40 Works

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...

The impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa

Dionne Argyropoulos, Shazia Ruybal‐Pesántez, Samantha L. Deed, Abraham R. Oduro, Samuel K. Dadzie, Maxwell A. Appawu, Victor Asoala, Mercedes Pascual, Kwadwo A. Koram, Karen P. Day, Maxwell A. Appawu, Kathryn E. Tiedje, Victor Asoala, Mercedes Pascual, Kwadwo A. Koram, Karen P. Day & Kathryn E. Tiedje
Here, we report the first population genetic study to examine the impact of indoor residual spraying (IRS) on Plasmodium falciparum in humans. This study was conducted in an area of high seasonal malaria transmission in Bongo District, Ghana. IRS was implemented during the dry season (November-May) in three consecutive years between 2013 and 2015 to reduce transmission and attempt to bottleneck the parasite population in humans towards lower diversity with greater linkage disequilibrium. The study...

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...

Microbial shotgun metagenomics from low microbial biomass human samples assisted by effective host depletion

Jacob T. Barlow, Natalie Wu-Woods, Dustin Shaw, Anna E. Romano, Bana Jabri & Rustem Ismagilov
Data and figures

The atomic-level physiochemical determinants of T cell receptor dissociation kinetics

Zachary Rollins, Roland Faller, Ilias Tagkopolous, Jun Huang & Steven George
The force-dependent bond lifetime of a T Cell Receptors (TCR) to 17 peptide-Major Histocompatibility Complexes (pMHCs) was simulated using Steered Molecular Dynamics. Physiochemical descriptors of the TCR-pMHC interaction during simulation were then filtered and selected to understand the best feature sets that predict bond lifetime. This methodology sets precedence on the rational design of TCRs via force-dependent bond lifetime enhancement.

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...

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...

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...

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,...

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...

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...

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...

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...

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...

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:...

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...

Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018

Yanqun Wang, Xin Li, Wenkuan Liu, Mian Gan, Lu Zhang, Jin Wang, Zhaoyong Zhang, Airu Zhu, Fang Li, Jing Sun, Guoxian Zhang, Zhen Zhuang, Jiaying Luo, Dehui Chen, Shuyan Qiu, Li Zhang, Duo Xu, Chris Ka Pun Mok, Fuchun Zhang, Jingxian Zhao, Rong Zhou & Jincun Zhao
Human coronavirus NL63 (HCoV-NL63) is primarily associated with common cold in children, elderly and immunocompromised individuals. Outbreaks caused by HCoV-NL63 are rare. Here we report a cluster of HCoV-NL63 cases with severe lower respiratory tract infection that arose in Guangzhou, China, in 2018. Twenty-three hospitalized children were confirmed to be HCoV-NL63 positive, and most of whom were hospitalized with severe pneumonia or acute bronchitis. Whole genomes of HCoV-NL63 were obtained using next-generation sequencing. Phylogenetic and...

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...

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...

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...

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...

Registration Year

  • 2021

Resource Types

  • Dataset


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