38 Works

A target enrichment probe set for resolving the flagellate land plant tree of life

Jesse W. Breinholt, Sarah B. Carey, George P. Tiley, E. Christine Davis, Lorena Endara, Stuart F. McDaniel, Leandro Neves, Emily B. Sessa, Matt Von Konrat, Susan Fawcett, Stefanie M. Ickert-Bond, Paulo H. Labiak, Juan Larraín, Marcus Lehnert, Lily R. Lewis, Nathalie S. Nagalingum, Nikisha Patel, Stefan A. Rensing, Weston Testo, Alejandra Vasco, Juan Carlos Villarreal, Evelyn Webb Williams, J. Gordon Burleigh, Sahut Chantanaorrapint, Leandro G. Neves … & Stefanie M. Ickert‐Bond
Premise of the Study: New sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. Methods and Results: We leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target...

Data from: Ultraconserved elements reconstruct the evolution of the Chagas disease-vectoring kissing bugs (Reduviidae: Triatominae)

Troy J. Kieran, Eric R. L. Gordon, Alejandro Zaldivar-Riveron, Carlos N. Ibarra-Cerdena, Travis C. Glenn & Christiane Weirauch
With about 150 species, Triatominae, the kissing bugs, are the largest radiation of hematophagous species within the Hemiptera. Kissing bugs are the sole vectors of the causative agent of Chagas disease, a tropical neglected disease that affects millions, mostly in Central and South America. Surprisingly, given the medical importance of this group, the evolutionary origin of Triatominae from predatory assassin bug ancestors is still under debate and phylogenetic relationships among and within the five tribes...

Microgeographic evolution of metabolic physiology in a salamander metapopulation

Sean Giery, Dana Drake & Mark Urban
The Metabolic Theory of Ecology explains ecological variation spanning taxonomic organization, space, and time based on universal physiological relationships. The theory depends on two core parameters: the normalization constant, a mass-independent measure of metabolic rate expected to be invariant among similar species, and the scaling coefficient, a measure of metabolic change with body mass commonly assumed to follow the universal ¾ scaling law. In this study, we explored evidence for evolved variation in these parameters...

Metabolism-related long non-coding RNAs (lncRNAs) as potential biomarkers for predicting risk of recurrence in breast cancer patients

Jian-ying Ma, Shao-hua Liu, Jie Chen & Qin Liu
Metabolism affects the development, progression, and prognosis of various cancers, including breast cancer (BC). Our aim was to develop a metabolism-related long non-coding RNA (lncRNA) signature to assess the prognosis of BC patients in order to optimize treatment. Metabolism-related genes between breast tumors and normal tissues were screened out, and Pearson correlation analysis was used to investigate metabolism-related lncRNAs. In total, five metabolism-related lncRNAs were enrolled to establish prognostic signatures. Kaplan-Meier plots and the receiver...

Identification of significant genes and therapeutic agents for breast cancer by integrated genomics

Xiao Sun, Zhenzhen Luo, Liuyun Gong, Xinyue Tan, Jie Chen, Xin Liang & Mengjiao Cai
Breast cancer is the most commonly diagnosed malignancy in women; thus, more cancer prevention research is urgently needed. The aim of this study was to predict potential therapeutic agents for breast cancer and determine their molecular mechanisms using integrated bioinformatics. Summary data from a large genome-wide association study of breast cancer was derived from the UK Biobank. The gene expression profile of breast cancer was from the Oncomine database. We performed a network-wide association study...

Geophyte ecophysiology and traits

Kerri Mocko & Cynthia Jones
Premise of the study: In semi-arid regions, decreasing rainfall presents a challenge to perennial seedlings that must reach sufficient size to survive the first year’s seasonal drought. Attaining a large storage organ size has been hypothesized to enhance drought resilience in geophytes, but building larger storage organs requires greater growth rates, and paradoxically, some traits conferring faster growth are highly sensitive to drought. We examine if tuber size confers greater drought resilience in seedlings of...

