451 Works

Data from: Body shape diversity in Triassic‒Early Cretaceous neopterygian fishes: sustained holostean disparity and predominantly gradual increases in teleost phenotypic variety

John T. Clarke & Matt Friedman
Comprising Holostei and Teleostei, the ~32,000 species of neopterygian fishes are anatomically disparate and represent the dominant group of aquatic vertebrates today. However, the pattern by which teleosts rose to represent almost all of this diversity, while their holostean sister group dwindled to 8 extant species and two broad morphologies, is poorly constrained. A geometric morphometric approach was taken to generate a morphospace from over 400 fossil taxa, representing almost all articulated neopterygian taxa known...

Data from: Chimpanzee cooperation is fast, and independent from self-control

Alexandra G. Rosati, Lauren M. DiNicola & Joshua W. Buckholtz
Large-scale cooperation is a hallmark of our species and appears to be unique among primates. Yet the evolutionary mechanisms that drove the emergence of humanlike patterns of cooperation remain unclear. Studying the cognitive processes underlying cooperative behavior in apes, our closest living relatives, can help identify these mechanisms. Accordingly, we employed a novel test battery to assess the willingness of 40 chimpanzees to donate resources, instrumentally help others, and punish a culpable thief. We found...

Data from: Parasite rearing and infection temperatures jointly influence disease transmission and shape seasonality of epidemics

Marta S. Shocket, Daniela Vergara, Andrew J. Sickbert, Jason M. Walsman, Alexander T. Strauss, Jessica L. Hite, Meghan A. Duffy, Carla E. Cáceres & Spencer R. Hall
Seasonal epidemics erupt commonly in nature and are driven by numerous mechanisms. Here, we suggest a new mechanism that could determine the size and timing of seasonal epidemics: rearing environment changes the performance of parasites. This mechanism arises when the environmental conditions in which a parasite is produced impact its performance—independently from the current environment. To illustrate the potential for ‘rearing effects’, we show how temperature influences infection risk (transmission rate) in a Daphnia-fungus disease...

Data from: Variations in HLA-B cell surface expression, half-life and extracellular antigen receptivity

Brogan Yarzabek, Anita J. Zaitouna, Eli Olson, Gayathri N. Silva, Jie Geng, Aviva Geretz, Rasmi Thomas, Sujatha Krishnakumar, Daniel S. Ramon & Malini Raghavan
The highly polymorphic human leukocyte antigen (HLA) class I molecules present peptide antigens to CD8+ T cells, inducing immunity against infections and cancers. Quality control mediated by peptide loading complex (PLC) components is expected to ensure the cell surface expression of stable peptide-HLA class I complexes. This is exemplified by HLA-B*08:01 in primary human lymphocytes, with both expression level and half-life at the high end of the measured HLA-B expression and stability hierarchies. Conversely, low...

Data from: Internal cranial anatomy of Early Triassic species of †Saurichthys (Actinopterygii: †Saurichthyiformes): implications for the phylogenetic placement of †saurichthyiforms

Thodoris Argyriou, Sam Giles, Matt Friedman, Carlo Romano, Ilja Kogan & Marcelo R. Sanchez-Villagra
Background: †Saurichthyiformes was a successful group of latest Permian-Middle Jurassic predatory actinopterygian fishes and constituted important and widely-distributed components of Triassic marine and freshwater faunas. Their systematic affinities have long been debated, with †saurichthyiforms often being aligned with chondrosteans, a group today comprising sturgeons and paddlefishes. However, their character-rich endocranial anatomy has not been investigated in detail since the first half of the 20th century. Since that time, major advances have occurred in terms of...

Data from: The nearshore cradle of early vertebrate diversification

Lauren Sallan, Matt Friedman, Robert S. Sansom, Charlotte M. Bird & Ivan J. Sansom
Ancestral vertebrate habitats are subject to controversy and obscured by limited, often contradictory paleontological data. We assembled fossil vertebrate occurrence and habitat datasets spanning the middle Paleozoic (480 million to 360 million years ago) and found that early vertebrate clades, both jawed and jawless, originated in restricted, shallow intertidal-subtidal environments. Nearshore divergences gave rise to body plans with different dispersal abilities: Robust fishes shifted shoreward, whereas gracile groups moved seaward. Fresh waters were invaded repeatedly,...

Data from: Terrestrial species adapted to sea dispersal: differences in propagule dispersal of two Caribbean mangroves

Richard G.J. Hodel, L. Lacey Knowles, Stuart F. McDaniel, Adam C. Payton, Jordan F. Dunaway, Pam S. Soltis, Douglas E. Soltis, Richard G. J. Hodel & Pamela S. Soltis
A central goal of comparative phylogeography is to understand how species-specific traits interact with geomorphological history to govern the geographic distribution of genetic variation within species. One key biotic trait with an immense impact on the spatial patterns of intraspecific genetic differentiation is dispersal. Here we quantify how species-specific traits directly related to dispersal affect genetic variation in terrestrial organisms with adaptations for dispersal by sea, not land—the mangroves of the Caribbean. We investigate the...

