121 Works

Large herbivores suppress liana infestation in an African savanna

Tyler C. Coverdale, Ryan D. O'Connell, Matthew C. Hutchinson, Amanda Savagian, Tyler R. Kartzinel, Todd M. Palmer, Jacob R. Goheen, David J. Augustine, Mahesh Sankaran, Corina E. Tarnita & Robert M. Pringle
African savannas are the last stronghold of diverse large-mammal communities, and a major focus of savanna ecology is to understand how these animals affect the relative abundance of trees and grasses. However, savannas support diverse plant life-forms, and human-induced changes in large-herbivore assemblages—declining wildlife populations and their displacement by livestock—may cause unexpected shifts in plant community composition. We investigated how herbivory affects the prevalence of lianas (woody vines) and their impact on trees in an...

Discordance in a South African Memecylon clade (Melastomataceae): Evidence for reticulate evolution

Prabha Amarasinghe, Phuc Pham, Robert Douglas Stone & Nico Cellinese
Premise of research. Evergreen forests in eastern South Africa have high biodiversity but are limited in extent and have a highly fragmented distribution. Populations of forest plants are thus geographically isolated, and fine-scale evolutionary studies of these lineages might yield important insights into the history and assembly of the forests themselves. Despite their morphological diversity, a prior study showed that three South African Memecylon taxa in Melastomataceae (M. natalense, M. bachmannii, and M. australissimum) had...

Arboreality drives heat tolerance while elevation drives cold tolerance in tropical rainforest ants

Lily Leahy, Brett Scheffers, Stephen Williams & Alan Andersen
Determining how species thermal limits correlate with climate is important for understanding biogeographic patterns and assessing vulnerability to climate change. Such analyses need to consider thermal gradients at multiple spatial scales. Here we relate thermal traits of rainforest ants to microclimate conditions from ground to canopy (microgeographic scale) along an elevation gradient (mesogeographic scale) and calculate warming tolerance in the Australian Wet Tropics Bioregion. We test the thermal adaptation and thermal niche asymmetry hypotheses to...

Bioinformatics-based identification of SPNS3 (Spinster homolog 3) as a prognostic biomarker of apoptosis resistance in acute myeloid leukemia

Yang Hong, Xiaopeng Tian, Mengmiao Wang, Cheng Chen & Aining Sun
Spinster homolog 3 (SPNS3) belongs to the Spinster (SPNS) family which participates in sphingolipid transportation through the cell membrane. However, the functions of SPNS3 in acute myeloid leukemia (AML) are unknown. This study obtained SPNS3 from a gene set that was related to AML relapse and evaluate whether high SPNS3 expression induced apoptosis resistance in an AML cell line, which is consistent with the role of SPNS3 as a marker of poor prognosis in the...

The probability of being infected with haemosporidian parasites increases with host age

Samuel Slowinski, Aidan Geissler, Nicole Gerlach, Britt Heidinger & Ellen Ketterson
In vertebrates, disease susceptibility often varies with age. Older individuals may be more susceptible than younger individuals due to senescent declines in immune function. Alternatively, disease susceptibility may decrease with age if older individuals are more likely to have had prior exposures to parasites and acquired adaptive immune responses that allowed them to resist future infections. Disease susceptibility can also vary with reproductive state, and reproductive hormones have been shown to increase infection susceptibility. Here...

Data from: Buxus and Tetracentron genomes

Andre Chanderbali
Ancient whole-genome duplications (WGDs) characterize many large clades of angiosperms, including angiosperms themselves. Prominently, the core eudicot clade accommodates 70% of all angiosperms and shares ancestral hexaploidy, termed gamma. Gamma arose via two WGDs that occurred early in eudicot history; however, the relative timing of these is unclear, largely due to the lack of high-quality genomes among early-diverging eudicots. We provide complete genomes for Buxus sinica (Buxales) and Tetracentron sinense (Trochodendrales), representing the lineages most...

Identification of a 3-gene signature based on differentially expressed invasion genes related to cancer molecular subtypes to predict the prognosis of osteosarcoma patients

Yue Wan, Ning Qu, Yang Yang, Jing Ma, Zhe Li & Zhenyu Zhang
Invasion is a critical pathway leading to tumor metastasis. This study constructed an invasion-related polygenic signature to predict osteosarcoma prognosis. We initially determined two molecular subtypes of osteosarcoma, Cluster1 (C1) and Cluster2 (C2).. A 3 invasive-gene signature was established by univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox regression analysis of the differentially expressed genes (DEGs) between the two subtypes, and was validated in internal and two external data sets (GSE21257...

Adaptations to light contribute to the ecological niches and evolution of the terrestrial avifauna

Ian Ausprey
The role of light in structuring the ecological niche remains a frontier in understanding how vertebrate communities assemble and respond to global change. For birds eyes represent the primary external anatomical structure specifically evolved to interpret light, yet eye morphology remains understudied compared to movement and dietary traits. Here, I use Stanley Ritland’s unpublished measurements of transverse eye diameter from preserved specimens to explore the ecological and phylogenetic drivers of eye morphology for a third...

