463 Works

New exceptionally-preserved panarthropods from the Drumian Wheeler Konservat-Lagerstätte of the House Range of Utah

Rudy Lerosey-Aubril, Julien Kimmig, Stephen Pates, Jacob Skabelund, Andries Weug & Javier Ortega-Hernández
The Drumian Wheeler Konservat-Lagerstätte of the House Range of Utah (Wheeler-HR) has yielded one of the most diverse exceptionally-preserved Cambrian biotas of North America. The discovery of soft-bodied fossils invariably provides precious insights on this remarkable Miaolingian biota, for most of its non-biomineralizing components are known from very few specimens. This contribution describes some 30 new exceptionally-preserved fossils of Wheeler panarthropods. Two new species are recognized, the radiodont Hurdia sp. nov. A and the megacheiran...

The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts

Patric Vaelli, Kevin Theis, Janet Williams, James Foster, Lauren O'Connell & Heather Eisthen
Rough-skinned newts (Taricha granulosa) use tetrodotoxin (TTX) to block voltage-gated sodium (Nav) channels as a chemical defense against predation. Interestingly, newts exhibit extreme population-level variation in toxicity attributed to a coevolutionary arms race with TTX-resistant predatory snakes, but the source of TTX in newts is unknown. Here, we investigated whether symbiotic bacteria isolated from toxic newts could produce TTX. We characterized the skin-associated microbiota from a toxic and non-toxic population of newts and established pure...

Recent hybrids recapitulate ancient hybrid outcomes

Zachariah Gompert, Samridhi Chaturvedi, Lauren Lucas, C. Alex Buerkle, James Fordyce, Matthew Forister & Chris Nice
Genomic outcomes of hybridization depend on selection and recombination in hybrids. Whether these processes have similar effects on hybrid genome composition in contemporary hybrid zones versus ancient hybrid lineages is unknown. Here we show that patterns of introgression in a contemporary hybrid zone in Lycaeides butterflies predict patterns of ancestry in geographically adjacent, older hybrid populations. We find a particularly striking lack of ancestry from one of the hybridizing taxa, Lycaeides melissa, on the Z...

Data from: Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex

Lacie Newton, James Starrett, Brent Hendrixson, Shahan Derkarabetian & Jason Bond
Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth’s quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, Antrodiaetus unicolor species complex which contains two sympatric species, exhibits this pattern of relative morphological stasis...

DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies

Gerard Talavera, Vladimir Lukhtanov, Naomi Pierce & Roger Vila
Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts...

Genetic control of collective behavior in zebrafish

Wenlong Tang, Jacob Davidson, Guoqiang Zhang, Katherine Conen, Jian Fang, Fabrizio Serluca, Jingyao Li, Xiaorui Xiong, Matthew Coble, Tingwei Tsai, Gregory Molind, Caroline Fawcett, Ellen Sanchez, Peixin Zhu, Iain Couzin & Mark Fishman
Many animals, including humans, have evolved to live and move in groups. In humans, disrupted social interactions are a fundamental feature of many psychiatric disorders. However, we know little about how genes regulate social behavior. Zebrafish may serve as a powerful model to explore this question. By comparing the behavior of wild-type fish to 90 genetic lines, we show that mutations of genes associated with human psychiatric disorders can alter the collective behavior of adult...

Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

Zachary Blount, Rohan Maddamsetti, Nkrumah Grant, Sumaya Ahmed, Tanush Jagdish, Brooke Sommerfeld, Alice Tillman, Jeremy Moore, Jessica Baxter, Joan L Slonczewski, Jeffrey E Barrick & Richard E Lenski
Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages...

Local and landscape scale variables shape insect diversity in an urban biodiversity hotspot.

Benjamin Adams, Enjie Li, Christine Bahlai, Emily Meineke, Terrence McGlynn & Brian Brown
Local community structure is shaped by processes acting at local and landscape scales. The relative importance of drivers operating across different spatial scales are difficult to test without observations across regional or latitudinal gradients. Cities exhibit strong but predictable environmental gradients overlaying a mosaic of highly variable but repeated habitat types within a constrained area. Thus, cities present a unique opportunity to explore how both local and landscape factors influence local biotic communities. We used...

Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/ Ya Tsie trial

Lerato Magosi, Yinfeng Zhang, Tanya Golubchik, Victor DeGruttola, Eric Tchetgen Tchetgen, Vladimir Novitsky, Janet Moore, Pam Bachanas, Tebogo Segolodi, Refeletswe Lebelonyane, Molly Pretorius Holme, Sikhulile Moyo, Joseph Makhema, Shahin Lockman, Christophe Fraser, Myron Essex & Marc Lipsitch
Background: Mathematical models predict that community-wide access to HIV testing-and-treatment can rapidly and substantially reduce new HIV infections. Yet several large universal test-and-treat HIV prevention trials in high-prevalence epidemics demonstrated variable reduction in population-level incidence. Methods: To elucidate patterns of HIV spread in universal test-and-treat trials we quantified the contribution of geographic-location, gender, age and randomized-HIV-intervention to HIV transmissions in the 30-community Ya Tsie trial in Botswana (estimated trial population: 175,664). Results: Deep-sequence phylogenetic analysis...