Data from: Two pulses of morphological diversification in Pacific pelagic fishes following the Cretaceous–Palaeogene mass extinction

Elizabeth Sibert, Matthew Friedman, Pincelli Hull, Gene Hunt, Richard Norris & Matt Friedman
Molecular phylogenies suggest some major radiations of open-ocean fish clades occurred roughly coincident with the K/Pg boundary, however the timing and nature of this diversification is poorly constrained. Here we investigate evolutionary patterns in ray-finned fishes across the Cretaceous-Palaeogene (K/Pg) Mass Extinction 66 million years ago (Ma), using microfossils (isolated teeth) preserved in a South Pacific sediment core spanning 72-43 Ma. Our record does not show significant turnover of fish tooth morphotypes at the K/Pg...

Data from: Ranking stressor impacts on periphyton structure and function with mesocosm experiments and environmental-change forecasts

David M. Costello, Konrad J. Kulacki, Mary E. McCarthy, Scott D. Tiegs & Bradley J. Cardinale
Streams are being subjected to physical, chemical, and biological stresses stemming from both natural and anthropogenic changes to the planet. In the face of limited time and resources, scientists, resource managers, and policy makers need ways to rank stressors and their impacts so that we can prioritize them from the most to least important (i.e., perform 'ecological triage'). We report results from an experiment in which we established a periphyton community from the Huron River...

Data from: The role of fish life histories in allometrically scaled food-web dynamics

Stephanie Bland, Fernanda Valdovinos, Jeffrey Hutchings & Anna Kuparinen
1. Body size determines key ecological and evolutionary processes of organisms. Therefore, organisms undergo extensive shifts in resources, competitors and predators as they grow in body size. While empirical and theoretical evidence show that these size-dependent ontogenetic shifts vastly influence the structure and dynamics of populations, theory on how those ontogenetic shifts affect the structure and dynamics of ecological networks is still virtually absent. 2. Here, we expand the Allometric Trophic Network (ATN) theory in...

Data from: Is permanent parasitism reversible? – Critical evidence from early evolution of house dust mites

Pavel B. Klimov & Barry OConnor
Long-term specialization may limit the ability of a species to respond to new environmental conditions and lead to a higher likelihood of extinction. For permanent parasites and other symbionts, the most intriguing question is whether these organisms can return to a free-living lifestyle and, thus, escape an evolutionary ‘dead end’. This question is directly related to Dollo's law, which stipulates that a complex trait (such as being free-living vs. parasitic) cannot re-evolve again in the...

Data from: Effects of vicariant barriers, habitat stability, population isolation and environmental features on species divergence in the south-western Australian coastal reptile community

Danielle L. Edwards, J. Scott Keogh & L. Lacey Knowles
Identifying explicit hypotheses regarding the factors determining genetic structuring within species can be difficult, especially in species distributed in historically dynamic regions. To contend with these challenges, we use a framework that combines species distribution models, environmental data and multi-locus genetic data to generate and explore phylogeographic hypotheses for reptile species occupying the coastal sand-dune and sand-plain habitats of the south-western Australian biodiversity hotspot; a community which has both a high diversity of endemics and...

Data from: Water stress strengthens mutualism among ants, trees, and scale insects

Elizabeth G. Pringle, Erol Akçay, Ted K. Raab, Rodolfo Dirzo & Deborah M. Gordon
Abiotic environmental variables strongly affect the outcomes of species interactions. For example, mutualistic interactions between species are often stronger when resources are limited. The effect might be indirect: water stress on plants can lead to carbon stress, which could alter carbon-mediated plant mutualisms. In mutualistic ant–plant symbioses, plants host ant colonies that defend them against herbivores. Here we show that the partners' investments in a widespread ant–plant symbiosis increase with water stress across 26 sites...

Logical inferences from visual and auditory information in ruffed lemurs and sifakas

Francesca De Petrillo & Alexandra Rosati
Inference by exclusion, or the ability to select a correct course of action by systematically excluding other potential alternatives, is a form of logical inference that allow individuals to solve problems without complete information. Current comparative research shows that several bird, mammal, and primate species can find hidden food through inference by exclusion. Yet there is also wide variation in how successful different species are, as well kinds of sensory information they can use to...

Antibiotic interactions shape short-term evolution of resistance in Enterococcus faecalis

Ziah Dean, Jeff Maltas & Kevin Wood
Antibiotic combinations are increasingly used to combat bacterial infections. Multidrug therapies are a particularly important treatment option for E. faecalis, an opportunistic pathogen that contributes to high-inoculum infections such as infective endocarditis. While numerous synergistic drug combinations for E. faecalis have been identified, much less is known about how different combinations impact the rate of resistance evolution. In this work, we use high-throughput laboratory evolution experiments to quantify adaptation in growth rate and drug resistance...

