34 Works

Genome-wide identification and functional prediction of circular RNAs in response to heat stress in Chinese Holstein cows

Ying Qi, Lin Zhang, Yuemei Guo, Jing Wang, Mingxing Chu, Yiming Zhang, Junfei Guo & Qiuling Li
Heat stress (HS) leads to substantial economic loss of dairy industry each year. The negative effect of HS in dairy cows is becoming one of the more urgent issue due to accelerating side-effects of global warming. Various genes are involved in HS response but the information about the role of noncoding RNAs, especially circular RNAs (circRNAs) is largely unknown. In our study, we aimed to investigate the different expression profile of circRNAs between HS and...

Phylogenomic species delimitation in the ants of the Temnothorax salvini Group (Hymenoptera: Formicidae): An integrative approach

Matthew Prebus
The members of the Temnothorax salvini species group are rarely collected, arboreally nesting ants of Central American forests. Previously thought to consist of two broadly dispersed species, recent collections have revealed a diversity of specimens that defy the two-species salvini group concept, but these are difficult to distinguish from each other based solely on morphology. I contrast several model-based approaches to species delimitation based on target-enriched genomic data. With molecular data from thousands of ultraconserved...

Supporting Data for: Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae)

Norman Wickett, Lindsey Bechen, Geoffrey Broadhead, Rachel Levin, Rick Overson, Tania Jogesh, Jeremie Fant, Robert Raguso & Krissa Skogen
Background: Plant volatiles play an important role in both plant-pollinator and plant-herbivore interactions. Intraspecific polymorphisms in volatile production are ubiquitous, but studies that explore underlying differential gene expression are rare. Oenothera harringtonii populations are polymorphic in floral emission of the monoterpene (R)-(-)-linalool; some plants emit (R)-(-)-linalool (linalool+ plants) while others do not (linalool- plants). However, the genes associated with differential production of this floral volatile in Oenothera are unknown. We used RNA-Seq to broadly characterize...

A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers

Yuxi Gu, Shouyi Tang, Zhen Wang, Luyao Cai, Haosen Lian, Yingqiang Shen & Yu Zhou
Beta-actin (ACTB), a highly conserved cytoskeleton structural protein, has been regarded as a common housekeep gene and used as a reference gene for years. However, accumulating evidence indicates that ACTB is abnormally expressed in multiple cancers and hence changes the cytoskeleton to affect the invasiveness and metastasis of tumors. This study aimed to investigate the function and clinical significance of ACTB in pan-cancer. The role of ACTB for prognosis and immune regulation across 33 tumors...

Phylogenomic reconstruction reveals new insights into the evolution and biogeography of Atta leaf-cutting ants (Hymenoptera: Formicidae)

Corina Barrera, Jeffrey Sosa-Calvo, Ted Schultz, Christian Rabeling & Maurício Bacci
Atta Fabricius is an ecologically dominant leaf-cutting ant genus, the major herbivore of the Neotropics, and an agricultural pest of great economic importance. Phylogenetic relationships within Atta have until now remained uncertain, and the delimitation and identification of a subset of Atta species are problematic. To address these phylogenetic uncertainties, we reconstruct the most comprehensive phylogenetic estimate to date of Atta by employing ultraconserved elements (UCEs). We recovered 2340 UCE loci from 224 Atta specimens,...

Shrub influence on soil carbon and nitrogen in a semi-arid grassland is mediated by precipitation and largely insensitive to livestock grazing

Heather Throop, Seth Munson, Nicole Hornslein & Mitchel McClaran
Dryland (arid and semi-arid) ecosystems globally provide more than half of livestock production and store roughly one-third of soil organic carbon (SOC). Biogeochemical pools are changing due toshrub encroachment, livestock grazing, and climate change. We assessed how vegetation microsite, grazing, and precipitation interacted to affect SOC and total nitrogen (TN) at a site with long-term grazing manipulations and well-described patterns of shrub encroachment across elevation and mean annual precipitation (MAP) gradients. We analyzed SOC and...

