326 Works

Data from: Screening sticky cards as a simple method for improving efficiency of Diaphorina citri (Hemiptera: Liviidae) monitoring and reducing non-target organisms

Mamoudou Sétamou, Robert R. Saldaña, James M. Hearn, Jon Dale, Teresa Patricia Feria Arroyo & Darek Czokajlo
Management of Diaphorina citri Kuwayama (Hemiptera: Liviidae) populations is one of the major strategies for reducing the spread and incidence of huanglongbing (HLB). HLB is putatively caused by Candidatus Liberibacter spp. (Rhizobiales: Phyllopbacteriaceae) that are transmitted to citrus by psyllid vectors. Diaphorina citri population monitoring is done to detect its presence and inform on management decisions. Various methods are used for detecting and estimating D. citri densities but trapping with yellow or lime-green sticky cards...

Data from: Phylogeography, population genetics, and distribution modeling reveal vulnerability of Scirpus longii (Cyperaceae) and the Atlantic Coastal Plain Flora to climate change.

Daniel Spalink, Ron MacKay & Kenneth J. Sytsma
A proactive approach to conservation must be predictive, anticipating how habitats will change and which species are likely to decline or prosper. We use composite species distribution modeling to identify suitable habitats for 18 members of the North American Atlantic Coastal Plain Flora (ACPF) since the Last Glacial Maximum and project these into the future. We then use Scirpus longii (Cyperaceae), a globally imperiled ACPF sedge with many of the characteristics of extinction vulnerability, as...

Data from: Meiotic drive shapes rates of karyotype evolution in mammals

Heath Blackmon, Joshua Justison, Itay Mayrose & Emma E. Goldberg
Chromosome number is perhaps the most basic characteristic of a genome, yet generalizations that can explain the evolution of this trait across large clades have remained elusive. Using karyotype data from over 1,000 mammals, we developed and applied a phylogenetic model of chromosome evolution that links chromosome number changes with karyotype morphology. Using our model, we infer that rates of chromosome number evolution are significantly lower in species with karyotypes that consist of either all...

Data from: Threshold elemental ratios and the temperature dependence of herbivory in fishes

Eric K. Moody, Nathan K. Lujan, Katherine A. Roach & Kirk O. Winemiller
1. Herbivorous ectothermic vertebrates are more diverse and abundant at lower latitudes. While thermal constraints may drive this pattern, its underlying cause remains unclear. We hypothesized that this constraint stems from an inability to meet the elevated phosphorus demands of bony vertebrates feeding on P-poor plant material at cooler temperatures because low gross growth efficiency at warmer temperatures facilitates higher P ingestion rates. We predicted that dietary carbon:phosphorus (C:P) should exceed the threshold elemental ratio...

Data from: Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, , Emily Jane McTavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams & Karen Ann Cranston
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly...

Data from: Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle

Matthew D. Littlejohn, Kristen M. Henty, Tiplady Kathryn, Thomas Johnson, Chad Harland, Thomas Lopdell, Richard G. Sherlock, Wanbo Li, Steven D. Lukefahr, Bruce C. Shanks, Dorian J. Garrick, Russel G. Snell, Richard J. Spelman & Stephen R. Davis
WGS Variants from 556 NZ Dairy Animals Chr23:30627379-40627379rtg_3.3.1_556_animal_Chr23:30627379-40627379_for_dryad.vcf.gzExome Variants in Multiple Breeds Chr20:34783594-42331973GATK-10MB-Window-Exomes.vcf.gzHairy syndrome genotypes and phenotypesGenotypes and phenotype used for genome-wide analysis of the hairy syndrome, Plink binary format (.bim .bed .fam)gen_phen_data_for_paper.zipHairy bull progeny TaqMan resultsHairy_bull_progeny_TaqMan_results.txtphysiological phenotypesphysiological_phenos.zipDFAM association results for 628,279 SNPDFAM_assoc_results.zipPhased genotypes and phenotypes for 82 Senepol crossbreedsphased_gen_phen_data_slick.zip