Data from: Co-evolving wing spots and mating displays are genetically separable traits in Drosophila

Jonathan H. Massey & Patricia Wittkopp
The evolution of sexual traits often involves correlated changes in morphology and behavior. For example, in Drosophila, divergent mating displays are often accompanied by divergent pigment patterns. To better understand how such traits co-evolve, we investigated the genetic basis of correlated divergence in wing pigmentation and mating display between the sibling species Drosophila elegans and D. gunungcola. Drosophila elegans males have an area of black pigment on their wings known as a wing spot and...

Redescription of the cranial skeleton of the Early Devonian (Emsian) sarcopterygian Durialepis edentatus Otto, 2007 (Dipnomorpha; Porolepiformes)

Sam Giles, Jorge Mondéjar-Fernández & Matt Friedman
Porolepiforms represent a clade of Devonian stem lungfishes, divided into the cosmine-bearing and likely paraphyletic ‘Porolepidae’ (e.g., Porolepis, Heimenia) and the cosmine-free and stratigraphically younger Holoptychiidae (e.g., Holoptychius, Glyptolepis, Laccognathus). Data on the dermoskeleton are available for both groups, but are more limited for ‘porolepids’. Here we present new information on the ‘porolepid’ Durialepis edentatus from the Emsian (Early Devonian) of Germany based on micro-CT scanning. The material comprises an articulated skull of a single...

Data from: Contemporaneous radiations of fungi and plants linked to symbiosis

François Lutzoni, Michael D. Nowak, Michael E. Alfaro, Valérie Reeb, Jolanta Miadlikowska, Michael Krug, A. Elizabeth Arnold, Louise A. Lewis, David L. Swofford, David Hibbett, Khidir Hilu, Timothy Y. James, Dietmar Quandt & Susana Magallón
Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma),...

Data from: Phylogenetic stability, tree shape, and character compatibility: a case study using early tetrapods

Massimo Bernardi, Kenneth D. Angielczyk, Jonathan S. Mitchell & Marcello Ruta
Phylogenetic tree shape varies as the evolutionary processes affecting a clade change over time. In this study, we examined an empirical phylogeny of fossil tetrapods during several time intervals, and studied how temporal constraints manifested in patterns of tree imbalance and character change. The results indicate that the impact of temporal constraints on tree shape is minimal and highlights the stability through time of the reference tetrapod phylogeny. Unexpected values of imbalance for Mississippian and...

Data from: X-rays and virtual taphonomy resolve the first Cissus (Vitaceae) macrofossils from Africa as early diverging members of the genus

Neil F. Adams, Margaret E. Collinson, Selena Y. Smith, Marion K. Bamford, Félix Forest, Panagiota Malakasi, Federica Marone & Dan Sykes
PREMISE OF THE STUDY: Fossilized seeds similar to Cissus (Vitaceae) have been recognized from the Miocene of Kenya, though some were previously assigned to the Menispermaceae. We undertook a comparative survey of extant African Cissus seeds to identify the fossils and consider their implications for the evolution and biogeography of Cissus and for African early Miocene paleoenvironments. METHODS: Micro-computed tomography (µCT) and synchrotron-based X-ray tomographic microscopy (SRXTM) were used to study seed morphology and anatomy....

Motion and heart rate from a wrist-worn wearable and labeled sleep from polysomnography

Olivia Walch
This project contains acceleration (in units of g) and heart rate (bpm, measured from photoplethysmography) recorded from the Apple Watch, as well as labeled sleep scored from gold-standard polysomnography. Data were collected at the University of Michigan from June 2017 to March 2019, and there are 31 subjects in total. Code to read and process these files is available on GitHub. The paper corresponding to the work is Walch et al., "Sleep stage prediction with...

2013 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

Data from: What makes a fang? phylogenetic and ecological controls on tooth evolution in rear-fanged snakes

Erin Westeen, Andrew Durso, Michael Grundler, Daniel Rabosky & Alison Davis Rabosky
Background: Fangs are a putative key innovation that revolutionized prey capture and feeding in snakes, and – along with their associated venom phenotypes – have made snakes perhaps the most medically-significant vertebrate animals. Several snake clades are known for their forward-positioned fangs, and these clades (Elapidae; Viperidae) contain the majority of snakes that are traditionally considered venomous. However, many other snakes are "rear-fanged": they possess potentially venom-delivering teeth situated at the rear end of the...

Framing the Dialogue: A New, Collaborative Approach to the Hazing Dilemma

Malinda M. Matney & Simone Himbeault Taylor

Alternative Trading Systems: Does One Shoe Fit All?

Nicolas Audet, Toni Gravelle & Jing Yang
This paper examines the factors that lead liquidity-motivated investors to choose the type of market structure they prefer. We assume that investors can choose between a dealership and a limit-order-book market. This study builds a theoretical model for both the dealership and order-book markets and develops a numerical method to solve the Nash equiibrium strategies of heterogeneous market participants. We find that a dealership market would be preferred by investors in an environment where customer...

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