The value of increased spatial resolution of pesticide usage data for assessing risk to endangered species: Data, notebooks, and results

Erin Murphy, Steffen Eikenberry, Gwen Iacona, Greg Watson & Leah Gerber
Decision makers often cite data quality as a limitation in environmental management. Value of information approaches evaluates the benefit of new data collection for management outcomes. Pesticide exposure risk assessment for endangered species is one context where data limitations may affect decisions and a value of information type approach could be useful for identifying optimal data quality and resolution. Under the U.S. Federal Insecticide, Fungicide and Rodenticide Act, the U.S. Environmental Protection Agency (EPA) is...

Biodiversity-productivity relationships in a natural grassland community vary under diversity loss scenarios

Qingmin Pan, Amy Symstad, Yongfei Bai, Jianhui Huang, Jianguo Wu, Shahid Naeem, Dima Chen, Dashuan Tian, Qibing Wang & Xingguo Han
Understanding the biodiversity-productivity relationship and underlying mechanisms in natural ecosystems under realistic diversity loss scenarios remains a major challenge for ecologists despite its importance for predicting impacts of rapid loss of biodiversity worldwide. Here we report the results of a plant functional group (PFG) removal experiment conducted on the Mongolian Plateau, the largest remaining natural grassland in the world. Our results demonstrated that the biodiversity-productivity relationship varied among positive linear, neutral, and unimodal forms under...

A global ecological signal of extinction risk in terrestrial vertebrates

Maya Munstermann, Noel Heim, Douglas McCauley, Jonathan Payne, Nathan Upham, Steve Wang & Matthew Knope
To determine the distribution and causes of extinction threat across functional groups of terrestrial vertebrates, we assembled a dataset on ecological traits for 18,016 species and tested, using phylogenetic comparative methods, which categories of habitat association, mode of locomotion, and feeding mode best predict extinction risk. We found that cave-dwelling amphibians, brachiating mammals (all of which are primates), aerial and scavenging birds, and pedal squamates are all disproportionately threatened with extinction. Across four vertebrate classes,...

A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers

Yuxi Gu, Shouyi Tang, Zhen Wang, Luyao Cai, Haosen Lian, Yingqiang Shen & Yu Zhou
Beta-actin (ACTB), a highly conserved cytoskeleton structural protein, has been regarded as a common housekeep gene and used as a reference gene for years. However, accumulating evidence indicates that ACTB is abnormally expressed in multiple cancers and hence changes the cytoskeleton to affect the invasiveness and metastasis of tumors. This study aimed to investigate the function and clinical significance of ACTB in pan-cancer. The role of ACTB for prognosis and immune regulation across 33 tumors...

Habitat structure mediates vulnerability to climate change through its effects on thermoregulatory behavior

Lauren Neel, Michael Logan, Daniel Nicholson, Christina Miller, Albert Chung, Inbar Maayan, Zach Degon, Madeline DuBois, John David Curlis, Q Taylor, Kaitlin Keegan, Owen McMillan, Jonathan Losos & Christian Cox
Tropical ectotherms are thought to be especially vulnerable to climate change because they are thermal specialists, having evolved in aseasonal thermal environments. However, even within the tropics, habitat structure can influence opportunities for behavioral thermoregulation. Open (and edge) habitats likely promote more effective thermoregulation due to the high spatial heterogeneity of the thermal landscape, while forests are thermally homogenous and may constrain opportunities for behavioral buffering of environmental temperatures. Nevertheless, the ways in which behavior...

Data from: Arthropod assemblages on small mammal carrion of the Kansas Flint Hills: an ecological approach

Emmy Engasser, Rachel Stone & Mary Liz Jameson
Arthropods are critical to the decomposition of carrion, but little is known about the biodiversity of arthropods attracted to carrion or environmental factors that shape communities. This research described carrion beetle (Coleoptera: Silphidae) and dung beetle (Coleoptera: Scarabaeidae: Scarabaeinae and Aphodiinae) community assemblages on rat carrion across a full annual cycle (twelve contiguous months, 2016-2017). Abiotic data (light availability, wind speed, soil surface humidity, soil surface temperature) complement the beetle biodiversity data. Together, these data...

