McAllister, Elaine Peskind, Ronald Petersen, Jennifer Wether, Ross Zafonte, Eimear Foley, Debra Babcock, Walter Koroshetz, Ann McKee, Martha Shenton … & Robert Stern
Objective: To develop evidence-informed, expert consensus research diagnostic criteria for Traumatic Encephalopathy Syndrome (TES), the clinical disorder associated with neuropathologically diagnosed Chronic Traumatic Encephalopathy (CTE). Methods: A panel of 20 expert clinician-scientists in neurology, neuropsychology, psychiatry, neurosurgery, and physical medicine and rehabilitation, from 11 academic institutions, participated in a modified Delphi procedure to achieve consensus, initiated at the First NINDS Consensus Workshop to Define the Diagnostic Criteria for TES, April, 2019. Prior to consensus, panelists...

Antagonistic effects of temperature and dissolved organic carbon on fish growth in California mountain lakes

Celia C. Symons, Marika A. Schulhof, Hamanda B. Cavalheri & Jonathan B. Shurin
Resources and temperature play major roles in determining biological production in lake ecosystems. Lakes have been warming and ‘browning’ over recent decades due to climate change and increased loading of terrestrial organic matter. Conflicting hypotheses and evidence have been presented about whether these changes will increase or decrease fish growth within lakes. Most studies have been conducted in low-elevation lakes where terrestrially derived carbon tends to dominate over carbon produced within lakes. Understanding how fish...

Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius

Luca Livraghi, Joseph J. Hanly, Ling Sheng Loh, Anna Ren, Ian A. Warren, Carolina Concha, Charlotte Wright, Jonah M. Walker, Jessica Foley, Henry Arenas-Castro, Arnaud Martin, William O. McMillan, Chris D. Jiggins, Steven M. Van Bellghem, Gabriela Montejo-Kovacevich, James J. Lewis, Micheal W. Perry, Zachary H. Goldberg, Laura H. Lopez, Riccardo Papa & Eva S.M. Van Der Heijden
In Heliconius butterflies, wing pattern diversity is controlled by a few genes of large effect that regulate colour pattern switches between morphs and species across a large mimetic radiation. One of these genes, cortex, has been repeatedly associated with colour pattern evolution in butterflies. Here we carried out CRISPR knock-outs in multiple Heliconius species and show that cortex is a major determinant of scale cell identity. Chromatin accessibility profiling and introgression scans identified cis-regulatory regions...

Experimental electrical resistivity values and computed thermal conductivities

Anne Pommier, Christopher Davies & Rong Zhang
We present a joint experimental-modeling investigation of core cooling in small terrestrial bodies. Significant amounts of light elements (S, O, Mg, Si) may compose the metallic cores of terrestrial planets and moons. However, the effect of multiple light elements on transport properties, in particular, electrical resistivity and thermal conductivity, is not well constrained. Electrical experiments were conducted at 10 GPa and up to 1850 K on high-purity powder mixtures in the Fe-S-O(+/-Mg, +/-Si) systems using...

Data from: FSHB transcription is regulated by a novel 5’ distal enhancer containing a fertility-associated single nucleotide polymorphism

Stephanie C. Bohaczuk, Varykina G. Thackray, Jia Shen, Dorota Skowronska-Krawczyk & Pamela L. Mellon
The pituitary gonadotropins, follicle-stimulating hormone (FSH) and luteinizing hormone, signal the gonads to regulate male and female fertility. FSH is critical for female fertility as it regulates oocyte maturation, ovulation, and hormone synthesis. Multiple genome-wide association studies (GWAS) link a 130 Kb locus at 11p14.1, which encompasses the FSH beta-subunit (FSHB) gene, with fertility-related traits including polycystic ovary syndrome, age of natural menopause, and dizygotic twinning. The most statistically significant single-nucleotide polymorphism from several GWAS...

DEPP: Deep learning enables extending species trees using single genes

Yueyu Jiang, Metin Balaban, Qiyun Zhu & Siavash Mirarab
Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. However, existing placement methods have a fundamental limitation: they assume that query sequences have evolved using specific models directly on the reference phylogeny. Thus, they can place single-gene data (e.g., 16S rRNA amplicons) onto their own gene tree. This practice is a proxy for a more ambitious goal: extending a (genome-wide) species tree given data from individual genes. No algorithm...

The Landscape of Connected Cancer Symptom Management in Rural America

Ming-Yuan Chih, Anna McCowan, Sadie Whittaker, Melinda Krakow, David K. Ahern, Eliah Aronoff-Spencer, Bradford W. Hesse, Timothy W. Mullett & Robin C. Vanderpool
Background: The 2016 President’s Cancer Panel called for projects focusing on improving cancer symptom management using connected health technologies (broadband and telecommunications). However, rural communities, like those in Appalachia, may experience a “double burden” of high cancer rates and lower rates of broadband access and adoption necessary for connected health solutions. Purpose: To better understand the current landscape of connected health in the management of cancer symptoms in rural America. Methods: A literature search was...

Dense seismic three-component nodal array at the Bud Wellman Ranch

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High-Resolution imaging and monitoring of the subsurface structure and seismicity at a site along the San Jacinto fault zone using a dense seismic nodal array. The site is located about 8 km southeast of the town of Anza, California. The type of nodal sensor employed is the Fairfield Zland 3-component geophone (records ground velocity continuously). The array consists of 108 sensors, with 54 located along a linear across-fault profile and the remaining 54 sensors scattered...

Dense seismic three-component nodal array at the Ramona Reservation

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High-Resolution imaging and monitoring of the subsurface structure and seismicity at a site along the San Jacinto fault zone using a dense seismic nodal array. The site is located about 6 km northwest of the town of Anza, California. The type of nodal sensor employed is the Fairfield Zland 3-component 5 Hz geophones (records ground velocity continuously at 500 sps). The array consists of 97 sensors, with 65 located along a linear across-fault profile and...

Photobehavior for octopus (‘Octopus bimaculatus’) and squid (‘Doryteuthis opalescens’) paralarvae during exposure to 9 light irradiance levels and 4 oxygen conditions in trials conducted in April of 2019

Lillian McCormick, Lisa Levin & Nicholas Oesch
This dataset gives the results of photobehavior experiments under different oxygen conditions in larvae of the market squid (‘Doryteuthis opalescens’) and two-spot octopus (‘Octopus bimaculatus’). Photobehavior experiments were conducted to determine whether the impairment of visual physiology observed in marine invertebrate larvae (McCormick et al., 2019) is subsequently affecting visual behavior in marine larvae.

Data from: APPLES: Scalable distance-based phylogenetic placement with or without alignments

Metin Balaban, Shahab Sarmashghi & Siavash Mirarab
Placing a new species on an existing phylogeny has increasing relevance to several applications. Placement can be used to update phylogenies in a scalable fashion and can help identify unknown query samples using (meta-)barcoding, skimming, or metagenomic data. Maximum likelihood (ML) methods of phylogenetic placement exist, but these methods are not scalable to reference trees with many thousands of leaves, limiting their ability to enjoy benefits of dense taxon sampling in modern reference libraries. They...

Data from: Parallel changes in gut microbiome composition and function during colonization, local adaptation and ecological speciation

Diana J. Rennison, Seth M. Rudman & Dolph Schluter
The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature....

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