Data from: Range-wide snow leopard phylogeography supports three subspecies

Jan E. Janecka, Yu-Quang Zhang, Di-Qiang Li, Munkhtsog Bariushaa, Bayaraa Munkhtsog, Galsandorj Naranbaatar, Wangchuk R. Tshewang, Karmacharya Dibesh, McCarthy Thomas, Li Juan, Zhi Lu, Zhumabai Uulu Kubanychbek, Gaur Ajay, Kumar Satish, B. Kumar Kesav, Hussain Shafqat, Muhammad Ghulam, Jevit Matthew, Hacker Charlotte, Burger Pamela, Wultsch Claudia, Janecka J. Mary, Helgen Kristofer, Murphy J. William & Jackson Rodney
The snow leopard, Panthera uncia, is an elusive high-altitude specialist that inhabits vast, inaccessible habitat across Asia. We conducted the first range-wide genetic assessment of snow leopards based on noninvasive scat surveys. Thirty-three microsatellites were genotyped and a total of 683-bp of mitochondrial DNA sequenced in 70 individuals. Snow leopards exhibited low genetic diversity at microsatellites (AN = 5.8, HO = 0.433, HE = 0.568), virtually no mtDNA variation, and underwent a bottleneck in the...

Data from: Pollination biology and reproductive phenology of the federally endangered endemic Physaria globosa (Brassicaceae) in Tennessee

James H. Thacker, Shawn E. Krosnick, Silas C. Maynord, Geoff P. Call & Joshua S. Perkin
A study on the reproductive biology of the federally endangered Physaria globosa was conducted near Hartsville, TN, at one of the largest known populations of the species from February through July 2016. Objectives included (a) establishment of baseline reproductive phenology for P. globosa, (b) documentation of the diversity and frequency of floral visitors, and (c) determination of effective insect pollen vectors. Flowers were open for three days and displayed characteristics typical of outcrossing. Six insect...

Data from: Mate quality and the temporal dynamics of breeding in a sex-role-reversed pipefish, S. typhle

Sarah P. Flanagan, Gunilla Rosenqvist & Adam G. Jones
The spatiotemporal dynamics of receptivity and breeding date, coupled with individual-level quality and attractiveness, are centrally important to mating system dynamics. These topics have been investigated in some detail in birds, but much less work has been devoted to other taxonomic groups, and almost no work has addressed spatiotemporal factors and individual quality in sex-role-reversed taxa. The broad-nosed pipefish, Syngnathus typhle, provides an excellent opportunity to investigate these ideas in a sex-role-reversed fish. Here, we...

Data from: Genetic variation in the Yolk protein expression network of Drosophila melanogaster: sex-biased negative correlations with longevity

Aaron M. Tarone, Lauren M. Mcintyre, Lawrence G. Harshman & Sergey V. Nuzhdin
One of the persistent problems in biology is understanding how genetic variation contributes to phenotypic variation. Associations at many levels have been reported, and yet causal inference has remained elusive. We propose to rely on the knowledge of causal relationships established by molecular biology approaches. The existing molecular knowledge forms a firm backbone upon which hypotheses connecting genetic variation, transcriptional variation and phenotypic variation can be built. The sex determination pathway is a well-established molecular...

Data from: Day/night upper thermal limits differ within Ectatomma ruidum ant colonies

Annika S. Nelson, Trey Scott, Maciej Barczyk, Terrence P. McGlynn, Arian Avalos, Elizabeth Clifton, Amlan Das, Andreia Figueiredo, Laura L. Figueroa, Mark Janowiecki, Sarah Pahlke, Jignasha D. Rana & Sean O'Donnell
In the tropics, daily temperature fluctuations can pose physiological challenges for ectothermic organisms, and upper thermal limits may affect foraging activity over the course of the day. Variation in upper thermal limits can occur among and within species, and for social insects such as ants, within colonies. Within colonies, upper thermal limits may differ among individuals or change for an individual throughout the day. Daytime foragers of the Neotropical ant Ectatomma ruidum have higher critical...

Data from: No evidence for size-assortative mating in the wild despite mutual mate choice in sex-role-reversed pipefishes

Kenyon B. Mobley, Maria Abou Chakra & Adam G. Jones
Size-assortative mating is a nonrandom association of body size between members of mating pairs and is expected to be common in species with mutual preferences for body size. In this study, we investigated whether there is direct evidence for size-assortative mating in two species of pipefishes, Syngnathus floridae and S. typhle, that share the characteristics of male pregnancy, sex-role reversal, and a polygynandrous mating system. We take advantage of microsatellite-based “genetic-capture” techniques to match wild-caught...