Code for: Environmental fluctuations dampen the effects of clonal reproduction on evolutionary rescue

James Peniston, Michael Barfield, Robert Holt & Maria Orive
Evolutionary rescue occurs when genetic change allows a population to persist in response to an environmental change that would otherwise have led to extinction. Most studies of evolutionary rescue assume that species have either fully clonal or fully sexual reproduction; however, many species have partially clonal reproductive strategies in which they reproduce both clonally and sexually. Furthermore, the few evolutionary rescue studies that have evaluated partially clonal reproduction did not consider fluctuations in the environment,...

Data from: Temperature and vegetation complexity structure mixed-species flocks along a gradient of elevation in the tropical Andes

Flavia A. Montaño-Centellas & Harrison Jones
Mixed-species flocks constitute community modules that can help test mechanisms driving changes to community composition across environmental gradients. Here, we examined elevational patterns of flock diversity (species richness, taxonomic diversity, species and guild composition) and asked if these patterns were reflections of the full bird community at a given elevation (open-membership hypothesis), or if they were instead structured by environmental variables. We surveyed both the overall avian community and mixed-species flocks across an undisturbed elevational...

Supplementary: Global continental and marine detrital εNd: an updated compilation for use in understanding marine Nd cycling

Suzanne Robinson, Ruza Ivanovic, Tina van de Flierdt, Cecile Blanchet, Kazuyo Tachikawa, Ellen E. Martin, Carys Falko, Trevor Williams, Lauren Gregoire, Yves Plancherel, Catherine Jeandel & Thomas Arsouze
Understanding the role of sediment-water interactions in the oceanic cycling of neodymium (Nd) isotopes is essential for its reliable use as a modern and palaeoceanographic tracer of ocean circulation. However, the exact processes that control Nd cycling in the ocean are poorly defined and require an up-to-date knowledge of the sources, sinks and transformation of this tracer to and within the ocean (e.g. as per the GEOTRACES core mission). We propose a considerable improvement of...

Data from: Colour use by tiny predators: jumping spiders exhibit colour biases during foraging

Lisa Taylor, Emily Maier, Kevin Byrne, Zareen Amin & Nathan Morehouse
The evolution of many animal colours is thought to be driven by selection from visually guided predators. Yet research has largely focused on large vertebrate predators such as birds while ignoring smaller, terrestrial invertebrate predators. This is despite clear evidence that small invertebrate predators are important regulators of prey densities in a variety of ecosystems. Jumping spiders are small voracious predators that feed on a wide variety of prey in the field. They are capable...

A reassessment of the little-known Amazonian fern Diplazium praestans based on molecular and morphological evidence

Weston Testo, Lindsey Riibe, Michael Sundue & Emily Sessa
Family- and genus-level circumscription of ferns in the suborder Aspleniineae (eupolypods II) has long been controversial, due in part to confusion about the relationship among the families Aspleniaceae and Athyriaceae. Recent studies have demonstrated that character states traditionally used to infer a close relationship between these two families are either symplesiomorphic or homoplastic, and re-examination of numerous taxa has led to the recircumscription of several clades, and the description of several new families and genera....

Power for balanced linear mixed models with complex missing data processes

Kevin P. Josey, Brandy M. Ringham, Anna E. Barón, Margaret Schenkman, Katherine A. Sauder, Keith E. Muller, Dana Dabelea & Deborah H. Glueck
When designing repeated measures studies, both the amount and the pattern of missing outcome data can affect power. The chance that an observation is missing may vary across measurements, and missingness may be correlated across measurements. For example, in a physiotherapy study of patients with Parkinson’s disease, increasing intermittent dropout over time yielded missing measurements of physical function. In this example, we assume data are missing completely at random, since the chance that a data...

Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

Rongsui Gao, Wenhong Zu, Yang Liu, Junhua Li, Zeyao Li, Yanling Wen, Haiyan Wang, Jing Yuan, Lin Cheng, Shengyuan Zhang, Yu Zhang, Shuye Zhang, Weilong Liu, Xun Lan, Lei Liu, Feng Li & Zheng Zhang
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies’...

Contrasting patterns of phylogenetic diversity and alpine specialization across the alpine flora of the American mountain range system

Hector Fox Figueroa, Hannah E. Marx, Maria Beatriz De Souza Cortez, Charles J. Grady, Nicholas Engle-Wrye, Jim Beach, Aimee Stewart, Ryan A. Folk, Douglas E. Soltis, Pamela S. Soltis & Stephen A. Smith
Although mountainous habitats contribute substantially to global biodiversity, comparatively little is known about biogeographic patterns of distributions of alpine species across multiple mountain ranges. Here, we present a detailed analysis of the distributions and phylogenetic affinities of alpine seed plant lineages across North, Central, and South American mountain systems. Using a comprehensive dataset that characterized the elevational niches of American seed plants in a continuously valued way, we were able to quantitatively investigate how the...

