277 Works

Data from: The unexpected depths of genome-skimming data: a case study examining Goodeniaceae floral symmetry genes

Brent A. Berger, Jiahong Han, Emily B. Sessa, Andrew G. Gardner, Kelly A. Shepherd, Vincent A. Ricigliano, Rachel S. Jabaily & Dianella G. Howarth
Premise of the study: The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. Methods: Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their...

Data from: Thresholds and gradients in a semi-arid grassland: long-term grazing treatments induce slow, continuous and reversible vegetation change

Lauren M. Porensky, Kevin E. Mueller, David J. Augustine & Justin D. Derner
1. Temporal changes in semi-arid ecosystems can include transitions between alternative stable states, involving thresholds and multiple domains of attraction, but can also include relatively continuous, symmetric and reversible shifts within a single stable state. Conceptual state-and-transition models (STMs) describe both types of ecosystem dynamics by including state transitions (plant community changes difficult-to-reverse without substantial input or effort) and phase shifts (easily reversible community changes) as consequences of management practices and environmental variability. Grazing management...

Data from: Genome-wide analysis of allele frequency change in sunflower crop-wild hybrid populations evolving under natural conditions

Jonathan Corbi, Eric J. Baack, Jennifer M. Dechaine, Gerald Seiler & John M. Burke
Crop-wild hybridization occurs in numerous plant species, and could alter the genetic structure and evolutionary dynamics of wild populations. Studying crop-derived alleles in wild populations is also relevant to assessing/mitigating the risks associated with transgene escape. To date, crop-wild hybridization has generally been examined via short-term studies, typically within a single generation, focusing on few traits or genetic markers. Little is known about patterns of selection on crop-derived alleles over multiple generations, particularly at a...

Data from: All roads lead to weediness: patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza

Zhongyun Huang, Nelson D. Young, Michael Reagon, Katie E. Hyma, Kenneth M. Olsen, Yulin Jia & Ana L. Caicedo
Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O. sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the “agricultural weed syndrome,” making this an ideal model to study the genetic basis of parallel evolution. Understanding parallel evolution hinges on accurate knowledge of the genetic background and origins of existing weedy rice groups. Using population structure analyses of South Asian and...

Data from: Phylogeny of xerophilic aspergilli (subgenus Aspergillus) and taxonomic revision of section Restricti

František Sklenář, Željko Jurjević, Polona Zalar, J. C. Frisvad, Cobus M. Visagie, Miroslav Kolařík, Jos Houbraken, Amanda J. Chen, Neriman Yilmaz, Keith A. Seifert, Monica Coton, Franck Déniel, Nina Gunde-Cimerman, Robert A. Samson, Stephen W. Peterson & Vít Hubka
Aspergillus section Restricti together with sister sect. Aspergillus (formerly Eurotium) comprises osmophilic species, that are able to grow on substrates with low water activity and in extreme environments. We adressed the monophyly of both sections within subgenus Aspergillus and applied a multidisciplinary approach for definition of species boundaries in sect. Restricti. The monophyly of sections Aspergillus and Restricti was tested on a set of 102 taxa comprising all currently accepted species and was strongly supported...

Data from: A novel molecular toolkit for rapid detection of the pathogen and primary vector of thousand cankers disease

Emel Oren, William Klingeman, Romina Gazis, John Moulton, Paris Lambdin, Mark Coggeshall, Jiri Hulcr, Steven J. Seybold & Denita Hadziabdic
Thousand Cankers Disease (TCD) of Juglans and Pterocarya (Juglandaceae) involves a fungal pathogen, Geosmithia morbida, and a primary insect vector, Pityophthorus juglandis. TCD was described originally from dying Juglans nigra trees in the western United States (USA), but it was reported subsequently from the eastern USA and northern Italy. The disease is often difficult to diagnose due to the absence of symptoms or signs on the bark surface of the host. Furthermore, disease symptoms can...

