174 Works

Data from: Postzygotic isolation involves strong mitochondrial and sex-specific effects in Tigriopus californicus, a species lacking heteromorphic sex chromosomes

Brad R. Foley, Colin G. Rose, Daniel E. Rundle, Wai Leong & Suzanne Edmands
Detailed studies of the genetics of speciation have focused on a few model systems, particularly Drosophila. The copepod Tigriopus californicus offers an alternative that differs from standard animal models in that it lacks heteromorphic chromosomes (instead, sex determination is polygenic) and has reduced opportunities for sexual conflict, because females mate only once. Quantitative trait loci (QTL) mapping was conducted on reciprocal F2 hybrids between two strongly differentiated populations, using a saturated linkage map spanning all...

Data from: Genetic variation in the Yolk protein expression network of Drosophila melanogaster: sex-biased negative correlations with longevity

Aaron M. Tarone, Lauren M. Mcintyre, Lawrence G. Harshman & Sergey V. Nuzhdin
One of the persistent problems in biology is understanding how genetic variation contributes to phenotypic variation. Associations at many levels have been reported, and yet causal inference has remained elusive. We propose to rely on the knowledge of causal relationships established by molecular biology approaches. The existing molecular knowledge forms a firm backbone upon which hypotheses connecting genetic variation, transcriptional variation and phenotypic variation can be built. The sex determination pathway is a well-established molecular...

Data from: The genomic trajectory of hybrid swarms: outcomes of repeated crosses between populations of Tigriopus californicus

Victoria L. Pritchard & Suzanne Edmands
Introgressive hybridization between genetically divergent populations is an important evolutionary process. The degree to which repeated hybridization events between the same parental taxa lead to similar genomic outcomes is unknown. This study addressed this question by following genomic trajectories of replicate hybrid swarms of the copepod Tigriopus californicus over many generations of free mating. Swarm composition was determined both by differential reproductive success of founder individuals and subsequent selection on hybrid genotypes. For one cross,...

Data from: Polymorphism pattern at a Miniature Inverted-repeat Transposable Element locus downstream of the domestication gene Teosinte-branched1 in wild and domesticated pearl millet

Yann Dussert, Marie-Stanislas Remigereau, Michael C. Fontaine, Alodie Snirc, Ghayas Lakis, Solenn Stoeckel, Thierry Langin, Aboubakry Sarr, Thierry Robert & M.-S. Remigereau
Unraveling the mechanisms involved in adaptation to understand plant morphological evolution is a challenging goal. For crop species, identification of molecular causal polymorphisms involved in domestication traits are central to this issue. Pearl millet, a domesticated grass mostly found in semi-arid areas of Africa and India, is an interesting model to address this topic: the domesticated form shares common derived phenotypes with some other cereals such as a decreased ability to develop basal and axillary...

Data from: Divergent transcriptional patterns are related to differences in hypoxia tolerance between the intertidal and the subtidal sculpins

Milica Mandic, Marina L. Ramon, Andrew Y. Gracey & Jeffrey G. Richards
Transcriptionally mediated phenotypic plasticity as a mechanism of modifying traits in response to an environmental challenge remains an important area of study. We compared the transcriptional responses to low-oxygen (hypoxia) of the hypoxia tolerant intertidal fish, the tidepool sculpin (Oligocottus maculosus) with the closely related hypoxia intolerant subtidal fish, the silverspotted sculpin (Blepsias cirrhosus) to determine if these species use different mechanisms to cope with hypoxia. Individuals from each species were exposed to environmental O2...

Data from: Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the southeastern United States and Caribbean Islands

Joyce Y. Kao, Asif Zubair, Matthew P. Salomon, Sergey V. Nuzhdin & Daniel Campo
Drosophila melanogaster is postulated to have colonized North America in the past several 100 years in two waves. Flies from Europe colonized the east coast United States while flies from Africa inhabited the Caribbean, which if true, make the south-east US and Caribbean Islands a secondary contact zone for African and European D. melanogaster. This scenario has been proposed based on phenotypes and limited genetic data. In our study, we have sequenced individual whole genomes...