Data from: Multiple mating and reproductive skew in parental and introgressed females of the live-bearing fish Xiphophorus birchmanni

Kimberly A. Paczolt, Courtney N. Passow, Pablo J. Delclos, Holly K. Kindsvater, Adam G. Jones & Gil G. Rosenthal
Just as mating patterns can promote speciation or hybridization, the presence of hybridization can shape mating patterns within a population. In this study, we characterized patterns of multiple mating and reproductive skew in a naturally hybridizing swordtail fish species, Xiphophorus birchmanni. We quantified multiple mating using microsatellite markers to genotype embryos from 43 females collected from 2 wild populations. We also used a suite of single-nucleotide polymorphism markers to categorize females and their inferred mates...

Data from: Spatial averaging and disturbance lead to high productivity in aquatic metacommunities

Evangelia Smeti, Daniel L. Roelke & Sofie Spatharis
Dispersal in heterogeneous ecosystems, such as coastal metacommunities, is a major driver of diversity and productivity. According to theory, both species richness and spatial averaging shape a unimodal relationship of productivity with dispersal. We experimentally tested the hypothesis that disturbances acting on local patches would buffer the loss of productivity at high dispersal by preventing synchronized species oscillations. To simulate these disturbances, our experimental assemblages involved species that self-organized in isolation under three inflow pulsing...

Data from: Sensory trait variation contributes to biased dispersal of threespine stickleback in flowing water

Yuexin Jiang, Catherine L. Peichel, Fei Ling, Daniel I. Bolnick, Z. Rizvi, S. Thompson, V. V. Palivela & L. Torrance
Gene flow is widely thought to homogenize spatially separate populations, eroding effects of divergent selection. The resulting theory of ‘migration-selection balance’ is predicated on a common assumption that all genotypes are equally prone to dispersal. If instead certain genotypes are disproportionately likely to disperse, then migration can actually promote population divergence. For example, previous work has shown that threespine stickleback (Gasterosteus aculeatus) differ in their propensity to move up- or down-stream (‘rheotactic response’), which may...

Data from: Multi-scale effects of habitat structure and landscape context on a vertebrate with limited dispersal ability (the brown-throated sloth, Bradypus variegatus)​

Kelsey D. Neam, & Thomas E. Lacher
As human population, food consumption, and demand for forest products continue to rise over the next century, the pressures of land use change on biodiversity are projected to intensify. In tropical regions, countryside habitats that retain abundant tree cover and structurally complex canopies may complement protected areas by providing suitable habitats and landscape connectivity for a significant portion of the native biota. Species with low dispersal capabilities are among the most at risk of extinction...

Data from: Community functional trait composition at the continental scale: the effects of non-ecological processes

A. Michelle Lawing, Jussi T. Eronen, Jessica L. Blois, Catherine H. Graham & P. David Polly
Ecological communities and their response to environmental gradients are increasingly being described by measures of trait composition at the community level – the trait-based approach. Whether ecological or non-ecological processes influence trait composition between communities has been debated. Understanding the processes that influence trait composition is important for reconstructing paleoenvironmental conditions from fossil deposits and for understanding changes in community functionality through time. Here, we assess the influence of ecological and non-ecological processes on the...

Data from: Interpreting and predicting the spread of invasive wild pigs

Nathan P. Snow, Marta A. Jarzyna & Kurt C. VerCauteren
The eruption of invasive wild pigs (IWPs) Sus scrofa throughout the world exemplifies the need to understand the influences of exotic and non-native species expansions. In particular, the continental USA is precariously threatened by a rapid expansion of IWPs, and a better understanding of the rate and process of spread can inform strategies that will limit the expansion. We developed a spatially and temporally dynamic model to examine three decades (1982–2012) of IWP expansion, and...

Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods

Kimberly Ballare, Nathaniel Pope, Antonio Castilla, Sarah Cusser, Richard Metz & Shalene Jha
DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non-model organisms for basic and applied questions. Despite these opportunities, many next-generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field-collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we...

