39 Works

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...

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...

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...

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...

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...

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...

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...

Sustainable use of groundwater may dramatically reduce irrigated production of maize, soybean, and wheat

Jose R. Lopez, Jonathan M. Winter, Joshua Elliott, Alex C. Ruane, Cheryl Porter, Gerrit Hoogenboom, Martha Anderson & Christopher Hain
Groundwater extraction in the United States (US) is unsustainable, making it essential to understand the impacts of limited water use on irrigated agriculture. Here, we integrate a gridded crop model with satellite observations, recharge estimates, and water survey data to assess the effects of sustainable groundwater withdrawals on US irrigated agricultural production. Our model agrees with satellite-based estimates of evapotranspiration (R2 = 0.68), as well as survey production estimates from the United States Department of...

Phylogenomics of bonytongue fishes (Osteoglossomorpha) shed light on the craniofacial evolution and biogeography of the weakly electric clade (Mormyridae)

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...

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:...

Evolutionary modularity, integration and disparity in an accretionary skeleton: Analysis of venerid Bivalvia

Stewart Edie, Safia Khouja, Katie Collins, Nicholas Crouch & David Jablonski
Modular evolution, the relatively independent evolution of body parts, may promote high morphological disparity in a clade. Conversely, integrated evolution via the stronger covariation of parts may limit disparity. However, integration can also promote high disparity by channeling morphological evolution along lines of least resistance—a process that may be particularly important in the accumulation of disparity among organisms with accretionary growth, as in many invertebrate systems. We use a time-calibrated phylogenetic hypothesis and high-density, 3D...

Data from: Twist and chew: three dimensional tongue kinematics during chewing in macaque primates

Kara Feilich, J.D. Laurence-Chasen, Courtney Orsbon, Nicholas Gidmark & Callum Ross
Three-dimensional (3D) tongue movements are central to performance of feeding functions by mammals and other tetrapods, but 3D tongue kinematics during feeding are poorly understood. Tongue kinematics were recorded during grape chewing by macaque primates using biplanar videoradiography. Complex shape changes in the tongue during chewing are dominated by a combination of flexion in the tongue’s sagittal planes and roll about its long axis. As hypothesized for humans, in macaques during tongue retraction the middle...

Data from: Postcrania of Borealestes (Mammaliformes: Docodonta) and the emergence of ecomorphological diversity in early mammals

Elsa Panciroli, Roger Benson, Vincent Fernandez, Matthew Humpage, Alberto Martin-Serra, Stig Walsh, Zhe-Xi Luo & Nick Fraser
The Middle Jurassic witnessed the early diversification of mammal groups, including the stem-mammalian clade, Docodonta. Recent discoveries in China indicate docodontans exhibited ecomorphological diversity akin to small-bodied mammals living >100 million years later, in the Cenozoic. Our understanding of the emergence of this ecological diversity is hindered by a lack of Middle Jurassic fossil material from other parts of the world. The two partial postcranial skeletons of Borealestes described here come from the Kilmaluag Formation,...

De novo genome assembly of Leptodactylus fuscus

Lu Yang, Peter Andolfatto, Andrew Crawford, Santiago Herrera-Álvarez, Maríadel Pilar Rodríguez-Ordoñez, Julie Peng, Shabnam Mohammadi, Jay Storz, Arbel Harpak & Susanne Dobler
This presents a de novo genome assembly of Leptodactylus fuscus. High molecular weight DNA was extracted from a L. fuscus embryo which had been preserved in ethanol upon collection in Garzón, Huila, Colombia. The library was prepared and sequenced with 10X Genomics Chromium. Linked reads were processed by Long Ranger basic v2.2.2 and assembled with Supernova v2.1.1. The assembled genome is 2.42 Gb with 16,530 scaffolds >=10 kb, and scaffold N50 = 363 kb. The...

Selection in males purges the mutation load on female fitness

Karl Grieshop, Paul Maurizio, Göran Arnqvist & David Berger
Theory predicts that the ability of selection and recombination to purge mutation load is enhanced if selection against deleterious genetic variants operates more strongly in males than females. However, direct empirical support for this tenet is limited, in part because traditional quantitative genetic approaches allow dominance and intermediate-frequency polymorphisms to obscure the effects of the many rare and partially recessive deleterious alleles that make up the main part of a population’s mutation load. Here, we...

Data from: Concerted evolution reveals co-adapted amino acid substitutions in Na+K+ ATPase of frogs that prey on toxic toads

Shabnam Mohammadi, Lu Yang, Arbel Harpak, Santiago Herrera-Álvarez, María Del Pilar Rodríguez-Ordoñez, Julie Peng, Karen Zhang, Jay Storz, Susanne Dobler, Andrew Crawford & Peter Andolfatto
Gene duplication is an important source of evolutionary innovation, but the functional distinction between duplicates can be opposed by ongoing gene conversion between them. Here we document a tandem duplication of Na+,K+-ATPase subunit α1 (ATP1A1) sharedby frogs in the genus Leptodactylus,a group of species that feeds on toxic toads. One ATP1A1 paralog evolved resistance to toad toxins while the other paralog retained ancestral susceptibility. Frequent non-allelic gene conversion homogenized most of the paralog sequences,yet the...