Data from: Biodiversity response to natural gradients of multiple stressors on continental margins

Erik A. Sperling, Christina A. Frieder & Lisa A. Levin
Sharp increases in atmospheric CO2 are resulting in ocean warming, acidification and deoxygenation that threaten marine organisms on continental margins and their ecological functions and resulting ecosystem services. The relative influence of these stressors on biodiversity remains unclear though, as well as the threshold levels for change and when secondary stressors become important. One strategy to interpret adaptation potential and predict future faunal change is to examine ecological shifts along natural gradients in the modern...

Data from: Social effects for locomotion vary between environments in Drosophila melanogaster females

Sarah A. Signor, Mohammad Abbasi, Paul Marjoram & Sergey V. Nuzhdin
Despite strong purifying or directional selection, variation is ubiquitous in populations. One mechanism for the maintenance of variation is indirect genetic effects, as the fitness of a given genotype will depend somewhat on the genes of its social partners. Indirect genetic effects (IGEs) describe the effect of genes in social partners on the expression of the phenotype of a focal individual. Here we ask what effect IGEs, and variation in IGEs between abiotic environments, has...

Data from: Cannabinoids disrupt memory encoding by functionally isolating hippocampal CA1 from CA3

Roman A. Sandler, Dustin Fetterhoff, Robert E. Hampson, Sam A. Deadwyler, Vasilis Z. Marmarelis & Roman Sandler
Much of the research on cannabinoids (CBs) has focused on their effects at the molecular and synaptic level. However, the effects of CBs on the dynamics of neural circuits remains poorly understood. This study aims to disentangle the effects of CBs on the functional dynamics of the hippocampal Schaffer collateral synapse by using data-driven nonparametric modeling. Multi-unit activity was recorded from rats doing an working memory task in control sessions and under the influence of...

Data from: Variation of stomatal traits from cold-temperate to tropical forests and association with water use efficiency

Congcong Liu, Nianpeng He, Jiahui Zhang, Ying Li, Qiufeng Wang, Lawren Sack & Guirui Yu
1.Stomata control carbon and water vapor exchange between leaves and the atmosphere, thus it can influence water use efficiency and reflect plant adaptation to climate. However, the spatial patterns of leaf stomatal traits and relationships between stomatal trait and water use efficiency across natural communities remain unclear. 2.We measured stomatal density, stomatal size, and stomatal area fraction for 737 plant species from nine forests ranging from tropical to cold-temperate forests. 3.Stomatal density, stomatal size, and...

Data from: Inferring individual-level processes from population-level patterns in cultural evolution

Anne Kandler, Bryan Wilder & Laura Fortunato
Our species is characterized by a great degree of cultural variation, both within and between populations. Understanding how group-level patterns of culture emerge from individual-level behaviour is a long-standing question in the biological and social sciences. We develop a simulation model capturing demographic and cultural dynamics relevant to human cultural evolution, focusing on the interface between population-level patterns and individual-level processes. The model tracks the distribution of variants of cultural traits across individuals in a...

Data from: Basic reversal-learning capacity in flies suggests rudiments of complex cognition

Brad R. Foley, Paul Marjoram & Sergey V. Nuzhdin
The most basic models of learning are reinforcement learning models (for instance, classical and operant conditioning) that posit a constant learning rate; however many animals change their learning rates with experience. This process is sometimes studied by reversing an existing association between cues and rewards, and measuring the rate of relearning. Augmented reversal-learning, where learning rates increase with practice, can be an important component of behavioral flexibility; and may provide insight into higher cognition. Previous...

