115 Works

Improving dryland seedling recruitment using fungicide seed coatings

Benjamin Hoose, Brad Geary, William Richardson, Steven Petersen & Matthew Madsen
The success of seed-based restoration in dryland regions of the world is often low or sporadic, with most mortality occurring between germination and emergence. Fungal pathogenesis is one process that may reduce seedling emergence and limit restoration success. Our objective was to determine whether fungicide seed coatings constitute an economically viable strategy for increasing emergence by reducing fungal pathogenesis and mortality. We performed an experiment across two sites and three years, using bluebunch wheatgrass (Pseudoroegneria...

Performance and social connection data for baseball and basketball from 2001 to 2020

Emily Evans, Benjamin Webb & Rebecca Jones
We examine whether social data can be used to predict how members of Major League Baseball (MLB) and members of the National Basketball Association (NBA) transition between teams during their career. We find that incorporating social data into various machine learning algorithms substantially improves the algorithms' ability to correctly determine these transitions in the NBA but only marginally in MLB. We also measure the extent to which player performance and team fitness data can be...

Morphometric Response of Galaxias maculatus (Jenyns) to Lake Colonization in Chile

Margaret Mercer, Peter C. Searle, Roberto Cifuentes, Evelyn Habit & Mark C. Belk
Body and head shape in fish responds to environmental factors such as water flow rate, food sources, and niche availability. However, the way in which fish respond to these environmental factors varies. In Central Chile, multiple river and lake systems along the coast provide an ideal study site to investigate these types of shape changes. We use geometric morphometrics to characterize shape differences in Galaxias maculatus (Jenyns) between river and lake populations. Lake fish converge...

Do dog breeds differ in pain sensitivity? Veterinarians and the public believe they do

Margaret Gruen, Brian Hare & Philip White
Humans do not respond to the pain of all humans equally; physical appearance and associated group identity affect how people respond to the pain of others. Here we ask if a similar differential response occurs when humans evaluate different individuals of another species. Beliefs about pain in pet dogs (Canis familiaris) provide a powerful test, since dogs vary so much in size, shape, and color, and are often associated with behavioral stereotypes. Using an on-line...

Data from: Warming alters surface soil organic matter composition despite unchanged carbon stock in a Tibetan permafrost ecosystem

Fei Li, Yunfeng Peng, Leiyi Chen, Guibiao Yang, Benjamin W Abbott, Dianye Zhang, Kai Fang, Guanqin Wang, Jun Wang, Jianchun Yu, Li Liu, Qiwen Zhang, Kelong Chen, Anwar Mohammat & Yuanhe Yang
1. Climate warming can alter ecosystem carbon (C) balance and also the composition of soil organic matter (SOM), with important local and global implications. However, the extent to which rising temperature affects SOM composition in permafrost ecosystems remains poorly understood. 2. Here, we experimentally warmed a permafrost ecosystem by open-top chambers (OTCs) on the Tibetan Plateau for four years to quantify the responses of C inputs via vegetation production, C losses via soil respiration, and...

Data from: Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata)

Bryce A. Richardson, Justin T. Page, Prabin Bajgain, Stewart C. Sanderson & Joshua A. Udall
PREMISE OF THE STUDY: Hybridization has played an important role in the evolution and ecological adaptation in diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata ssp. wyomingensis, or as autotetraploids of diploid subspecies tridentata and vaseyana. Few details are available as to how these tetraploids are formed or how they are related to diploid subspecies. METHODS: We used...

Data from: Climate drives adaptive genetic responses associated with survival in big sagebrush (Artemisia tridentata)

Lindsay Chaney, Bryce A. Richardson & Matthew J. Germino
A genecological approach was used to explore genetic variation for survival in Artemisia tridentata (big sagebrush). Artemisia tridentata is a widespread and foundational shrub species in western North America. This species has become extremely fragmented, to the detriment of dependent wildlife, and efforts to restore it are now a land management priority. Common garden experiments were established at three sites with seedlings from 55 source-populations. Populations included each of the three predominant subspecies, and cytotype...

Data from: How lizards survived blizzards: phylogeography of the Liolaemus lineomaculatus group (Liolaemidae) reveals multiple breaks and refugia in southern Patagonia, and their concordance with other co-distributed taxa

Maria Breitman, Luciano Avila, Jack Sites, Mariana Morando & Jack W. Sites
Patagonia was shaped by a complex geological history, including the Miocene uplift of the Andes, followed by volcanism, marine introgressions, and extreme climatic oscillations during Pleistocene glaciation–deglaciation cycles. The distributional patterns and phylogenetic relationships of southern patagonian animals and plants were affected in different ways, and those imprints are reflected in the seven phylogeographic breaks and eight refugia that have been previously proposed. In this study we estimated time-calibrated phylogenetic/phylogeographic patterns in lizards of the...

Data from: Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil

Marcelo Gehara, Adrian Antoinio Garda, Fernanda P. Werneck, Eliana F. Oliveira, Emanuel M. Da Fonseca, Felipe Camurugi, Felipe De M. Magalhães, Flavia Mol Lanna, Jack W. Sites, Ricardo Marques, Ricardo Silveira-Filho, Vinícius A. São-Pedro, Guarino R. Colli, Gabriel C. Costa & Frank T. Burbrink
Many studies propose that Quaternary climatic cycles contracted and /or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the...