Juvenile survival of a burned forest specialist in response to variation in fire characteristics

Andrew Stillman, Teresa Lorenz, Philip Fischer, Rodney Siegel, Robert Wilkerson, Matthew Johnson & Morgan Tingley
1. Pyrodiversity, defined as variation in fire history and characteristics, has been shown to catalyze post-fire biodiversity in a variety of systems. However, the demographic and behavioral mechanisms driving the responses of individual species to pyrodiversity remain largely unexplored. 2. We used a model post-fire specialist, the black-backed woodpecker (Picoides arcticus), to examine the relationship between fire characteristics and juvenile survival while controlling for confounding factors. 3. We radio-tracked fledgling black-backed woodpeckers in burned forests...

Terrestrial green algae show higher tolerance to dehydration than do their aquatic sister-species: Raw data and analysis files

Elizaveta Terlova, Andreas Holzinger & Louise Lewis
Diverse algae possess the ability to recover from extreme desiccation without forming specialized resting structures. Green algal genera such as Tetradesmus (Sphaeropleales, Chlorophyceae) contain temperate terrestrial, desert, and aquatic species, providing an opportunity to compare physiological traits associated with the transition to land in closely related taxa. We subjected six species from distinct habitats to three dehydration treatments varying in relative humidity (RH 5%, 65%, 80%) followed by short- and long-term rehydration. We tested the...

The Phanerozoic aftermath of the Cambrian information revolution: sensory and cognitive complexity in marine faunas

Shannon Hsieh, Roy Plotnick & Andrew Bush
The Cambrian information revolution describes how biotically-driven increases in signals, sensory abilities, behavioral interactions, and landscape spatial complexity drove a rapid increase in animal cognition concurrent with the Cambrian radiation. Here, we compare cognitive complexity in Cambrian and post-Cambrian marine ecosystems, documenting changes in animal cognition after the initial Cambrian increase. In a comparison of Cambrian and post-Cambrian Lagerstätten, we find no strong trend in the proportion of genera possessing two types of macroscopic sense...

Out from under the wing: reconceptualizing the insect wing gene regulatory network as a versatile, general module for body-wall lobes in arthropods

Cera Fisher, Justin Kratovil, David Angelini & Elizabeth Jockusch
Body plan evolution often occurs through the differentiation of serially homologous body parts, particularly in the evolution of arthropod body plans. Recently, homeotic transformations resulting from experimental manipulation of gene expression have been interpreted as evidence that portions of dorsal and lateral arthropod body-wall are serially homologous to wings. These results, along with comparative data on the expression and function of genes in the wing regulatory network, provided a new perspective on an old question...

Both source and recipient range phylogenetic community structure can predict the outcome of avian introductions

Brian Maitner, Daniel Park, Brian Enquist & Katrina Dlugosch
Competing phylogenetic models have been proposed to explain the success of species introduced to other communities. Here, we present a study predicting the establishment success of birds introduced to Florida, Hawaii, and New Zealand using several alternative models, considering species’ phylogenetic relatedness to source and recipient range taxa, propagule pressure, and traits. We find consistent support for the predictive ability of source region phylogenetic structure. However, we find that the effects of recipient region phylogenetic...

Road salt inputs alter biogeochemistry but not plant community composition in exurban forested wetlands

Beth Lawrence & Samantha Walker
Forested wetlands of the temperate north are increasingly exposed to deicing salts, but it is unclear how this may alter wetland biogeochemistry and plant community composition. To investigate potential effects of deicing salts on exurban forested wetlands in southern New England, we employed a multi-site field study to describe spatiotemporal patterns of soil physiochemical, water quality, and vegetation characteristics with distance from road deicing salt source. We surveyed nine road-adjacent, red maple-dominated wetlands to quantify...

Limited plasticity in thermally tolerant ectotherm populations: evidence for a trade-off

Jordanna Barley, Brian S. Cheng, Matthew Sasaki, Sarah Gignoux-Wolfsohn, Cynthia G. Hays, Alysha B. Putnam, Seema Sheth, Andrew Villeneuve, Morgan Kelly, Jordanna M. Barley & Andrew R. Villeneuve
Many species face extinction risks owing to climate change, and there is an urgent need to identify which species' populations will be most vulnerable. Plasticity in heat tolerance, which includes acclimation or hardening, occurs when prior exposure to a warmer temperature changes an organism's upper thermal limit. The capacity for thermal acclimation could provide protection against warming, but prior work has found few generalizable patterns to explain variation in this trait. Here, we report the...

