274 Works

Dataset for 'Auditory Activity is Diverse and Widespread Throughout the Central Brain of Drosophila'

DIEGO PACHECO PINEDO, Stephan Thiberge, Eftychios Pnevmatikakis & Mala Murthy
Sensory pathways are typically studied starting at receptor neurons and following postsynaptic neurons into the brain. However, this leads to a bias in analysis of activity towards the earliest layers of processing. Here, we present new methods for volumetric neural imaging with precise across-brain registration, to characterize auditory activity throughout the entire central brain of Drosophila and make comparisons across trials, individuals, and sexes. We discover that auditory activity is present in most central brain...

Shakespeare and Company Project Dataset: Lending Library Members, Books, Events

Joshua Kotin, Rebecca Sutton Koeser, Carl Adair, Serena Alagappan, Jean Bauer, Oliver J. Browne, Nick Budak, Harriet Calver, Jin Chow, Ian Davis, Gissoo Doroudian, Currie Engel, Elspeth Green, Benjamin Hicks, Madeleine E. Joelson, Carolyn Kelly, Sara Krolewski, Xinyi Li, Ellie Maag, Cate Mahoney, Jesse D. McCarthy, Mary Naydan, Isabel Ruehl, Sylvie Thode, Camey VanSant … & Clifford E. Wulfman
The Shakespeare and Company Project makes three datasets available to download in CSV and JSON formats. The datasets provide information about lending library members; the books that circulated in the lending library; and lending library events, including borrows, purchases, memberships, and renewals. The datasets may be used individually or in combination site URLs are consistent identifiers across all three. The DOIs for each dataset are as follows: Members (https://doi.org/10.34770/ht30-g395); Books (https://doi.org/10.34770/g467-3w07); Events (https://doi.org/10.34770/2r93-0t85).

Agincourt Integrated Family Survey 2004

Anne Case

Agincourt Integrated Family Survey 2002

Anne Case

Fluorescence Reconstruction Microscopy Data: Keratinocyte (10x) Phase to Nuclei (DAPI)

Julienne LaChance & Daniel Cohen
The data provided in this DataSpace consists of sample training data to be used for Fluorescence Reconstruction Microscopy (FRM) testing. We provide a subset of the keratinocyte (10x magnification) dataset used in our paper, in which interested parties may find more complete information about our data collection methods. Matched pairs of phase contrast and fluorescent images are given. The nuclei were stained using Hoechst 33342 and imaged using a standard DAPI filter set.

Daily ranging and den usage patterns structure fission-fusion dynamics and social associations in spotted hyenas

Eli Strauss, Frants Jensen, Andrew Gersick, Mara Thomas, Kay Holekamp & Ariana Strandburg-Peshkin
Environment structure often shapes social interactions. Spatial attractors that draw multiple individuals may play a particularly important role in dispersed groups, where individuals must first encounter one another to interact. We use GPS data recorded simultaneously from five spotted hyenas (Crocuta crocuta) within a single clan to investigate how communal dens and daily ranging patterns shape fission-fusion dynamics (subgroup splits and merges). We introduce a species-general framework for identifying and characterizing dyadic fission-fusion events and...

Data from: Mechanisms of plant–plant interactions: concealment from herbivores is more important than abiotic-stress mediation in an African savannah

Allison M. Louthan, Daniel F. Doak, Jacob R. Goheen, Todd M. Palmer & Robert M. Pringle
Recent work on facilitative plant–plant interactions has emphasized the importance of neighbours’ amelioration of abiotic stress, but the facilitative effects of neighbours in reducing plant apparency to herbivores have received less attention. Whereas theory on stress reduction predicts that competition should be more important in less stressful conditions, with facilitation becoming more important in harsh environments, apparency theory suggests that facilitation should be greater in the presence of herbivores, where it is disadvantageous to be...

Data from: Does primary productivity modulate the indirect effects of large herbivores? A global meta-analysis

Joshua H. Daskin & Robert M. Pringle
1. Indirect effects of large mammalian herbivores (LMH), while much less studied than those of apex predators, are increasingly recognized to exert powerful influences on communities and ecosystems. The strength of these effects is spatiotemporally variable, and several sets of authors have suggested that they are governed in part by primary productivity. However, prior theoretical and field studies have generated conflicting results and predictions, underscoring the need for a synthetic global analysis. 2. We conducted...

Data from: Infanticide and within-clutch competition select for reproductive synchrony in a cooperative bird

Christina Riehl
Reproduction among members of social animal groups is often highly synchronized, but neither the selective advantages nor the proximate causes of synchrony are fully understood. Here I investigate the evolution of hatching synchrony in the Greater Ani (Crotophaga major), a communally nesting bird in which several unrelated females contribute eggs to a large, shared clutch. Hatching synchrony is variable, ranging from complete synchrony to moderate asynchrony, and is determined by the onset of incubation of...