Data from: Randomized phase 2 study of FcRn antagonist efgartigimod in generalized myasthenia gravis

James F. Howard, Vera Bril, Ted M. Burns, Renato Mantegazza, Malgorzata Bilinska, Andrzej Szczudlik, Said Beydoun, Francisco Javier Rodriguez De Rivera Garrido, Fredrik Piehl, Mariarosa Rottoli, Philip Van Damme, Tuan Vu, Amelia Evoli, Miriam Freimer, Tahseen Mozaffar, E. Sally Ward, Torsten Dreier, Peter Ulrichts, Katrien Verschueren, Antonio Guglietta, Hans De Haard, Nicolas Leupin & Jan J. G. M. Verschuuren
Objective: To investigate safety and explore efficacy of efgartigimod (ARGX-113), an anti-neonatal Fc receptor immunoglobulin G1 Fc fragment, in patients with generalized myasthenia gravis (gMG) with a history of anti-acetylcholine receptor (AChR) autoantibodies, who were on stable standard-of-care myasthenia gravis (MG) treatment. Methods: A phase 2, exploratory, randomized, double-blind, placebo-controlled, 15-center study is described. Eligible patients were randomly assigned (1:1) to receive 4 doses over a 3-week period of either 10 mg/kg IV efgartigimod or...

Data from: Augmented reality powers a cognitive assistant for the blind

Yang Liu, Noelle R.B. Stiles, Markus Meister & Noelle RB Stiles
To restore vision for the blind several prosthetic approaches have been explored that convey raw images to the brain. So far these schemes all suffer from a lack of bandwidth. An alternate approach would restore vision at the cognitive level, bypassing the need to convey sensory data. A wearable computer captures video and other data, extracts important scene knowledge, and conveys that to the user in compact form. Here we implement an intuitive user interface...

Data from: A GWAS approach identifies Dapp1 as a determinant of air pollution-induced airway hyperreactivity

Hooman Allayee
Asthma is a chronic inflammatory disease of the airways with contributions from genes, environmental exposures, and their interactions. While genome-wide association studies (GWAS) in humans have identified ~200 susceptibility loci, the genetic factors that modulate risk of asthma through gene-environment (GxE) interactions remain poorly understood. Using the Hybrid Mouse Diversity Panel (HMDP), we sought to identify the genetic determinants of airway hyperreactivity (AHR) in response to diesel exhaust particles (DEP), a model traffic-related air pollutant....

Founder effects shape linkage disequilibrium and genomic diversity of a partially clonal invader

Ben Flanagan, Stacy Krueger-Hadfield, Courtney Murren, Chris Nice, Allan Strand & Erik Sotka
Genomic variation of an invasive species may be affected by complex demographic histories and evolutionary changes during invasions. Here, we describe the relative influence of bottlenecks, clonality, and population expansion in determining genomic variability of the widespread red macroalga Agarophyton vermiculophyllum. Its introduction from mainland Japan to the estuaries of North America and Europe coincided with shifts from predominantly sexual to partially clonal reproduction and rapid adaptive evolution. A survey of 62,285 SNPs for 351...

2018 FaultScan San Jacinto Fault dense array experiment

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This experiment is part of the FaultScan project (UGA, UCSD, USC). It targets the San Jacinto Fault by using passive seismic interferometry measurements across the fault using permanent and dense array stations. This preliminary experiment in 2018 will be followed by longer-term arrays deployments starting 2022.

Congestion reduction via personalized incentives

Ali Ghafelebashi, Meisam Razaviyayn & Maged Dessouky
The purpose of this research is to develop real-time algorithms to reduce traffic congestion and improve routing efficiency via offering personalized incentives to drivers. The incentives and alternative routes should be chosen smartly in order to maximize the probability of acceptance by drivers and to avoid the creation of new congestion in other areas of the network. To this end, we propose to exploit the wide-accessibility of smart communication devices and develop a real-time look-ahead...

Transgenerational plasticity and the capacity to adapt to low salinity in the eastern oyster, Crassostrea virginica

Joanna Griffiths, Kevin Johnson, Kyle Sirovy, Mark Yeats, Francis Pan, Jerome La Peyre & Morgan Kelly
Salinity conditions in oyster breeding grounds in the Gulf of Mexico are expected to drastically change due to increased precipitation from climate change and anthropogenic changes to local hydrology. We determined the capacity of the eastern oyster, Crassostrea virginica, to adapt via standing genetic variation or acclimate through transgenerational plasticity. We outplanted oysters to either a low or medium salinity site in Louisiana for two years. We then crossed adult parents using a North Carolina...