Conditional natal dispersal provides a mechanism for populations tracking resource pulses after fire

Andrew Stillman, Teresa Lorenz, Rodney Siegel, Robert Wilkerson, Matthew Johnson & Morgan Tingley
Animals that persist in spatially structured populations face the challenge of tracking the rise and fall of resources across space and time. To combat these challenges, theory predicts that species should use conditional dispersal strategies that allow them to emigrate from patches with declining resources and colonize new resource patches as they appear. We studied natal dispersal movements in the black-backed woodpecker (Picoides arcticus), a species known for its strong association with recent post-fire forests...

Metabolism-related long non-coding RNAs (lncRNAs) as potential biomarkers for predicting risk of recurrence in breast cancer patients

Jian-ying Ma, Shao-hua Liu, Jie Chen & Qin Liu
Metabolism affects the development, progression, and prognosis of various cancers, including breast cancer (BC). Our aim was to develop a metabolism-related long non-coding RNA (lncRNA) signature to assess the prognosis of BC patients in order to optimize treatment. Metabolism-related genes between breast tumors and normal tissues were screened out, and Pearson correlation analysis was used to investigate metabolism-related lncRNAs. In total, five metabolism-related lncRNAs were enrolled to establish prognostic signatures. Kaplan-Meier plots and the receiver...

Body size and environment influence both intraspecific and interspecific variation in daily torpor use across hummingbirds

Austin Spence & Morgan Tingley
1. Torpor, or a regulated drop in body temperature and metabolic rate, allows animals to inhabit energetically costly environments, but among torpor-using species, we have a poor understanding of how plasticity in torpor use relates to the experienced environment. 2. To better understand the ecology of daily torpor, we completed the largest study to date on the intraspecific variation of daily torpor use in hummingbirds by exposing 149 individuals of two hummingbird species to ambient...

Genetic data disagree with described subspecies ranges for Seaside Sparrows on the Atlantic coast

Mackenzie Roeder, Christopher Hill, Chris Elphick, Meaghan Conway, Alison Kocek, Amy Tegeler & Stefan Woltmann
Seaside Sparrows (Ammospiza maritima) are tidal salt marsh endemic passerines found along the Atlantic and Gulf coasts of North America. Currently there are 7 described subspecies and "MacGillivray's" Seaside Sparrow (A. m. macgillivraii) is the name given to the Atlantic coast subspecies breeding from North Carolina to northern Florida. In 2019 the US Fish and Wildlife Service received a petition to list this subspecies under the Endangered Species Act due to shrinking populations and loss...

Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Non-Parametric Bootstrap Support

Sean Gosselin, Matthew Fullmer, Yutien Feng & J Peter Gogarten
Whole genome comparisons based on Average Nucleotide Identities (ANI) and the Genome-to-genome distance calculator have risen to prominence in rapidly classifying prokaryotic taxa using whole genome sequences. Some implementations have even been proposed as a new standard in species classification and have become a common technique for papers describing newly sequenced genomes. However, attempts to apply whole genome divergence data to delineation of higher taxonomic units and to phylogenetic inference have had difficulty matching those...

Effects of salt marsh vegetation zonation on carbon and nitrogen cycling in Connecticut

Beth Lawrence, Ashley Helton, Chris Elphick, Aidan Barry & Sean Ooi
Coastal marshes fringing the Long Island Sound (Connecticut, USA) are dynamic ecosystems positioned at the interface between land and sea, and provide an array of essential ecosystem services to society associated with improved water quality, carbon sequestration, and disturbance regulation. However, these wetlands are increasingly altered by rising seas and invasive species, and have been affected by historical management such as tidal manipulation. We conducted a survey of 20 Connecticut salt marshes (10 tidally restored,...

