265 Works

Induction of Minimalist Grammars over Morphemes

Marina Ermolaeva

Analyzing Default Risk and Liquidity Demand during a Financial Crisis: The Case of Canada

Jason Allen, Ali Hortaçsu & Jakub Kastl
This paper explores the reliability of using prices of credit default swap contracts (CDS) as indicators of default probabilities during the 2007/2008 financial crisis. We use data from the Canadian financial system to show that these publicly available risk measures, while indicative of initial problems of the financial system as a whole, do not seem to correspond to risks implied by the cross-sectional heterogeneity in bank behavior in short-term lending markets. Strategies in, and reliance...

Market Concentration and Uniform Pricing: Evidence from Bank Mergers

João Granja & Nuno Paixao
"In recent years there has been considerable debate about the economic impact of rising levels of market concentration across many industries. In this paper, we focus on the US deposit market. Greater market concentration is usually associated with lower deposit rates. As a result, anti-trust authorities tend to block mergers and acquisitions that could significantly increase concentration in local markets. However, we don’t find that deposit rates necessarily decrease after a merger, even in areas...

Shared patterns of spatial accumulation of lineages across terrestrial vertebrates

Nicholas Crouch
Aim: Whether species co-occur with closely related taxa has long been thought to influence both the rate of species formation and maximum clade diversity. However, it is unclear whether these processes act concordantly across entire clades, and between taxa with disparate dispersal and life history strategies. Quantifying these patterns will yield a better understanding of the factors regulating biodiversity. I investigate whether allopatry promotes lineage diversification leading to greater clade richness. I also test whether...

Raw images of targeted gearshifting in actin-based active nematic liquid crystals

Steven Redford, Rui Zhang, Paul Ruijgrok, Nitin Kumar, Ali Mozaffari, Sasha Zemsky, Aaron Dinner, Vincenzo Vitelli, Zev Bryant, Margaret Gardel & Juan De Pablo
Active materials are capable of converting free energy into mechanical work to produce autonomous motion, and exhibit striking collective dynamics that biology relies on for essential functions. Controlling those dynamics and transport in synthetic systems has been particularly challenging. Here, we introduce the concept of spatially structured activity as a means to control and manipulate transport in active nematic liquid crystals consisting of actin filaments and light-sensitive myosin motors. Simulations and experiments are used to...

Image stack, PLY-files and a NEX-file accompanying: A new symmoriiform from the Late Devonian of Morocco: novel jaw function in ancient sharks

Linda Frey, Michael I. Coates, Kristen Tietjen, Martin Rücklin & Christian Klug
We describe the small chondrichthyan Ferromirum oukherbouchi n.gen. et sp. from the Famennian (Late Devonian) of the Maïder region in Morocco. This chondrichthyan is exceptionally well preserved and displays not only mineralized soft tissues but also undeformed cartilages of the head, gills, and shoulder girdle. A reconstruction of the head using 3D-prints revealed a previously unknown kind of jaw articulation. Here, we make the original cropped image stack and PLY-files of the single cartilaginous elements...

Phylogenetic and ecological correlates of pollen morphological diversity in a neotropical rainforest

Luke Mander, Caroline Parins-Fukuchi, Christopher W. Dick, Surangi W. Punyasena & Carlos Jaramillo.
Morphology varies enormously across clades, and the morphology of a trait may reflect ecological function or the retention of ancestral features. We examine the tension between ecological and phylogenetic correlates of morphological diversity through a case study of pollen grains produced by angiosperms in Barro Colorado Island, Panama (BCI). Using a molecular phylogeny of 730 taxa we demonstrate a statistically significant association between morphological and genetic distance for these plants. However, the relationship is non-linear,...

Disease seasonality estimation dataset for: Do psychiatric diseases follow annual cyclic seasonality?

Hanxin Zhang
Seasonal affective disorder famously follows annual cycles, with incidence elevation in the fall and spring. Should some version of cyclic annual pattern be expected from other psychiatric disorders? Would annual cycles be similar for distinct psychiatric conditions? This study probes these questions using two very large datasets describing the health histories of 150 million unique Americans and the entire Swedish population. We performed two types of analysis, using “uncorrected” and “corrected” observation. The former analysis...