DatasetS2 Intramidbrain macroconnection reports for rat

Larry Swanson
This file contains data used to construct connection matrices for network analysis of the rat intra-midbrain axonal connections from one gray matter region to another. The data was expertly collated from the peer-reviewed neuroanatomical literature. The Connection Reports are listed in an Excel Worksheet and are self-explanatory.

A dataset for pollinator diversity and their interactions with plants in the Pacific NorthWest

Laura Melissa Guzman, Tyler Kelly & Elizabeth Elle
Pollinator populations have declined substantially in recent years. The resulting loss in pollination services has both ecological and economic consequences including reductions in plant diversity and crop production and lower food security. Datasets that identify pollinators and their plant hosts are of utmost importance in order to understand the main causes of pollinator declines. Here we present a dataset, which contains 67,954 individual pollinator records. The data has been collected across the Pacific Northwest, primarily...

A new genus of treeshrew and other micromammals from the middle Miocene hominoid locality of Ramnagar, Udhampur District, Jammu & Kashmir, India

Ramesh Sehgal, Abhishek Singh, Christopher Gilbert, Biren Patel, Christopher Campisano, Keegan Selig, Rajeev Patnaik & Ningthoujam Premjit Singh
The fossil record of treeshrews, hedgehogs, and other micromammals from the Lower Siwaliks of India is sparse. Here, we report on a new genus and species of fossil treeshrew, specimens of the hedgehog Galerix, and other micromammals from the middle Miocene (Lower Siwalik) deposits surrounding Ramnagar (Udhampur District, Jammu & Kashmir), at a fossil locality known as Dehari. The treeshrew from Dehari (Sivatupaia ramnagarensis gen. nov. et sp. nov.) currently represents the oldest record of...

Combining metabolomics and experimental evolution reveals key mechanisms underlying longevity differences in laboratory evolved Drosophila melanogaster populations

Mark Phillips, Kenneth R. Arnold, Zer Vue, Heather K. Beasley, Edgar Garza-Lopez, Andrea G. Marshall, Derrick J. Morton, Melanie R. McReynolds, Thomas T. Barter & Antentor Hinton
Experimental evolution with Drosophila melanogaster has been used extensively for decades to study aging and longevity. In recent years, the addition of DNA and RNA sequencing to this framework has allowed researchers to leverage the statistical power inherent to experimental evolution to study the genetic basis of longevity itself. Here, we incorporated metabolomic data into to this framework to generate even deeper insights into the physiological and genetic mechanisms underlying longevity differences in three groups...

Supplementary information for: A biased fossil record can preserve reliable phylogenetic signal

C. Henrik Woolley, Jeffrey Thompson, Yun-Hsin Wu, David Bottjer & Nathan Smith
Abstract.­­––The fossil record is notoriously imperfect and biased in representation, hindering our ability to place fossil specimens into an evolutionary context. For groups with fossil records mostly consisting of disarticulated parts (e.g., vertebrates, echinoderms, plants), the limited morphological information preserved sparks concerns about whether fossils retain reliable evidence of phylogenetic relationships, and lends uncertainty to analyses of diversification, paleobiogeography, and biostratigraphy in Earth history. To address whether a fragmentary past can be trusted, we need...

Additional file 1 of Gene Identification, expression analysis and molecular docking of ATP sulfurylase in the selenization pathway of Cardamine hupingshanensis

Zhijing Xiao, Yanke Lu, Yi Zou, Chi Zhang, Li Ding, Kai Luo, Qiaoyu Tang & Yifeng Zhou
Supplementary Figure S1: Multiple sequence alignment of all the ChATPS proteins; Supplementary Table S1: Physicochemical properties of ATPS proteins in C. hupingshanensis. Supplementary Table S2: The gene coding sequences and protein sequences of ChATPS. Supplementary Table S3: Secondary structure analysis of the nine proteins. Supplementary Table S4: Primers used in qRT-PCR analysis for ChATPS. Table S5: The binding energy of each ligand to each protein at the catalytic site (unit: kcal mol-1). Table S6: At...

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Affiliations

  • University of Southern California
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  • Chinese Academy of Sciences
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