Data from: Can ancestry and morphology be used as surrogates for species niche relationships?

Friedrich Keppeler & Kirk Winemiller
Species interactions are difficult to quantify, and, consequently, many studies have used species traits and phylogeny as proxies under an assumption of niche conservatism (i.e., closely related and morphologically similar species should have similar niches). However, few studies have investigated whether niches actually are conserved within and across diverse communities. Here, we tested the degree to which phylogenetic relatedness and morphological similarity predict diets and stable isotopic ratios (δ15N and δ13C), two common descriptors of...

Data from: The upper thermal tolerance for a Texas population of the hairy maggot blow fly Chrysomya rufifacies Macquart (Diptera: Calliphoridae)

Travis Rusch, Ashleigh Faris, Lauren Beebe, Jeffery Tomberlin & Aaron Tarone
The hairy maggot blow fly (Chrysomya rufifacies: Macquart) is an invasive necrophagous fly found throughout the continental United States. Chrysomya rufifacies is of medical/veterinary, forensic, and ecological importance due to its ability to cause myiasis, colonize human remains, and displace native Diptera. However, little is known about their upper thermal tolerance, which could be used to better predict their invasion potential. We investigated the upper thermal tolerance of C. rufifacies exposed to different temperatures (20...

Under the radar: genetic assessment of Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), two Rio Grande basin endemic cyprinids that have experienced recent range contractions

Megan Osborne, David Portnoy, Andrew Fields, Kevin Conway, Megan Bean & Christopher Hoagstrom
The Rio Grande drainage of the southwestern United States and Mexico has undergone intense anthropogenic alteration by water diversions, extraction and associated habitat changes. These alterations have disproportionately impacted the pelagic broadcast spawning guild of minnows (pelagophils). Several Rio Grande endemic pelagophils, including the co-occurring Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), have experienced dramatic recent range-wide declines yet have slipped under the radar of conservation efforts. The status of N. jemezanus...

SARS-CoV-2 transmission and control in a hospital setting: an individual-based modelling study

Qimin Huang, Anirban Mondal, Xiaobing Jiang, Mary Ann Horn, Fei Fan, Peng Fu, Xuan Wang, Hongyang Zhao, Martial Ndeffo Mbah & David Gurarie
Background: Development of strategies for mitigating the severity of COVID-19 is now a top public health priority. We sought to assess strategies for mitigating the COVID-19 outbreak in a hospital setting via the use of non-pharmaceutical interventions. Methods: We developed an individual-based model for COVID-19 transmission in a hospital setting. We calibrated the model using data of a COVID-19 outbreak in a hospital unit in Wuhan. The calibrated model was used to simulate different intervention...

Data from: Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing

A. Millie Burrell, Alan E. Pepper, George Hodnett, John A. Goolsby, William A. Overholt, Alexis E. Racelis, Rodrigo Diaz & Patricia E. Klein
Imperata cylindrica (Cogongrass, Speargrass) is a diploid C4 grass that is a noxious weed in 73 countries and constitutes a significant threat to global biodiversity and sustainable agriculture. We used a cost-effective genotyping-by-sequencing (GBS) approach to identify the reproductive system, genetic diversity and geographic origins of invasions in the south-eastern United States. In this work, we demonstrated the advantage of employing the closely related, fully sequenced crop species Sorghum bicolor (L.) Moench as a proxy...

Data from: Stick insect genomes reveal natural selection's role in parallel speciation

Victor Soria-Carrasco, Zachariah Gompert, Aaron A. Comeault, Timothy E. Farkas, Thomas L. Parchman, J. Spencer Johnston, C. Alex Buerkle, Jeffrey L. Feder, Jens Bast, Tanja Schwander, Scott P. Egan, Bernard J. Crespi & Patrik Nosil
Natural selection can drive the repeated evolution of reproductive isolation, but the genomic basis of parallel speciation remains poorly understood. We analyzed whole-genome divergence between replicate pairs of stick insect populations that are adapted to different host plants and undergoing parallel speciation. We found thousands of modest-sized genomic regions of accentuated divergence between populations, most of which are unique to individual population pairs. We also detected parallel genomic divergence across population pairs involving an excess...

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