Convergent craniofacial evolution and biogeography of weakly electric Mormyridae and Bonytongue Fishes (Osteoglossomorpha)

Rose Peterson, John Sullivan, Carl Hopkins, Aintzane Santaquiteria, Casey Dillman, Stacy Pirro, Ricardo Betancur, Dahiana Arcila, Lily C. Hughes & Guillermo Ortí
Bonytongues (Osteoglossomorpha) constitute an ancient clade of teleost fishes distributed in freshwater habitats throughout the world. The group includes well-known species such as arowanas, featherbacks, pirarucus, and the weakly electric fishes in the family Mormyridae. Their disjunct distribution, extreme morphologies, and electrosensory capabilities (Notopteridae and Mormyroidea) have attracted interest by many, yet a comprehensive phylogenetic framework for comparative analysis is missing. We provide a phylogenomic analysis of 179 species (out of 260), 28 out of...

Historical rice farming in China linked to contemporary polygenic score differences

Chen Zhu, Thomas Talhelm, Yingxiang Li, Gang Chen, Jiong Zhu & Jun Wang
Following domestication in the lower Yangtze River valley 9,400 years ago, rice farming spread throughout China and changed lifestyle patterns among Neolithic populations. Here we report evidence that the advent of rice domestication and cultivation may have shaped humans not only culturally but also genetically. Leveraging recent findings from molecular genetics, we construct a number of polygenic scores of behavioural traits and examine their associations with rice cultivation based on a sample of 4,101 individuals...

Spatially displaced excitation contributes to the encoding of interrupted motion by the retinal direction-selective circuit

Jennifer Ding
Spatially distributed excitation and inhibition collectively shape a visual neuron’s receptive field (RF) properties. In the direction-selective circuit of the mammalian retina, the role of strong null-direction inhibition of On-Off direction-selective ganglion cells (ON-OFF DSGCs) on their direction selectivity is well-studied. However, how excitatory inputs influence the On-Off DSGC’s visual response is underexplored. Here, we report that On-Off DSGCs have a spatially displaced glutamatergic receptive field along their horizontal preferred-null motion axes. This displaced receptive...

OTU data and analysis files for interspecies comparison of Philippine terrestrial small mammal diets

Anna Petrosky, Dakota Rowsey & Lawrence Heaney
Island radiations represent unique evolutionary histories in unique ecological contexts. These radiations provide opportunities to investigate ecological diversification in groups that typically exhibit niche partitioning among their constituents, including partitioning of food resources. DNA metabarcoding produces finer levels of diet identification than traditional methods, allowing us to examine dietary niche partitioning in communities or clades in which species share superficially similar diets. Here we use DNA metabarcoding to investigate dietary niche partitioning in an endemic...

Key roles for the freezing line and disturbance in driving the low plant species richness of temperate regions

Suresh K Rana, Alexander E White & Trevor D Price
Aim: At the macroscale, climate strongly correlates with species richness gradients, resulting from differences in in-situ diversification and dispersal. One historical explanation for the pattern is that regions spanning temperate climates contain few species because past disturbances have generated high extinction rates, and species from tropical regions are unable to easily colonize temperate regions. We test these postulates for Himalayan plants, which span subtropical to temperate climates over steep elevational gradients. Location: Himalaya Time period:...

Data from: Mechanosensation is evolutionarily tuned to locomotor mechanics

Brett R. Aiello, Mark W. Westneat & Melina E. Hale
The biomechanics of animal limbs has evolved to meet the functional demands for movement associated with different behaviors and environments. Effective movement relies not only on limb mechanics but also on appropriate mechanosensory feedback. By comparing sensory ability and mechanics within a phylogenetic framework, we show that peripheral mechanosensation has evolved with limb biomechanics, evolutionarily tuning the neuromechanical system to its functional demands. We examined sensory physiology and mechanics of the pectoral fins, forelimb homologs,...

Data from: Morphology of the petrosal and stapes of Borealestes (Mammaliaformes, Docodonta) from the Middle Jurassic of Skye, Scotland

Elsa Panciroli, Julia A. Schultz & Zhe-Xi Luo
\We describe, in unprecedented detail, the petrosals and stapes of the docodont Borealestes from the Middle Jurassic of Scotland, using high resolution μCT and phase‐contrast synchrotron imaging. We describe the inner ear endocast and the vascularized interior structure of the petrosal, and provide the first endocranial view of a docodontan petrosal. Our study confirms some similarities in petrosal and stapedial morphology with the better known Haldanodon of the Late Jurassic of Portugal, including: (1) the...