Limited increases in savanna carbon stocks over decades of fire suppression

Yong Zhou, Jenia Singh, John Butnor, Corli Coetsee, Peter Boucher, Madelon Case, Evan Hockridge, Andrew Davies & Carla Staver
Savannas cover a fifth of the land surface and contribute a third of terrestrial net primary production, accounting for three quarters of global area burned and over half of global fire-driven carbon emissions. Fire suppression and afforestation have been proposed as tools to increase carbon sequestration in these ecosystems. A robust quantification of whole-ecosystem carbon storage in savannas is lacking, however, especially under altered fire regimes. Here, we provide the first direct estimates of whole-ecosystem...

Data from: Nonlinearities between inhibition and T-type calcium channel activity bidirectionally regulate thalamic oscillations

Adam Lu, Christine Lee, Max Kleiman-Weiner, Brian Truong, Megan Wang, John Huguenard & Mark Beenhakker
Absence seizures result from 3-5 Hz generalized thalamocortical oscillations that depend on highly regulated inhibitory neurotransmission in the thalamus. Efficient reuptake of the inhibitory neurotransmitter GABA is essential, and reuptake failure worsens seizures. Here, we show that blocking GABA transporters (GATs) in acute brain slices containing key parts of the thalamocortical seizure network modulates epileptiform activity. As expected, we found that blocking either GAT1 or GAT3 prolonged oscillations. However, blocking both GATs unexpectedly suppressed oscillations....

A dataset of ovariole number from more than 2,000 insect species

Samuel H. Church, Bruno A. S. De Medeiros, Seth Donoughe, Nicole L. Márquez Reyes & Cassandra G. Extavour
The number of offspring an organism can produce is a key component of its evolutionary fitness and life-history. This number differs widely between organisms, and its variation is the foundation for several hypotheses about life-history evolution, including the prediction that there is an evolutionary trade off between the number of offspring and their size. In insects, the number of egg-producing compartments in the ovary, called ovarioles, has been used as a proxy for potential offspring...

Dopamine activity in the tail of the striatum, DeepLabCut and MoSeq during novel object exploration

Mitsuko Watabe-Uchida, Korleki Akiti, Iku Tsutsui-Kimura, Yudi Xie, Alexander Mathis, Jeffrey Markowitz, Rockwell Anyoha, Sandeep Robert Datta, Mackenzie Weygandt Mathis & Naoshige Uchida
In this study, we characterized dynamics of novelty exploration using multi-point tracking (DeepLabCut) and behavioral segmentation (MoSeq). Mice were habituated in an arena, and then a object was placed at the corner of the arena. We compared 4 groups of mice: one with presentation of a novel object (stimulus novelty), one with a presentation of a familiar object (contextual novelty), one with presentation of a novel object after ablation of dopamine neuorns that project to...

Data for: A hypothesis to explain polarization color vision in butterflies, with an example from the Australian Imperial Blue, Jalmenus evagoras

Richard Rabideau Childers
The Australian lycaenid butterfly, Jalmenus evagoras, has iridescent wings that are sexually dimorphic in both spectral reflection and degree of polarization, suggesting that these wing properties are likely to be important in mate recognition. We first describe the results of a field experiment showing that free-flying individuals of J. evagoras can discriminate between visual stimuli that vary in polarization content in a wavelength-dependent manner. We then present detailed reflectance spectrophotometry measurements of the polarization content...

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...

Exploration of marine lichenized fungi as bioindicators of coastal ocean pollution in the Boston Harbor Islands National Recreation Area

Liam Nokes, Danny Haelewaters & Donald Pfister
This preliminary exploration of marine lichenized fungi (lichens) as bioindicators of water pollution examined the distribution of intertidal lichen communities in the Boston Harbor Islands National Recreation Area with respect to recorded pollution throughout the harbor. We found significant negative associations between pollution measurements and the health of the lichen community based on cover and species richness. We also observed significant differences in species composition between areas of higher pollution and areas of lower pollution,...

Data from: Species tree estimation and the impact of gene loss following whole-genome duplication

Liang Liu, Haifeng Xiong, Danying Wang, Chen Shao, Xuchen Yang, Jialin Yang, Tao Ma, Charles Davis & Zhenxiang Xi
Whole-genome duplication (WGD) has been demonstrated to occur broadly and repeatedly in the evolutionary history of eukaryotes, and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD, however, differential loss of paralogs may lead to spurious phylogenetic inference resulting...