Data from: The global antigenic diversity of swine influenza A viruses

Nicola S. Lewis, Colin A. Russell, Tavis K. Anderson, Kathryn Berger, David F. Burke, Judith M. Fonville, Ronald A.M. Fouchier, Paul Kellam, Bjorn F. Koel, Tung Nguyen, Bundit Nuansrichy, J. S. Malik Peiris, Takehiko Saito, Gaelle Simon, Eugene Skepner, Nobuhiro Takemae, ESNIP3 Consortium, Richard J. Webby, Kristien Van Reeth, Sharon M. Brookes, Lars Larsen, Ian H. Brown, Amy L. Vincent, Pinky Langat, Filip Bielejec … & JS Malik Peiris
Swine influenza presents a substantial disease burden for pig populations worldwide and poses a potential pandemic threat to humans. There is considerable diversity in both H1 and H3 influenza viruses circulating in swine due to the frequent introductions of viruses from humans and birds coupled with geographic segregation of global swine populations. Much of this diversity is characterized genetically but the antigenic diversity of these viruses is poorly understood. Critically, the antigenic diversity shapes the...

Data from: Direct effects dominate responses to climate perturbations in grassland plant communities

Chengjin Chu, Andrew R. Kleinhesselink, Kris M. Havstad, Mitchel P. McClaran, Debra P. Peters, Lance T. Vermeire, Haiyan Wei & Peter B. Adler
Theory predicts that strong indirect effects of environmental change will impact communities when niche differences between competitors are small and variation in the direct effects experienced by competitors is large, but empirical tests are lacking. Here we estimate negative frequency dependence, a proxy for niche differences, and quantify the direct and indirect effects of climate change on each species. Consistent with theory, in four of five communities indirect effects are strongest for species showing weak...

Data from: The Genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos)

Jacqueline M. Doyle, Todd E. Katzner, Peter H. Bloom, Yanzhu Ji, Bhagya K. Wijayawardena & J. Andrew DeWoody
Biologists routinely use molecular markers to identify conservation units, to quantify genetic connectivity, to estimate population sizes, and to identify targets of selection. Many imperiled eagle populations require such efforts and would benefit from enhanced genomic resources. We sequenced, assembled, and annotated the first eagle genome using DNA from a male golden eagle (Aquila chrysaetos) captured in western North America. We constructed genomic libraries that were sequenced using Illumina technology and assembled the high-quality data...

Data from: Origins of cattle on Chirikof Island, Alaska, elucidated from genome-wide SNP genotypes

Jared E. Decker, Jeremy F. Taylor, Leeson J. Alexander, Juha Kantanen, Ann Millbrooke, Robert D. Schnabel & Michael D. MacNeil
Feral livestock may harbor genetic variation of commercial, scientific, historical or esthetic value. The origins and uniqueness of feral cattle on Chirikof Island, Alaska, are uncertain. The island is now part of the Alaska Maritime Wildlife Refuge and Federal wildlife managers want grazing to cease, presumably leading to demise of the cattle. Here we characterize the cattle of Chirikof Island relative to extant breeds and discern their origins. Our analyses support the inference that Yakut...

Data from: Modeling multi-species and multi-mode contact networks: implications for persistence of bovine tuberculosis at the wildlife-livestock interface

Mark Q. Wilber, Kim M. Pepin, , Scott E. Hygnstrom, Michael J. Lavelle, Tatiana Xifara, Kurt C. Vercauteren & Coleen T. Webb
1. Individual- and species-level heterogeneity in contact rates can alter the ability of a pathogen to invade a host community. Many pathogens have multiple modes of transmission -- by direct or indirect contact. It is important to identify the role of heterogeneity in different types of transmission when managing the risk of disease spillover at the interface among different host species. 2. We developed a network-based analysis to explore how individual- and species-level heterogeneity shape...

Data from: Interactions among morphotype, nutrition, and temperature impact fitness of an invasive fly.

Dalila Rendon, Vaughn Walton, Gabriella Tait, Jessica Buser, Ivana Lemos Souza, Anna Wallingford, Greg Loeb & Jana Lee
Invasive animals depend on finding a balanced nutritional intake to colonize, survive, and reproduce in new environments. This can be especially challenging during situations of fluctuating cold temperatures and food scarcity, but phenotypic plasticity may offer an adaptive advantage during these periods. We examined how lifespan, fecundity, pre-oviposition periods, and body nutrient contents were affected by dietary protein and carbohydrate (P:C) ratios at variable low temperatures in two morphs (winter morphs WM and summer morphs...

