44 Works

A new pipeline for removing paralogs in target enrichment data

Wenbin Zhou, John Soghigian &
Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper...

Data From: Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae)

Xuankun Li, Luisa C. Teasdale, Keith M. Bayless, Allan G. Ellis, Brian M. Wiegmann, Carlos José E. Lamas, Christine L. Lambkin, Neal L. Evenhuis, James A. Nicholls, Diana Hartley, Seunggwan Shin, Michelle Trautwein, Andreas Zwick, Bryan D. Lessard & David K. Yeates
Bombyliidae is a very species-rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present-day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the...

Detecting flying insects using car nets and DNA metabarcoding

Cecilie Svenningsen, Tobias Guldberg Frøslev, Jesper Bladt, Lene Bruhn Pedersen, Jonas Colling Larsen, Rasmus Ejrnæs, Camilla Fløjgaard, Anders Hansen, Jacob Heilmann-Clausen, Robert Dunn & Anders Tøttrup
Monitoring insects across space and time is challenging, due to their vast taxonomic and functional diversity. This study demonstrates how nets mounted on rooftops of cars (car nets) and DNA metabarcoding can be applied to sample flying insect richness and diversity across large spatial scales within a limited time period. During June 2018, 365 car net samples were collected by 151 volunteers during two daily time intervals on 218 routes in Denmark. Insect bulk samples...

Combining epidemiological and ecological methods to quantify social effects on E. coli transmission

Trevor Farthing, Daniel Dawson, Michael Sanderson, Hannah Seger & Cristina Lanzas
Enteric microparasites like Escherichia coli utilize multiple transmission pathways to propagate within and between host populations. Characterizing the relative transmission risk attributable to host social relationships, and direct physical contact between individuals is paramount for understanding how microparasites like E. coli spread within affected communities and estimating colonization rates. To measure these effects, we carried out commensal E. coli transmission experiments in two cattle (Bos taurus) herds, wherein all individuals were equipped with real-time location...

Uncertainty in health impact assessments of smoke from a wildfire event

Megan Johnson & Fernando Garcia-Menendez
Manuscript abstract: Wildfires cause elevated air pollution that can be detrimental to human health. However, health impact assessments associated with emissions from wildfire events are subject to uncertainty arising from different sources. Here, we quantify and compare major uncertainties in mortality and morbidity outcomes of exposure to fine particulate matter (PM2.5) pollution estimated for a series of wildfires in the Southeastern U.S. We present an approach to compare uncertainty in estimated health impacts specifically due...

Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur

Ryan Campbell, George Tiley, Jelmer Poelstra, Kelsie Hunnicutt, Peter Larsen, Hui-Jie Lee, Jeffrey Thorne, Mario Dos Reis & Anne Yoder
Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of de novo mutations have been directly characterized in relatively few lineages. Our study provides the first direct mutation rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprise nearly half of the primate clade. Using high-coverage...

Data from: Variation in predation regime drives sex-specific differences in mosquitofish foraging behaviour

Varpu Pärssinen, Kaj Hulthén, Christer Brönmark, Gustaf Ekelund Ugge, Raphael Gollnisch, Simon David Herzog, Nan Hu, Marcus Lee, Yongcui Sha, Martin Škerlep, Jerker Vinterstare, R. Brian Langerhans, P. Anders Nilsson, Caroline Björnerås, Lars-Anders Hansson, Emma Johansson, Karin Rengefors & Huan Zhang
Predation is a well-studied driver of ecological selection on prey traits, which frequently drives divergence in anti-predator performance across environments that vary in predation risk. However, predation also alters prey mortality regimes, where low predation risk often results in higher prey densities and consequently higher intensities of intraspecific resource competition. In addition, predation risk alters the foraging context, as acquiring food can be risky in the presence of predators. Thus, different predation regimes can drive...

PacBio IsoSeq reference transcriptomes for Pinus taeda L.

Edwin Lauer & Fikret Isik
Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f. sp. fusiforme, is the most damaging disease affecting economically important pine species in the southeast United States. In this report, we detail the genomic localization and sequence-level discovery of candidate race-nonspecific broad-spectrum fusiform rust resistance genes in Pinus taeda L. Two full-sib families, each with ~1000 progeny, were challenged with a complex inoculum consisting of over 150 pathogen isolates. High-density linkage mapping revealed three...

Knockdown resistance (kdr) genotypes and collection information for Aedes aegytpi from Iquitos, Peru (2000 - 2017)

Jennifer Baltzegar
This study describes the evolution of knockdown resistance (kdr) haplotypes in Aedes aegypti in response to pyrethroid insecticide use over the course of 18 years in Iquitos, Peru. Based on the duration and intensiveness of sampling (~10,000 samples), this is the most thorough study of kdr population genetics in Ae. aegypti to date within a city. We provide evidence for the direct connection between programmatic citywide pyrethroid spraying and the increase in frequency of specific...