TCCON data from Park Falls (US), Release GGG2020.R0

P. O. Wennberg, C. M. Roehl, D. Wunch, G. C. Toon, J.-F. Blavier, R. Washenfelder, G. Keppel-Aleks & N. T. Allen
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This is the GGG2020 data release of observations from the TCCON station at Park Falls, Wisconsin, USA

Data from: Molecular physiology of chemical defenses in a poison frog

Stephanie N Caty, Aurora Alvarez-Buylla, Gary` D Byrd, Charles Vidoudez, Alexandre B Roland, Elicio E Tapia, Bogdan Bodnik, Sunia A Trauger, Luis A Coloma & Lauren A O'Connell
Poison frogs sequester small molecule lipophilic alkaloids from their diet of leaf litter arthropods for use as chemical defenses against predation. Although the dietary acquisition of chemical defenses in poison frogs is well-documented, the physiological mechanisms of alkaloid sequestration has not been investigated. Here, we used RNA sequencing and proteomics to determine how alkaloids impact mRNA or protein abundance in the Little Devil Frog (Oophaga sylvatica) and compared wild caught chemically defended frogs to laboratory...

Data from: Extracting spatio-temporal patterns in animal trajectories: an ecological application of sequence analysis methods

Johannes De Groeve, Nico Van De Weghe, Nathan Ranc, Tijs Neutens, Lino Ometto, Omar Rota-Stabelli & Francesca Cagnacci
Digital tracking technologies have considerably increased the amount and quality of animal trajectories, enabling the study of habitat use and habitat selection at a fine spatial and temporal scale. However, current approaches do not yet explicitly account for a key aspect of habitat use, namely the sequential variation in the use of different habitat features. To overcome this limitation, we propose a tree-based approach that makes use of sequence analysis methods, derived from molecular biology,...

Data from: How many routes lead to migration? Comparison of methods to assess and characterise migratory movements

Francesca Cagnacci, Stefano Focardi, Anne Ghisla, Bram Van Moorter, Eliezer Gurarie, Marco Heurich, Atle Mysterud, John Linnell, Manuela Panzacchi, Evelyn Merrill, Roel May, Torgeir Nygård, Christer Rolandsen, Mark Hebblewhite & Evelyn H. Merrill
1. Decreasing rate of migration in several species as a consequence of climate change and anthropic pressure, together with increasing evidence of space-use strategies intermediate between residency and complete migration, are very strong motivations to evaluate migration occurrence and features in animal populations. 2. The main goal of this paper was to perform a relative comparison between methods for identifying and characterising migration at the individual and population level on the basis of animal location...

Data from: Towards a worldwide wood economics spectrum

Amy E. Zanne, G. Lopez-Gonzalez, David A. Coomes, Jugo Ilic, Steven Jansen, Simon L. Lewis, Regis B. Miller, Nathan G. Swenson, Michael C. Wiemann & Jerome Chave
Wood performs several essential functions in plants, including mechanically supporting aboveground tissue, storing water and other resources, and transporting sap. Woody tissues are likely to face physiological, structural and defensive trade-offs. How a plant optimizes among these competing functions can have major ecological implications, which have been under-appreciated by ecologists compared to the focus they have given to leaf function. To draw together our current understanding of wood function, we identify and collate data on...

Data from: The biomechanical basis of evolutionary change in a territorial display

Terry J. Ord, David C. Collar & Thomas J. Sanger
1. Few studies have examined how the anatomy of an animal signal contributes to, or limits, the evolution of signal differentiation among closely related species. 2. In Anolis lizards, adult males extend a large, conspicuous dewlap as part of a territorial advertisement display. Males of species from the island of Jamaica rely on the rapid extension of the dewlap to facilitate display detection by territorial neighbours and conspecific females. Males of other species on the...

Data from: Ant-plant mutualism: a dietary by-product of a tropical ant's macronutrient requirements

Lina M. Arcila Hernández, Jon G. Sanders, Gabriel A. Miller, Alison Ravenscraft & Megan E. Frederickson
Many arboreal ants depend on myrmecophytic plants for both food and shelter; in return, these ants defend their host plants against herbivores, which are often insects. Ant-plant and other mutualisms do not necessarily involve the exchange of costly rewards or services; they may instead result from by-product benefits, or positive outcomes that do not entail a cost for one or both partners. Here, we examined whether the plant-ant Allomerus octoarticulatus pays a short-term cost to...

Data from: Sexual selection constrains the body mass of male but not female mice

James S. Ruff, Douglas H. Cornwall, Linda C. Morrison, Joseph W. Cauceglia, Adam C. Nelson, Shannon M. Gaukler, Shawn Meagher, Lara S. Carroll & Wayne K. Potts
Sexual size dimorphism results when female and male body size is influenced differently by natural and sexual selection. Typically, in polygynous species larger male body size is thought to be favored in competition for mates and constraints on maximal body size are due to countervailing natural selection on either sex; however, it has been postulated that sexual selection itself may result in stabilizing selection at an optimal mass. Here we test this hypothesis by retrospectively...

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