Data from: Can butterflies evade fire? Pupa location and heat tolerance in fire prone habitats of Florida

Matthew D. Thom, Jaret C. Daniels, Leda N. Kobziar & Jonathan R. Colburn
Butterflies such as the atala hairstreak, Eumaeus atala Poey, and the frosted elfin, Callophrys irus Godart, are restricted to frequently disturbed habitats where their larval host plants occur. Pupae of these butterflies are noted to reside at the base of host plants or in the leaf litter and soil, which may allow them to escape direct mortality by fire, a prominent disturbance in many areas they inhabit. The capacity of these species to cope with...

Data from: More than one way to evolve a weed: Parallel evolution of U.S. weedy rice through independent genetic mechanisms

Xinshuai Qi, Yan Liu, Cynthia C. Vigueira, Nelson D. Young, Ana L. Caicedo, Yulin Jia, David R. Gealy & Kenneth M. Olsen
Many different crop species were selected for a common suite of ‘domestication traits’, which facilitates their use for studies of parallel evolution. Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of parallel weed evolution and the extent to which this process occurs through shared genetic mechanisms. We performed comparative QTL mapping of weediness traits using two...

Data from: Mediating water temperature increases due to livestock and global change in high elevation meadow streams of the Golden Trout Wilderness

Sébastien Nusslé, Kathleen R. Matthews & Stephanie M. Carlson
Rising temperatures due to climate change are pushing the thermal limits of many species, but how climate warming interacts with other anthropogenic disturbances such as land use remains poorly understood. To understand the interactive effects of climate warming and livestock grazing on water temperature in three high elevation meadow streams in the Golden Trout Wilderness, California, we measured riparian vegetation and monitored water temperature in three meadow streams between 2008 and 2013, including two “resting”...

Data from: Molecular analyses identify hybridization-mediated nuclear evolution in newly discovered fungal hybrids

Fabiano Sillo, Paolo Gonthier, Blakey Lockman, Takao Kasuga & Matteo Garbelotto
Hybridization may be a major driver in the evolution of plant pathogens. In a high elevation Alpine larch stand in Montana, a novel hybrid fungal pathogen of trees originating from the mating of Heterobasidion irregulare with H. occidentale has been recently discovered. In this study, sequence analyses of one mitochondrial and four nuclear loci from 11 Heterobasidion genotypes collected in the same Alpine larch stand indicated that hybridization has increased allelic diversity by generating novel...

Data from: Strong patterns of intraspecific variation and local adaptation in Great Basin plants revealed through a review of 75 years of experiments

Owen W. Baughman, Alison C. Agneray, Matthew L. Forister, Francis F. Kilkenny, Erin K. Espeland, Rob Fiegener, Matthew E. Horning, Richard C. Johnson, Thomas N. Kaye, Jeffery Ott, John Bradley St. Clair & Elizabeth A. Leger
Variation in natural selection across heterogeneous landscapes often produces 1) among-population differences in phenotypic traits, 2) trait-by-environment associations, and 3) higher fitness of local populations. Using a broad literature review of common garden studies published between 1941 and 2017, we documented the commonness of these three signatures in plants native to North America’s Great Basin, an area of extensive restoration and revegetation efforts, and asked which traits and environmental variables were involved. We also asked,...

Data from: The importance of growing up: juvenile environment influences dispersal of individuals and their neighbours

Stacy B. Endriss, Megan L. Vahsen, Ellyn V. Bitume, J. Grey Monroe, Kathryn G. Turner, Andrew P. Norton & Ruth A. Hufbauer
Dispersal is a key ecological process that is strongly influenced by both phenotype and environment. Here, we show that juvenile environment influences dispersal not only by shaping individual phenotypes, but also by changing the phenotypes of neighbouring conspecifics, which influence how individuals disperse. We used a model system (Tribolium castaneum, red flour beetles) to test how the past environment of dispersing individuals and their neighbours influences how they disperse in their current environment. We found...