Natural and anthropogenic sources of habitat variation influence exploration behaviour, stress response, and brain morphology in a coastal fish

R. Brian Langerhans, Matthew Jenkins, John Cummings, Alex Cabe, Kaj Hulthén & M. Nils Peterson
1. Evolutionary ecology aims to better understand how ecologically important traits respond to environmental heterogeneity. Environments vary both naturally and as a result of human activities, and investigations that simultaneously consider how natural and human-induced environmental variation affect diverse trait types grow increasingly important as human activities drive species endangerment. 2. Here, we examine how habitat fragmentation and structural habitat complexity, affect disparate trait types in Bahamas mosquitofish (Gambusia hubbsi) inhabiting tidal creeks. We tested...

Supplemental information for: An early burst in brachiopod evolution corresponding with significant climatic shifts during the great Ordovician biodiversification event

Curtis Congreve, Mark Patzkowsky & Peter Wagner
We employ modified tip-dating methods to date divergence times within the Strophomenoidea, one of the most abundant and species-rich brachiopod clades to radiate during the Great Ordovician Biodiversification Event (GOBE), to determine if significant environmental changes at this time correlate with the diversification of the clade. Models using origination, extinction and sampling rates to estimate prior probabilities of divergence times strongly support both high rates of anatomical change per million-years and rapid divergences shortly before...

Data from: Long-term trends in the occupancy of ants revealed through use of multi-sourced datasets

Julie Sheard, Carsten Rahbek, Robert Dunn, Nathan Sanders & Nick Isaac
We combined participatory science data and museum records to understand long-term changes in occupancy for 29 ant species in Denmark over 119 years. Bayesian occupancy modelling indicated change in occupancy for 15 species: five increased, four declined and six showed fluctuating trends. We consider how trends may have been influenced by life-history and habitat changes. Our results build on an emerging picture that biodiversity change in insects is more complex than implied by the simple...

Frankliniella fusca activity patterns in wheat

Anders Huseth, James Goethe, Seth Dorman, George Kennedy & Hehe Wang
Tobacco thrips (Frankliniella fusca Hinds) are an important seedling pest of many agricultural crops including, but not limited to cotton, tomato, and tobacco. This insect is mobile and completes several generations on both crop and non-crop plants each growing season in the southern United States. We do know that this insect disperses through a predictable sequence of these habitats each spring, however, it is not well known how abundant early season host crops affect population...

NDVI time series - early warning signals

Melinda Martinez, Marcelo Ardon & Joshua Gray
Many freshwater forested wetlands along the southeastern U.S. coastline are rapidly transitioning from forest to marsh or open water, due to climate change related disturbances, such as saltwater intrusion and increasing flooding frequency. These changes in wetland state are considered a regime shift, and the timing and trajectory of change are not well understood. Recent studies have found early warning signals (EWS) of regime shifts in other ecosystems, but it is unclear if these can...

Measuring phylogenetic information of incomplete sequence data

Tae-Kun Seo, Olivier Gascuel & Jeffrey Thorne
Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of columns in the sequence alignment and will be decreased when the alignment contains gaps due to insertion or deletion events. Motivated by the measurement of information loss, we suggest assessment of the Effective Sequence Length (ESL) of an aligned data...

Wild bumble bee colony abundance, scaled by field size, predicts pollination services

Shelby Fleischer, James Strange, Margarita Lopez-Uribe & Carley McGrady
Although bee visitation rate to flowers is often used to assess both pollination services and bee abundance, the abundance of social species needs to be assessed by quantifying the number of colonies instead of the number of foraging individuals. Because accurately quantifying the number of wild bee colonies can be difficult, the relationship of visitation rates provided by foragers and the abundance of colonies contributing those foragers from the surrounding landscape is poorly documented for...

Cooperative communication with humans evolved to emerge early in domestic dogs

Hannah Salomons, Kyle C.M. Smith, Megan Callahan-Beckel, Margaret Callahan, Kerinne Levy, Brenda S. Kennedy, Emily E. Bray, Gitanjali E. Gnanadesikan, Daniel J. Horschler, Margaret Gruen, Jingzhi Tan, Philip White, Bridgett M. VonHoldt, Evan L. MacLean & Brian Hare
While we know that dogs evolved from wolves, it remains unclear how domestication affected dog cognition. One hypothesis suggests dog domestication altered social maturation by a process of selecting for an attraction to humans. Under this account, dogs became more flexible in using inherited skills to cooperatively-communicate with a new social partner that was previously feared and expressed these unusual social skills early in development. Here we tested dog (N=44) and wolf (N=37) puppies, 5-18...

Data from: Estimating encounter location distributions from animal tracking data

Michael Noonan, Ricardo Martinez-Garcia, Grace H. Davis, Margaret C. Crofoot, Roland Kays, Ben T. Hirsch, Damien Caillaud, Eric Payne, Andrew Sih, David L. Sinn, Orr Spiegel, William F. Fagan, Christen H. Fleming & Justin M. Calabrese
1. Ecologists have long been interested in linking individual behavior with higher-level processes. For motile species, this 'upscaling' is governed by how well any given movement strategy maximizes encounters with positive factors, and minimizes encounters with negative factors. Despite the importance of encounter events for a broad range of ecological processes, encounter theory has not kept pace with developments in animal tracking or movement modeling. Furthermore, existing work has focused primarily on the relationship between...