Data from: Intraspecific correlations between growth and defense vary with resource availability and differ within- and among-populations

Philip Hahn, Ken Keefover-Ring, Linh Nguyen & John Maron
A paradigm in the plant defense literature is that defending against herbivores comes at a cost to growth, resulting in a growth-defense tradeoff. However, while there is strong evidence for growth-defense tradeoffs across species, evidence is mixed within species. Several mechanisms can account for this equivocal support within species, but teasing them apart requires examining growth-defense relationships both within and among populations, an approach seldom employed. We examined correlations between plant biomass (growth) and terpene...

Coordination of movement via complementary interactions of leaders and followers in termite mating pairs.

Nobuaki Mizumoto, Sang-Bin Lee, Gabriele Valentini, Thomas Chouvenc & Stephen Pratt
Leadership of animal group movements depends on social feedback, hence leader’s signals and follower’s responses should be attuned to each other. However, leader and follower roles are difficult to disentangle in species with high levels of coordination. To overcome this challenge, we investigated a simple case of movement coordination: termite pairs in which a female leads a male as they search for a nest site. To tease apart leader and follower roles, we created conspecific...

Evidence of a rapid and adaptive response of hemipteran mouthparts to a physical barrier

Pablo Allen, Quentin Cui & Christine Miller
Animals have encountered novel foods at points throughout history, due to factors such as range expansions and niche shifts driven by competition. One of the first challenges presented by novel foods is how to eat them. Mouthpart morphology is thus critical during the process of host shifts. Developmental plasticity in mouthparts is one potential mechanism that may allow animals to tolerate new foods and eventually to thrive upon them. Here, we investigated the extent to...

Fruit hardness, size, and weight for wild fruits in Uganda and Madagascar

Kim Valenta & Omer Nevo
Fleshy fruits have evolved to be attractive to frugivorous seed dispersers. As a result, many fruit traits like size, color, scent and nutritional content are assumed to be the result of selective pressures exerted by frugivores. At the same time, fruit traits are also subjected to a set of other selective pressures and constraints. One such trait is fruit hardness. On one hand, haptic cues have been suggested to play a role in frugivore behavior,...

Amborella pangenome and supplementary tables v4

, Ricky Hu, Armin Patrick Scheben, Brent Verpaalen, Soodeh Tirnaz, Jacqueline Batley, Douglas E. Soltis, Dave Edwards & Richard G.J. Hodel

Data for pith width, leaf size, and twig thickness of trees and shrubs

Kalindhi Larios Mendieta, Gordon Burleigh & Francis Putz
Premise of the study: As an extension of E. J. H. Corner’s Rule that twig diameter increases with leaf size, we hypothesized that pith width also increases with leaf size. The benefit to the plant from the proposed relationship is that pith is a low-cost tissue that reduces the metabolic cost of large diameter twig production. Methods: Leaf sizes and cross-sectional areas of bark, xylem, and pith of 81 species of trees and shrubs growing...

Therapeutic genome screen in AsPC1

Chris Vulpe
Pancreatic adenocarcinoma generally does not respond to our current therapeutic approaches of surgical resection, radiation and chemotherapy with an overall five-year survival of only 8%. In an effort to identify potential new therapeutic approaches for pancreatic cancer, we carried out a targeted synthetic lethal CRISPR screens in the pancreatic cell line AsPC1. A custom CRISPR knockout library, termed the Therapeutic Genome (RxG) Library, which targets genes for which a current drug already exists was utilized...

Disparities in pediatric patient portal adoption and feature use

Jennifer LeLaurin, Oliver Nguyen, Lindsay Thompson, Jaclyn Hall, Jiang Bian, Hee Deok Cho, Ratna Acharya, Christopher Harle & Ramzi Salloum
Objective: Disparities in adult patient portal adoption are well-documented; however, less is known about disparities in portal adoption in pediatrics. This study examines the prevalence and factors associated with patient portal activation and use of specific portal features in general pediatrics. Materials and Methods: We analyzed electronic health record (EHR) data from 2012-2020 in a large academic medical center that offers both parent and adolescent portals. We summarized portal activation and use of select portal...

Bioinformatics-based identification of SPNS3 (Spinster homolog 3) as a prognostic biomarker of apoptosis resistance in acute myeloid leukemia

Yang Hong, Xiaopeng Tian, Mengmiao Wang, Cheng Chen & Aining Sun
Spinster homolog 3 (SPNS3) belongs to the Spinster (SPNS) family which participates in sphingolipid transportation through the cell membrane. However, the functions of SPNS3 in acute myeloid leukemia (AML) are unknown. This study obtained SPNS3 from a gene set that was related to AML relapse and evaluate whether high SPNS3 expression induced apoptosis resistance in an AML cell line, which is consistent with the role of SPNS3 as a marker of poor prognosis in the...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Florida
  • Chinese Academy of Agricultural Sciences
  • Shanghai Jiao Tong University
  • West China Second University Hospital of Sichuan University
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Sichuan University
  • University of Electronic Science and Technology of China
  • West China Hospital of Sichuan University
  • Central South University
  • University of Hong Kong