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...

Tracking the Impact of Diseases of Despair in Appalachia—2015 to 2018

Megan Heffernan, Michael Meit, Margaret Cherney & Victoria A. Hallman
Introduction: This study provides an update on mortality due to diseases of despair within the Appalachian Region, comparing 2015 to 2018. Methods: Diseases of despair include: alcohol, prescription drug and illegal drug overdose, suicide, and alcoholic liver disease/cirrhosis of the liver. Analyses are based on National Vital Statistics System (NVSS) mortality data for individuals aged 15-64. Results: Between 2015 and 2017, the diseases of despair mortality rate increased in both Appalachia and the non-Appalachian U.S.,...

A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses

Graeme Lloyd & Graham Slater
Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species--rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely...

Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how dietary convergence and parallelism obfuscate traditional morphological taxonomy

Matthew Kolmann & Lily Hughes
The Amazon and neighboring South American river basins harbor the world’s most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of the top riverine predators as well as the primary seed dispersers in the flooded forest. Despite their widespread occurrence and notable ecologies, serrasalmid evolutionary history and systematics are controversial....

Experimental evolution of ancestrally reconstructed BCL2 family proteins

Brian Metzger, Victoria Xie, Jinyue Pu, Joseph Thornton & Bryan Dickinson
The roles of chance, contingency, and necessity in evolution is unresolved, because they have never been assessed in a single system or on timescales relevant to historical evolution. We combined ancestral protein reconstruction and a new continuous evolution technology to mutate and select B-cell-lymphoma-2-family proteins to acquire protein-protein-interaction specificities that occurred during animal evolution. By replicating evolutionary trajectories from multiple ancestral proteins, we found that contingency generated over long historical timescales steadily erased necessity and...

Data from two dimensional electronic spectroscopy showing that photosynthesis tunes quantum-mechanical mixing of electronic and vibrational states to steer exciton energy transfer

Jacob Higgins, Lawson Lloyd, Sara Sohail, Marco Allodi, John Otto, Rafael Saer, Ryan Wood, Sara Massey, Po-Chieh Ting, Robert Blankenship & Gregory Engel
Raw data from an ultrafast two dimensional electronic spectrometer investigating a series of mutants from the Fenna-Matthews Olson photosynthetic complex from Chlorobaculum tepidum is included here. This data was analyzed and reduced using the enclosed matlab scripts to show that this complex responds to changing oxidation conditions by breaking a resonance between a gap between electronic states and an attendant vibration within the bacteriochlorophyll molecules. Breaking this resonance steers energy differently through the complex and...

Evolutionary history of quadrupedal walking gaits shows mammalian release from locomotor constraint

Alexa Wimberly, Graham Slater & Michael Granatosky
Vertebrates employ an impressive range of strategies for coordinating their limb movements while walking. Although this gait variation has been quantified and hypotheses for its origins tested in select tetrapod lineages, a comprehensive understanding of gait evolution in a macroevolutionary context is currently lacking. We used freely-available internet videos to nearly double the number of species with quantitative gait data and used phylogenetic comparative methods to test key hypotheses about gait origin and evolution. We...

Dataset S1 - Noelaerhabdaceae organic carbon isotope culture data compilation

Samuel Phelps, Gwenn Hennon, Sonya Dyhrman, María Hernández-Limón, Olivia Williamson & Pratigya Polissar
The carbon isotope fractionation in algal organic matter (Ep), including the long-chain alkenones produced by the coccolithophorid family Noelaerhabdaceae, is used to reconstruct past atmospheric CO2 levels. The conventional proxy linearly relates Ep to changes in cellular carbon demand relative to diffusive CO2 supply, with larger Ep values occurring at lower carbon demand relative to supply (i.e. abundant CO2). However, the response of Gephyrocapsa oceanica, one of the dominant alkenone producers of the last few...

Differential impacts of alternate primary producers on carbon cycling

Khashiff Miranda, Brooke Weigel, Sophie McCoy & Catherine Pfister
Disturbance impacts the spatial distribution of primary producers, which can have cascading effects on ecosystem function. The lower-intertidal zone on the rocky shores of the Pacific Northwest is one such place where wave energy creates a mosaic-like distribution between two assemblages: surfgrass (Phyllospadix scouleri) meadows and macroalgal forests dominated by kelp. We simulated wave disturbance by experimentally removing patches of surfgrass monocultures, resulting in a macroalgal assemblage with increased diversity, biomass, and net primary productivity...

Registration Year

  • 2021

Resource Types

  • Dataset
  • Text
  • Journal Article
  • Report


  • University of Chicago
  • George Washington University
  • Smithsonian Institution
  • Cornell University
  • Wellcome Sanger Institute
  • Stanford University
  • Universität Hamburg
  • The University of Texas at Austin
  • Columbia University
  • Princeton University