A novel body plan alters diversification of body shape and genitalia in live-bearing fish

R. Brian Langerhans & Eduardo Rosa-Molinar
Major evolutionary innovations can greatly influence subsequent evolution. While many major transitions occurred in the deep past, male live-bearing fishes (family Poeciliidae) more recently evolved a novel body plan. This group possesses a three-region axial skeleton, with one region—the ano-urogenital region—representing a unique body region accommodating male genitalic structures (gonopodial complex). Here we evaluate several hypotheses for the evolution of diversity in this region and examine its role in the evolution of male body shape....

Low-level updraft intensification in response to environmental wind profiles

Nicholas A. Goldacker & Matthew D. Parker
Supercell storms can develop a “dynamical response” whereby upward accelerations in the lower troposphere amplify as a result of rotationally induced pressure falls aloft. These upward accelerations likely modulate a supercell’s ability to stretch near-surface vertical vorticity to achieve tornadogenesis. This study quantifies such a dynamical response as a function of environmental wind profiles commonly found near supercells. Self-organizing maps (SOMs) were used to identify recurring low-level wind profile patterns from 20,194 model-analyzed, near-supercell soundings....

Facilitation by isolated trees triggers woody encroachment and a biome shift at the savanna-forest transition

Rodolfo Abreu, Giselda Durigan, Antônio Carlos Melo, Natashi Pilon & William Hoffmann
1. Woody encroachment into grassy biomes is a global phenomenon, often resulting in a nearly complete turnover of species, with savanna specialists being replaced by forest-adapted species. Understanding the mechanisms involved in this change is important for devising strategies for managing savannas. 2. We examined how isolated trees favor woody encroachment and species turnover by overcoming dispersal limitation and environmental filtering. In a savanna released from fire in southeastern Brazil (Cerrado) we sampled woody plants...

Variant discovery in full-sibling families of Pinus taeda L

Eddie Lauer
Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f. sp. fusiforme, is the most damaging disease affecting economically important pine species in the southeast United States. In this report, we detail the genomic localization and sequence-level discovery of candidate race-nonspecific broad-spectrum fusiform rust resistance genes in Pinus taeda L. Two full-sib families, each with ~1000 progeny, were challenged with a complex inoculum consisting of over 150 pathogen isolates. High-density linkage mapping revealed three...

Prevalence of Ranavirus, Batrachochytrium dendrobatidis, B. salamandrivorans, and Ophidiomyces ophiodiicola in Amphibians and Reptiles of North Carolina, USA

Thomas Lentz, Stephanie Thi, Andrew Duncan, Adam Miranda, Jeffrey Beane, Daniel Dombrowski, Brenna Forester, Christopher Akcali, Nathan Shepard, , Alvin Braswell, Lori Williams, Charles Lawson, Christopher Jenkins, Joseph Pechmann, Jacqueline Blake, Melissa Hooper, Keenan Freitas, Ann Somers & Bryan Stuart
The viral pathogen Ranavirus (Rv) and the fungal pathogens Batrachochytrium dendrobatidis (Bd), B. salamandrivorans (Bsal), and Ophidiomyces ophiodiicola (Oo) infect amphibians and reptiles. In recent years, there has been increased interest in reporting the occurrences of these pathogens. North Carolina, USA has a rich diversity of amphibians and reptiles, and is notably the most species-rich U.S. state in salamanders. We assessed prevalence of Rv, Bd, Bsal, and Oo in a broad taxonomic and geographic representation...

Data from: Salivary digestion extends the range of sugar-aversions in the German cockroach

Ayako Wada-Katsumata
Saliva has diverse functions in feeding behavior of animals. However, the impact of salivary digestion of food on insect gustatory information processing is poorly documented. Glucose-aversion (GA) in the German cockroach, Blattella germanica, is a highly adaptive heritable behavioral resistance trait that protects the cockroach from ingesting glucose-containing-insecticide-baits. In this study, we confirmed that GA cockroaches rejected glucose, but they accepted oligosaccharides. However, whereas wild-type cockroaches that accepted glucose also satiated on oligosaccharides, GA cockroaches...

Avian Response to Hurricane Maria in Coffee Plantations

Jaime Collazo, Amarilys Irizarry, Ivette Perfecto & John Vandermeer
Insights on impacts and resiliency of avian species with respect to hurricanes in the Caribbean have largely focused on responses measured in protected habitats. We assessed avian responses in non-protected habitat, specifically shade-restored coffee plantations, because their structural complexity retains many attributes of secondary forests, and may contribute to landscape scale species resiliency. We tallied species richness and estimated occupancy probability of 12 resident avian species, after adjusting for imperfect detection, to assess the impact...

Registration Year

  • 2021
    44

Resource Types

  • Dataset
    44

Affiliations

  • North Carolina State University
    44
  • Lund University
    4
  • Duke University
    3
  • Pennsylvania State University
    3
  • University of Michigan-Ann Arbor
    2
  • Universidade Federal Rural do Rio de Janeiro
    2
  • University of North Carolina
    2
  • University of North Carolina at Chapel Hill
    2
  • University of Minnesota
    2
  • University of Copenhagen
    2