Data from: Tree circumference dynamics in four forests characterized using automated dendrometer bands

Valentine Herrmann, Sean M. McMahon, Matteo Detto, James A. Lutz, Stuart J. Davies, Chia-Hao Chang-Yang & Kristina J. Anderson-Teixeira
Stem diameter is one of the most commonly measured attributes of trees, forming the foundation of forest censuses and monitoring. Changes in tree stem circumference include both irreversible woody stem growth and reversible circumference changes related to water status, yet these fine-scale dynamics are rarely leveraged to understand forest ecophysiology and typically ignored in plot- or stand-scale estimates of tree growth and forest productivity. Here, we deployed automated dendrometer bands on 12–40 trees at four...

Data from: Admixture mapping identifies introgressed genomic regions in North American canids

Bridgett M. VonHoldt, Roland W. Kays, John P. Pollinger & Robert K. Wayne
Hybrid zones typically contain novel gene combinations that can be tested by natural selection in a unique genetic context. Parental haplotypes that increase fitness can introgress beyond the hybrid zone, into the range of parental species. We used the Affymetrix canine SNP genotyping array to identify genomic regions tagged by multiple ancestry informative markers that are more frequent in an admixed population than expected. We surveyed a hybrid zone formed in the last 100 years...

Data from: The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves

Ilana Janowitz Koch, Michelle M. Creek, Michael J. Thompson, Kerry A. Deere-Machemer, Jun Wang, Lionel Duarte, Gitanjali E. Gnanadesikan, Eskender L. McCoy, Liudmilla Rubbi, Daniel R. Stahler, Matteo Pellegrini, Elaine A. Ostrander, Robert K. Wayne, Janet S. Sinsheimer, Bridgett M. VonHoldt & Michelle M. Clark
The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified...

Data from: Responses of interspecific associations in mixed-species bird flocks to selective logging

Binod Borah, Suhel Quader & Umesh Srinivasan
1. Non-trophic interactions (or, inter-species associations) play a prominent role in determining community structure and function. Mixed-species bird flocks are networks of non-trophic associations that confer foraging and anti-predator benefits to participant species. Yet, the responses of these interspecific associations to anthropogenic environmental change are poorly understood. 2. Selective logging is pervasive in the tropics, and can affect associations in mixed-species bird flocks by altering resource availability and/or predation risk, or through the altered abundances...

Data from: A comprehensive analysis of autocorrelation and bias in home range estimation

Michael J. Noonan, Marlee A. Tucker, Christen H. Fleming, Tom S. Akre, Susan C. Alberts, Abdullahi H. Ali, Jeanne Altmann, Pamela C. Antunes, Jerrold L. Belant, Dean Beyer, Niels Blaum, Katrin Böhning-Gaese, , Rogerio De Paula Cunha, Jasja Dekker, Jonathan Drescher-Lehman, Nina Farwig, Claudia Fichtel, Christina Fischer, Adam T. Ford, Jacob R. Goheen, René Janssen, Florian Jeltsch, Matthew Kauffman, Peter M. Kappeler … & Justin M. Calabrese
Home range estimation is routine practice in ecological research. While advances in animal tracking technology have increased our capacity to collect data to support home range analysis, these same advances have also resulted in increasingly autocorrelated data. Consequently, the question of which home range estimator to use on modern, highly autocorrelated tracking data remains open. This question is particularly relevant given that most estimators assume independently sampled data. Here, we provide a comprehensive evaluation of...

Data from: On the evolutionary interplay between dispersal and local adaptation in heterogeneous environments

Andrew M. Berdahl, Colin J. Torney, Emmanuel Schertzer, Simon A. Levin & Andrew Berdahl
Dispersal, whether in the form of a dandelion seed drifting on the breeze, or a salmon migrating upstream to breed in a non-natal stream, transports genes between locations. At these locations, local adaptation modifies the gene frequencies so their carriers are better suited to particular conditions, be those of newly disturbed soil or a quiet river pool. Both dispersal and local adaptation are major drivers of population structure; however, in general, their respective roles are...

Worldwide evidence of a unimodal relationship between productivity and plant species richness

Lauchlan H. Fraser, Jason Pither, Anke Jentsch, Marcelo Sternberg, Martin Zobel, Diana Askarizadeh, Sandor Bartha, Carl Beierkuhnlein, Jonathan A. Bennett, Alex Bittel, Bazartseren Boldgiv, Ilsi I. Boldrini, Edward Bork, Leslie Brown, Marcelo Cabido, James Cahill, Cameron N. Carlyle, Giandiego Campetella, Stefano Chelli, Ofer Cohen, Anna-Maria Csergo, Sandra Diaz, Lucas Enrico, David Ensing, Alessandra Fidelis … & Szilárd Szentes
The search for predictions of species diversity across environmental gradients has challenged ecologists for decades. The humped-back model (HBM) suggests that plant diversity peaks at intermediate productivity; at low productivity few species can tolerate the environmental stresses, and at high productivity a few highly competitive species dominate. Over time the HBM has become increasingly controversial, and recent studies claim to have refuted it. Here, by using data from coordinated surveys conducted throughout grasslands worldwide and...

