39 Works

Data from: Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila

Heather E. Machado, Alan O. Bergland, Ryan Taylor, Susanne Tilk, Emily Behrman, Kelly Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Iryna Kozeretska, Brian P. Lazzaro, Thomas JS Merritt, John E. Pool, Katherine O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul Schmidt, Dmitri Petrov & Bernard Kim
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched at...

Slower environmental cycles maintain greater life-history variation within populations

John Park & Tim Wootton
Populations in nature are comprised of individual life histories, whose variation underpins ecological and evolutionary processes. Yet the forces of environmental selection that shape intrapopulation life-history variation are still not well understood, and efforts have largely focused on random (stochastic) fluctuations of the environment. However, a ubiquitous mode of environmental fluctuation in nature is cyclical, whose periodicities can change independently of stochasticity. Here we test theoretically-based hypotheses for whether shortened (‘Fast’) or lengthened (‘Slow’) environmental...

Sound velocities and P-V-T data of phase A obtained at GSECARS beamline 13-ID-D

Nao Cai, Xintong Qi, Ting Chen, Siheng Wang, Tony Yu, Yanbing Wang, Toru Inoue, Duojun Wang & Baosheng Li
The sound velocities and lattice parameters for sample in the under review paper, "Enhanced visibility of subduction slabs by the formation of dense hydrous phase A", submitted to the journal 'Geophysical Research Letters', are published. The high pressure and high-temperature experiment was conducted in the 1000-ton Kawai type large volume apparatus (T-25) installed at the GSECARS beamline 13-ID-D of Advanced Photon Source, Argonne National Laboratory. The datasets were obtained at conditions up to 11 GPa...

Adult facilitation becomes competition as juvenile soapberry bugs age

Meredith Cenzer
Intraspecific interactions can change from facilitative to competitive depending on the organism’s ontogeny. In plant-feeding insects, host plant defenses can be strengthened or weakened by insect feeding, and can therefore be important for determining whether two insects feeding on the same plant help or harm each other’s fitness. Here I conducted two experiments looking at the direct effect of a physical seed defense and the role of intraspecific facilitation in reducing the effects of that...

Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families

Nicholas Crouch, Stewart Edie, Katie Collins, Rüdiger Bieler & David Jablonski
Analyses of evolutionary dynamics can be profoundly affected by age calibrations of phylogenetic nodes under different models of lineage branching. Most time-calibrated molecular phylogenies of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. Lineages can also split via budding, in which a parent lineage persists following the origin of a daughter lineage, and nodes are calibrated using the age...

Derivation and validation of a model to predict acute kidney injury following cardiac surgery in patients with normal renal function

Penghua Hu, Zhiming Mo, Yuanhan Chen, Yanhua Wu, Li Song, Li Zhang, Zhilian Li, Lei Fu, Huaban Liang, Yiming Tao, Shuangxin Liu, Zhiming Ye & Xinling Liang
The study aimed to construct a clinical model based on preoperative data for predicting acute kidney injury (AKI) following cardiac surgery in patients with normal renal function. A total of 22,348 consecutive patients with normal renal function undergoing cardiac surgery were enrolled. Among them, 15,701 were randomly selected for the training group and the remaining for the validation group. To develop a model visualized as a nomogram for predicting AKI, logistic regression was performed with...

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....

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...

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...

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...

Identification of microRNA hsa-miR-30c-5p as an inhibitory factor in the progression of hepatocellular carcinoma and investigation of its regulatory network via comprehensive analysis

Shangshang Hu, Jinyan Zhang, Xiaoyu Fang, Guoqing Guo, Jing Dai, Zhiyong Sheng, Dongdong Li, Jiasheng Chen, Li Zhang, Chuanmiao Liu & Yu Gao
Hepatocellular carcinoma (HCC) is a primary liver cancer with high morbidity and mortality. An increasing number of abnormal gene expressions were identified to be associated with the progression of HCC. Previous studies showed that the hsa-miR-30 c-5p (miR-30 c), one of the miR-30 family members, might play a role in suppressing tumor progression in a variety of tumors. The present study aims to examine miR-30 c effects in the development of HCC. The role of...

Identification of microRNA hsa-miR-30c-5p as an inhibitory factor in the progression of hepatocellular carcinoma and investigation of its regulatory network via comprehensive analysis

Shangshang Hu, Jinyan Zhang, Xiaoyu Fang, Guoqing Guo, Jing Dai, Zhiyong Sheng, Dongdong Li, Jiasheng Chen, Li Zhang, Chuanmiao Liu & Yu Gao
Hepatocellular carcinoma (HCC) is a primary liver cancer with high morbidity and mortality. An increasing number of abnormal gene expressions were identified to be associated with the progression of HCC. Previous studies showed that the hsa-miR-30 c-5p (miR-30 c), one of the miR-30 family members, might play a role in suppressing tumor progression in a variety of tumors. The present study aims to examine miR-30 c effects in the development of HCC. The role of...

Registration Year

  • 2021
    39

Resource Types

  • Dataset
    39

Affiliations

  • University of Chicago
    39
  • Sun Yat-sen University
    5
  • West China Hospital of Sichuan University
    5
  • Zhejiang University
    5
  • Southwest Medical University
    5
  • The University of Texas at Austin
    5
  • Jilin University
    5
  • Chinese University of Hong Kong
    5
  • International Agency for Research on Cancer
    5
  • Inner Mongolia University
    5