Genome-wide identification and functional prediction of circular RNAs in response to heat stress in Chinese Holstein cows

Ying Qi, Lin Zhang, Yuemei Guo, Jing Wang, Mingxing Chu, Yiming Zhang, Junfei Guo & Qiuling Li
Heat stress (HS) leads to substantial economic loss of dairy industry each year. The negative effect of HS in dairy cows is becoming one of the more urgent issue due to accelerating side-effects of global warming. Various genes are involved in HS response but the information about the role of noncoding RNAs, especially circular RNAs (circRNAs) is largely unknown. In our study, we aimed to investigate the different expression profile of circRNAs between HS and...

Mammalian intestinal allometry, phylogeny, trophic level and climate

María Duque-Correa, Daryl Codron, Carlo Meloro, Amanda McGrosky, Christiann Schiffmann, Mark Edwards & Marcus Clauss
An often-stated ecomorphological assumption that has the status of ‘textbook knowledge’ is that the dimensions of the digestive tract correlate with diet, where herbivores – consuming diets of lower digestibility – have longer intestinal tracts than faunivores – consuming diets of higher digestibility. However, statistical approaches have so far failed to demonstrate this link. Here, we collated data on the length of intestinal sections and body mass of 519 mammal species, and test for various...

Data for: Human food use increases plant geographic ranges in the Sonoran Desert

Benjamin Blonder, Carolyn Flower, Wendy Hodgson, Andrew Salywon, Brian Maitner, Brian Enquist & Matthew Peeples
Aim. Climate is usually regarded as the main determinant of plant species’ distributions. However, past human use of species for food also may have influenced distributions. We hypothesized that human-mediated dispersal has resulted in food plants occupying more of their potential geographic range. We also hypothesized that key ecological traits could predispose a species to occupy more of its potential climatic geographic range and be selected by humans for food. Location. The Sonoran Desert of...

Cytotype and genotype predict mortality and recruitment in Colorado quaking aspen (Populus tremuloides)

Benjamin Blonder, Courtenay Ray, James Walton, Marco Castaneda, K. Dana Chadwick, Michael Clyne, Pierre Gaüzere, Lars Iversen, Madison Lusk, G. Richard Strimbeck, Savannah Troy & Karen Mock
Species responses to climate change depend on environment, genetics, and interactions among these factors. Intraspecific cytotype (ploidy level) variation is a common type of genetic variation in many species. However, the importance of intraspecific cytotype variation in determining demography across environments is poorly known. We studied the tree species quaking aspen (Populus tremuloides), which occurs in diploid and triploid cytotypes. This widespread species is experiencing contractions in its western range, which could potentially be linked...

Data from: Sexually dimorphic dorsal coloration in a jumping spider: testing a potential case of sex-specific mimicry

Collette Cook, Erin Powell, Kevin McGraw & Lisa Taylor
To avoid predation, many animals mimic behaviors and/or coloration of dangerous prey. Here we examine potential sex-specific mimicry in the jumping spider Habronattus pyrrithrix. Previous work proposed that males’ conspicuous dorsal coloration paired with characteristic leg-waving behavior (i.e., false antennation) may imperfectly mimic hymenopteran insects, affording protection to males during mate-searching and courtship. In contrast, less active females are cryptic and display less leg-waving. Here we test the hypothesis that sexually dimorphic dorsal color patterns...

Distinguishing between unreliability and dishonesty: a comparative study of aggressive communication in crayfish

Zackary Graham & Michael Angilletta
A major challenge in the study of animal communication is distinguishing whether signals convey honest or dishonest information. Biologists infer the honesty of a signal from its correlation with the information being signaled (e.g., fecundity or fighting ability) — the better the correlation, the more honest the signal. However, this view of signaling potentially conflates unreliable indicators with dishonest signals. Just because a trait conveys unreliable information does not mean that the structure serves as...

Social consequences of energetically costly nest construction in a facultatively social bee

Madeleine Ostwald, Trevor Fox, Jon Harrison & Jennifer Fewell
Social groups form when the costs of breeding independently exceed fitness costs imposed by group living. The costs of independent breeding can often be energetic, especially for animals performing expensive behaviors, such as nest construction. To test the hypothesis that nesting costs can drive sociality by disincentivizing independent nest founding, we measured the energetics of nest construction and inheritance in a facultatively social carpenter bee (Xylocopa sonorina Smith), which bores tunnel nests in wood. We...