Data from: Phylogenetic relationships and the evolution of BMP4 in triggerfishes and filefishes (Balistoidea)

Charlene L. McCord & Mark W. Westneat
The triggerfishes (family Balistidae) and filefishes (family Monacanthidae) comprise a charismatic superfamily (Balistoidea) within the diverse order Tetraodontiformes. This group of largely marine fishes occupies an impressive ecological range across the world’s oceans, and is well known for its locomotor and feeding diversity, unusual body shapes, small genome size, and ecological and economic importance. In order to investigate the evolutionary history of these important fish families, we used multiple phylogenetic methods to analyze molecular data...

Data from: Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours

John M. Jumper, Nabil F. Faruk, Karl F. Freed & Tobin R. Sosnick
An ongoing challenge in protein chemistry is to identify the underlying interaction energies that capture protein dynamics. The traditional trade-off in biomolecular simulation between accuracy and computational efficiency is predicated on the assumption that detailed force fields are typically well-parameterized, obtaining a significant fraction of possible accuracy. We re-examine this trade-off in the more realistic regime in which parameterization is a greater source of error than the level of detail in the force field. To...

Data from: Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America

Katherine Silliman
Effective management of threatened and exploited species requires an understanding of both the genetic connectivity among populations and local adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from Baja California to the central coast of Canada, has a long history of population declines due to anthropogenic stressors. For such coastal marine species, population structure could follow a continuous isolation-by-distance model, contain regional blocks of genetic similarity separated by barriers to gene flow, or be consistent...

Data from: Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal

Choongwon Jeong, David B. Witonsky, Buddha Basnyat, Maniraj Neupane, Cynthia M. Beall, Geoff Childs, Sienna R. Craig, John Novembre & Anna Di Rienzo
Adaptive evolution in humans has rarely been characterized for its whole set of components, i.e. selective pressure, adaptive phenotype, beneficial alleles and realized fitness differential. We combined approaches for detecting selective sweeps and polygenic adaptations and for mapping the genetic bases of physiological and fertility phenotypes in approximately 1000 indigenous ethnically Tibetan women from Nepal, adapted to high altitude. We performed genome-wide association analysis and tests for polygenic adaptations which showed evidence of positive selection...

Data from: Genome-wide association study of Arabidopsis thaliana leaf microbial community

Matthew W. Horton, Natacha Bodenhausen, Kathleen Beilsmith, Dazhe Meng, Brian D. Muegge, Sathish Subramanian, M. Madlen Vetter, Bjarni J. Vilhjálmsson, Magnus Nordborg, Jeffrey I. Gordon & Joy Bergelson
Identifying the factors that influence the outcome of host–microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the...

Data from: Consequences of divergence and introgression for speciation in Andean cloud forest birds

Benjamin M. Winger
Divergence with gene flow is well documented and reveals the influence of ecological adaptation on speciation. Yet it remains intuitive that gene exchange inhibits speciation in many scenarios, particularly among ecologically similar populations. The influence of gene flow on the divergence of populations facing similar selection pressures has received less empirical attention than scenarios where differentiation is coupled with local environmental adaptation. I used a paired study design to test the influence of genomic divergence...

Data from: Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers

George H. Perry, Matthieu Foll, Jean-Christophe Grenier, Etienne Patin, Yohann Nédélec, Alain Pacis, Maxime Barakatt, Simon Gravel, Xiang Zhou, Sam L. Nsobya, Laurent Excoffier, Lluis Quintana-Murci, Nathaniel J. Dominy & Luis B. Barreiro
The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (east central Africa). The identified genomic regions have multiple attributes that provide supporting evidence of genuine association with the pygmy phenotype, including...

Data from: How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography

Jakob S. Jørgensen, Emil Y. Sidky & J. S. Jorgensen
We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in...

Data from: Diversity-dependent evolutionary rates in early Paleozoic zooplankton

Michael Foote, Roger A. Cooper, James S. Crampton & Peter M. Sadler
The extent to which biological diversity affects rates of diversification is central to understanding macroevolutionary dynamics, yet no consensus has emerged on the importance of diversity-dependence of evolutionary rates. Here we analyse the species-level fossil record of early Paleozoic graptoloids, documented with high temporal resolution, to test directly whether rates of diversification were influenced by levels of standing diversity within this major clade of marine zooplankton. To circumvent the statistical regression-to-the-mean artefact, whereby higher- and...

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