Data from: Meta-analysis reveals lower genetic diversity in overfished populations

Malin L. Pinsky & Stephen R. Palumbi
While population declines can drive the loss of genetic diversity under some circumstances, it has been unclear whether this loss is a general consequence of overharvest in highly abundant marine fishes. Here, we use a phylogenetic approach across 160 species and 11,658 loci to show that allelic richness was on average 11% lower (p < 0.0001) in overharvested populations, even after accounting for the effects of body size, latitude, and other factors. Heterozygosity was 2%...

Data from: A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution

Wendy C. Clement, Mónica Arakaki, Patrick W. Sweeney, Erika J. Edwards & Michael J. Donoghue
Premise of the study: Despite recent progress, significant uncertainties remain concerning relationships among early-branching lineages within Viburnum (Adoxaceae). This has prohibited a new classification, and has hindered studies of character evolution and the increasing use of Viburnum in addressing a wide range of ecological and evolutionary questions. We hoped to resolve these issues by sequencing whole plastid genomes for representative species and combining these with molecular data previously obtained from an expanded taxon sample. Methods:...

Data from: Cascading impacts of large-carnivore extirpation in an African ecosystem

Justine L. Atkins, Ryan A. Long, Johan Pansu, Joshua H. Daskin, Arjun B. Potter, Marc E. Stalmans, Corina E. Tarnita & Robert M. Pringle
The world’s largest carnivores are declining and now occupy mere fractions of their historical ranges. Theory predicts that when apex predators disappear, large herbivores should become less fearful, occupy new habitats, and modify those habitats by eating new food plants. Yet experimental support for this prediction has been difficult to obtain in large-mammal systems. Following the extirpation of leopards and African wild dogs from Mozambique’s Gorongosa National Park, forest-dwelling antelopes (bushbuck, Tragelaphus sylvaticus) expanded into...

Data from: Disentangling serology to elucidate henipa‐ and filovirus transmission in Madagascar fruit bats

Cara E. Brook, Hafaliana C. Ranaivoson, Christopher C. Broder, Andrew A. Cunningham, Jean-Michel Heraud, Alison J. Peel, Louise Gibson, James L. N. Wood, C. Jessica Metcalf & Andrew P. Dobson
Bats are reservoirs for emerging human pathogens, including Hendra and Nipah henipaviruses and Ebola and Marburg filoviruses. These viruses demonstrate predictable patterns in seasonality and age structure across multiple systems; previous work suggests that they may circulate in Madagascar's endemic fruit bats, which are widely consumed as human food. We aimed to (a) document the extent of henipa‐ and filovirus exposure among Malagasy fruit bats, (b) explore seasonality in seroprevalence and serostatus in these bat...

Data from: Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network

Feng Liu, Alexander H. Morrison & Thomas Gregor
Patterning of body parts in multicellular organisms relies on the interpretation of transcription factor (TF) concentrations by genetic networks. To determine the extent by which absolute TF concentration dictates gene expression and morphogenesis programs that ultimately lead to patterns in Drosophila embryos, we manipulate maternally supplied patterning determinants and measure readout concentration at the position of various developmental markers. When we increase the overall amount of the maternal TF Bicoid 5-fold, Bicoid concentrations in cells...

Data from: Cutting through the complexity of cell collectives

Carey D. Nadell, Vanni Bucci, Knut Drescher, Simon A. Levin, Bonnie L. Bassler & Joao B. Xavier
Via strength in numbers, groups of cells can influence their environments in ways that individual cells cannot. Large-scale structural patterns and collective functions underpinning virulence, tumour growth and bacterial biofilm formation are emergent properties of coupled physical and biological processes within cell groups. Owing to the abundance of factors influencing cell group behaviour, deriving general principles about them is a daunting challenge. We argue that combining mechanistic theory with theoretical ecology and evolution provides a...

Data from: Incomplete host immunity favors the evolution of virulence in an emergent pathogen

Arietta E. Fleming-Davies, Paul D. Williams, André A. Dhondt, Andrew P. Dobson, Wesley A. Hochachka, Ariel E. Leon, David H. Ley, Erik E. Osnas & Dana M. Hawley
Immune memory evolved to protect hosts from reinfection, but incomplete responses that allow future reinfection might inadvertently select for more harmful pathogens. We present empirical and modeling evidence that incomplete immunity promotes the evolution of higher virulence in a natural host-pathogen system. We performed sequential infections of house finches with Mycoplasma gallisepticum strains of varying virulence. Virulent bacterial strains generated stronger host protection against reinfection than less virulent strains, and thus excluded less virulent strains...

Data from: Only accessible information is useful: insights from gradient-mediated patterning

Mikhail Tikhonov, Shawn C. Little & Thomas Gregor
Information theory is gaining popularity as a tool to characterise performance of biological systems. However, information is commonly quantified without reference to whether or how a system could extract and use it; as a result, information-theoretic quantities are easily misinterpreted. Here we take the example of pattern-forming developmental systems which are commonly structured as cascades of sequential gene expression steps. Such a multi-tiered structure appears to constitute sub-optimal use of the positional information provided by...

Data from: Error-robust modes of the retinal population code

Adrianna R. Loback, Gašper Tkačik, Jason S. Prentice, Mark L. Ioffe, , Olivier Marre & Michael J. Berry
Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the...

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