Data from: Host use dynamics in a heterogeneous fitness landscape generates oscillations in host range and diversification

Mariana P. Braga, Sabrina B.L. Araujo, Salvatore Agosta, Daniel Brooks, Eric Hoberg, Soren Nylin, Niklas Janz & Walter A. Boeger
Colonization of novel hosts is thought to play an important role in parasite diversification, yet little consensus has been achieved about the macroevolutionary consequences of changes in host use. Here we offer a mechanistic basis for the origins of parasite diversity by simulating lineages evolved in silico. We describe an individual-based model in which (i) parasites undergo sexual reproduction limited by genetic proximity, (ii) hosts are uniformly distributed along a one-dimensional resource gradient, and (iii)...

Data from: How topography induces reproductive asynchrony and alters gypsy moth invasion dynamics

Jonathan A. Walter, Marcia S. Meixler, Thomas Mueller, William F. Fagan, Patrick C. Tobin & Kyle J. Haynes
1. Reproductive asynchrony, a temporal mismatch in reproductive maturation between an individual and potential mates, may contribute to mate-finding failure and Allee effects that influence the establishment and spread of invasive species. Variation in elevation is likely to promote variability in maturation times for species with temperature-dependent development, but it is not known how strongly this influences reproductive asynchrony or the population growth of invasive species. 2. We examined whether spatial variation in reproductive asynchrony,...

Data from: Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle

Jared Egan Decker, Stephanie D. McKay, Megan M. Rolf, JaeWoo Kim, Antonio Molina Alcalá, Tad S. Sonstegard, Olivier Hanotte, Anders Götherström, Christopher M. Seabury, Lisa Praharani, Masroor Ellahi Babar, Luciana Correia De Almieda Regitano, Mehmet Ali Yildiz, Michael P. Heaton, Wan-Sheng Liu, Chu-Zhao Lei, James M. Reecy, Muhammad Saif-Ur-Rehman, Robert D. Schnabel & Jeremy F. Taylor
The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns...

Data from: Intercomparison of photogrammetry software for three-dimensional vegetation modelling

Alexandra Probst, Demetrios Gatziolis & Nikolay Strigul
Photogrammetry-based 3D reconstruction of objects is becoming increasingly appealing in research areas unrelated to computer vision. It has the potential to facilitate the assessment of forest inventory-related parameters by enabling or expediting resource measurements in the field. We hereby compare several implementations of photogrammetric algorithms (CMVS/PMVS, CMPMVS, MVE, OpenMVS, SURE, and Agisoft PhotoScan) with respect to their performance in vegetation assessment. The evaluation is based on (a) a virtual scene where the precise location and...

Data from: Invasion complexity at large spatial scales is an emergent property of interactions among landscape characteristics and invader traits

Ranjan Muthukrishnan, Adam S. Davis, Nicholas R. Jordan & James D. Forester
Invasion potential should be part of the evaluation of candidate species for any species introduction. However, estimating invasion risks remains a challenging problem, particularly in complex landscapes. Certain plant traits are generally considered to increase invasive potential and there is an understanding that landscapes influence invasions dynamics, but little research has been done to explore how those drivers of invasions interact. We evaluate the relative roles of, and potential interactions between, plant invasiveness traits and...

Data from: Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen

Simren Brar, Clement K. M. Tsui, Braham Dhillon, Marie-Josée Bergeron, David L. Joly, P. J. Zambino, Yousry A. El-Kassaby & Richard C. Hamelin
White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C. ribicola....

Data from: Geosmithia associated with bark beetles and woodborers in the western USA: taxonomic diversity and vector specificity

Miroslav Kolařík, Steven J. Seybold, Ned Tisserat, Wilhelm De Beer, David M. Rizzo, Jiri Hulcr & Martin Kostovčík
Fungi in the genus Geosmithia (Ascomycota: Hypocreales) are frequent associates of bark beetles and woodborers that colonize hardwood and coniferous trees. One species, Geosmithia morbida, is an economically damaging invasive species. The authors surveyed the Geosmithia species of California and Colorado, USA, to (i) provide baseline data on taxonomy of Geosmithia and beetle vector specificity across the western USA; (ii) investigate the subcortical beetle fauna for alternative vectors of the invasive G. morbida; and (iii)...

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  • United States Department of Agriculture
  • Cornell University
  • University of Florida
  • University of Montana
  • University of Georgia
  • Oregon State University
  • University of Minnesota
  • Colorado State University
  • Iowa State University
  • University of Washington