The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes

Chaehee Lee, In-Su Choi, Domingos Cardoso, Haroldo De Lima, Luciano De Queiroz, Martin Wojciechowski, Robert Jansen & Tracey Ruhlman
The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused...

APOE4 is associated with elevated blood lipids and lower levels of innate immune biomarkers in a tropical Amerindian subsistence population

Angela Garcia
In post-industrial settings, APOE4 is associated with increased cardiovascular and neurological disease risk. However, the majority of human evolutionary history occurred in environments with higher pathogenic diversity and low cardiovascular risk. We hypothesize that in high-pathogen and energy-limited contexts, the APOE4 allele confers benefits by reducing innate inflammation when uninfected, while maintaining higher lipid levels that buffer costs of immune activation during infection. Among Tsimane forager-farmers of Bolivia (N=1266), APOE4 is associated with 30% lower...

Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients

Yong Xiong, Yuan Liu, Liu Cao, Dehe Wang, Ming Guo, Ao Jiang, Dong Guo, Wenjia Hu, Jiayi Yang, Zhidong Tang, Honglong Wu, Yongquan Lin, Meiyuan Zhang, Qi Zhang, Mang Shi, Yingle Liu, Yu Zhou, Ke Lan & Yu Chen
Circulating in China and 158 other countries and areas, the ongoing COVID-19 outbreak has caused devastating mortality and posed a great threat to public health. However, efforts to identify effectively supportive therapeutic drugs and treatments has been hampered by our limited understanding of host immune response for this fatal disease. To characterize the transcriptional signatures of host inflammatory response to SARS-CoV-2 (HCoV-19) infection, we carried out transcriptome sequencing of the RNAs isolated from the bronchoalveolar...

Critical angle reflection imaging for quantification of molecular interactions on glass surface

Guangzhong Ma & Shaopeng Wang
Quantification of molecular interactions on a surface is typically achieved via label-free techniques such as surface plasmon resonance (SPR). The sensitivity of SPR originates from the characteristic that the SPR angle is sensitive to the surface refractive index change. Analogously, in another interfacial optical phenomenon, total internal reflection, the critical angle is also refractive index dependent. Therefore, surface refractive index change can also be quantified by measuring the reflectivity near critical angle. Based on this...

Data from: Effects of food intake and hydration state on behavioral thermoregulation and locomotor activity in the tropidurid lizard Tropidurus catalanensis

Dylan J. Padilla Perez, Jose Eduardo De Carvalho & Carlos Navas
Theoretical models predict that lizards adjust their body temperature through behavioral thermoregulation as a function of food availability. However, behavioral thermoregulation is also governed by interactions among physiological and ecological factors other than food availability, such as hydration state, and sometimes it can even conflict with the locomotor activity of animals. Here, we aimed to investigate the role of food intake and hydration state on behavioral thermoregulation and voluntary locomotor activity in the lizard Tropidurus...

Data from: Urban links to molt schedule, body condition, and carotenoid-based coloration in the house finch (Haemorhous mexicanus)

Pierce Hutton, Jennifer McKenna & Kevin McGraw
Animals in urban environments are exposed to novel conditions, such as habitat and dietary alterations, and night-time light pollution, that can shift the timing and expression of life-history traits. Birds are popular urban-ecological study subjects, and in these feathered animals regular plumage molt is a critical process for maintenance of feather quality and their associated functions (e.g., thermoregulation, aerodynamics, and communicative coloration). We hypothesized that environmental changes associated with urbanization might affect the timing and...

Registration Year

  • 2021
    34

Resource Types

  • Dataset
    34

Affiliations

  • Arizona State University
    34
  • West China Hospital of Sichuan University
    6
  • Jilin University
    6
  • Sichuan University
    5
  • Chinese Academy of Sciences
    5
  • Shanghai University
    4
  • Xiamen University
    4
  • Hebei GEO University
    4
  • Shanghai Jiao Tong University
    4
  • Huazhong Agricultural University
    4