High-resolution CONUS-wide downscaled rainfall estimates (HRCDRE)

Stergios Emmanouil, Andreas Langousis, Efthymios I. Nikolopoulos & Emmanouil N. Anagnostou
The spatiotemporal character of rainfall is particularly important for hydrologic modeling, as well as hydroclimatic risk estimation and impact assessment. Existing atmospheric reanalysis datasets offer extensive record lengths and global coverage, but usually their spatial resolution is coarse for distributed hydrologic simulations at small spatial scales. On the other hand, the temporal coverage of high-resolution radar-based rainfall estimates can be rather short for risk applications. To address these shortcomings, we simultaneously bias-correct and downscale a...

Microgeographic divergence of functional responses among salamanders under antagonistic selection from apex predators

Mark C. Urban, Nicole Friedenfelds & Jonathan Richardson
A predator's functional response determines predator–prey interactions by describing the relationship between the number of prey available and the number eaten. Its shape and parameters fundamentally govern the dynamic equilibrium of predator–prey interactions and their joint abundances. Yet, estimates of these key parameters generally assume stasis in space and time and ignore the potential for local adaptation to alter feeding responses and the stability of trophic dynamics. Here, we evaluate if functional responses diverge among...

Long-term trends in gastropod abundance and biodiversity: disentangling effects of press versus pulse disturbances

Michael Willig & Steven Presley
Aim: Climate-induced pulse (e.g., hurricanes) and press (e.g., global warming) disturbances represent threats to populations, communities, and the ecosystem services that they provide. We leveraged three decades of annual data on tropical gastropods to quantify the effects of major hurricanes, associated secondary succession, and global warming on abundance, biodiversity, and species composition. Location: Luquillo Mountains, Puerto Rico. Methods: Gastropod abundance, biodiversity, and composition were estimated annually for each of 27 years in a tropical montane...

What evolutionary processes maintain MHCIIβ diversity within and among populations of stickleback?

Foen Peng, Kimberly Ballare, S. Hollis Woodard, Stijn Haan & Daniel Bolnick
Major Histocompatibility Complex (MHC) genes encode for proteins that recognize foreign protein antigens to initiate T-cell mediated adaptive immune responses. They are often the most polymorphic genes in vertebrate genomes. How evolution maintains this diversity is still an unsettled issue. Three main hypotheses seek to explain the maintenance of MHC diversity by invoking pathogen-mediated selection: heterozygote advantage, frequency-dependent selection, and fluctuating selection across landscapes or through time. Here, we use a large-scale field parasite survey...

Negative relationship between thermal tolerance and plasticity in tolerance emerges during experimental evolution in a widespread marine invertebrate

Matthew Sasaki
Whether populations can adapt to predicted climate change conditions, and how rapidly, are critical questions for the management of natural systems. Experimental evolution has become an important tool to answer these questions. In order to provide useful, realistic insights into the adaptive response of populations to climate change, there needs to be careful consideration of how genetic differentiation and phenotypic plasticity interact to generate observed phenotypic changes. We exposed three populations of the widespread copepod...

Towards a stable global Noctuidae (Lepidoptera) taxonomy

Kevin Keegan, Jadranka Rota, Reza Zahiri, Alberto Zilli, Niklas Wahlberg, B. Christian Schmidt, J. Donald Lafontaine, Paul Goldstein & David Wagner
The family Noctuidae is one of the world’s most diverse, ecologically successful, and economically important animal lineages; with over 12,000 species in ~1150 genera. We inferred a phylogeny based on eight protein-coding genes (>6,400 base pairs) for the global fauna, greatly expanding upon previous attempts to stabilize the higher classification of Noctuidae by sampling 70 of the 76 widely recognized family-group taxa: 20 of the 21 subfamilies, 32 of the 35 tribes, and 18 of...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Connecticut
  • Sun Yat-sen University
  • West China Hospital of Sichuan University
  • Zhejiang University
  • Central South University
  • Zunyi Medical University
  • Wenzhou Medical University
  • Fudan University
  • Capital Medical University
  • Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University