Data from: An in silico comparison of protocols for dated phylogenomics

Rupert A. Collins & Tomas Hrbek
In the age of genome-scale DNA sequencing, choice of molecular marker arguably remains an important decision in planning a phylogenetic study. Using published genomes from 23 primate species, we make a standardized comparison of four of the most frequently used protocols in phylogenomics, viz., targeted sequence-enrichment using ultraconserved element and exon-capture probes, and restriction-site-associated DNA sequencing (RADseq and ddRADseq). Here we present a procedure to perform in silico extractions from genomes and create directly comparable...

Data from: Limitations of species delimitation based on phylogenetic analyses: a case study in the (Hypogymnia hypotrypa) group (Parmeliaceae, Ascomycota)

Xinli Wei, Bruce McCune, H. Thorsten Lumbsch, Hui Li, Steven Leavitt, Yoshikazu Yamamoto, Svetlana Tchabanenko & Jiangchun Wei
Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which...

Data from: A gene for genetic background in Zea mays: fine-mapping enhancer of teosinte branched1.2 to a YABBY class transcription factor

Chin Jian Yang, Lisa E. Kursel, Anthony J. Studer, Madelaine E. Bartlett, Clinton J. Whipple & John F. Doebley
The effects of an allelic substitution at a gene often depend critically on genetic background, i.e., the genotypes at other genes in the genome. During the domestication of maize from its wild ancestor (teosinte), an allelic substitution at teosinte branched (tb1) caused changes in both plant and ear architecture. The effects of tb1 on phenotype were shown to depend on multiple background loci, including one called enhancer of tb1.2 (etb1.2). We mapped etb1.2 to a...

Data from: Use of auto-germ to model germination timing in the Sagebrush-steppe

William C. Richardson, Dallin R. Whitaker, Kyler P. Sant, Nicholas S. Barney, Ryan S. Call, Bruce A. Roundy, Zachary T. Aanderud & Matthew D. Madsen
Germination timing has a strong influence on direct seeding efforts, and therefore is a closely tracked demographic stage in a wide variety of wildland and agricultural settings. Predictive seed germination models, based on soil moisture and temperature data in the seed zone are an efficient method of estimating germination timing. We utilized Visual Basic for Applications (VBA) to create Auto-Germ, which is an Excel workbook that allows a user to estimate field germination timing based...

Data from: \"Transcriptome resources for the marmot flea and plague vector, Oropsylla silantiewi\" in Genomic Resources Notes accepted 1 February 2014 to 31 March 2014

Gonghua Lin, Zuyun Wang, Michael F. Whiting, Jianping Su, Fang Zhao, Junying Ma, Hongjian Chen & Tongzuo Zhang
This article documents the public availability of raw transcriptome sequence data, 47,882 assembled unigenes as well as their functional annotations, and 13,052 deduced ORFs (open reading frame) of a plague vector Oropsylla silantiewi.

Data from: Plotting for change: an analytic framework to aid decisions on which lineages are candidate species in phylogenomic species discovery

Arthur Georges, Peter Unmack, Mark Adams, Michael Hammer, Jerald Johnson, Bernd Gruber, André Gilles & Matthew Young
A recent study argued that coalescent-based models of species delimitation mostly delineate population structure not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable, or uninformative. For de novo genomic studies of species...

Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies

Anton Suvorov, Celine Scornavacca, M. Stanley Fujimoto, Paul Bodily, Mark Clement, Keith Crandall, Michael Whiting, Daniel Schrider & Seth Bybee
Introgression is arguably one of the most important biological processes in the evolution of groups of related species, affecting at least 10% of the extant species in the animal kingdom. Introgression reduces genetic divergence between species, and in some cases can be highly beneficial, facilitating rapid adaptation to ever-changing environmental pressures. Introgression also significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we...

Decreased coevolutionary potential and increased symbiont fecundity during the biological invasion of a legume-rhizobium mutualism

Camille Wendlandt, Emily Helliwell, Miles Roberts, Kyle Nguyen, Maren Friesen, Eric Von Wettberg, Paul Price, Joel Griffitts & Stephanie Porter
Although most invasive species engage in mutualism, we know little about how mutualism evolves as partners colonize novel environments. Selection on cooperation and standing genetic variation for mutualism traits may differ between a mutualism's invaded and native ranges, which could alter cooperation and coevolutionary dynamics. To test for such differences, we compare mutualism traits between invaded- and native-range host-symbiont genotype combinations of the weedy legume, Medicago polymorpha, and its nitrogen-fixing rhizobium symbiont, Ensifer medicae, which...

Identification of Wright fishhook cactus using drone and remote sensing technology

Steven Petersen
Obtaining accurate population estimates of plants has been an integral part of the listing, recovery, and delisting of species under the U.S. Endangered Species Act (ESA) of 1973 and for monitoring vegetation in response to livestock grazing management. However, obtaining such estimates for many plant species remains a daunting and labor-intensive task. The use of small unmanned aircraft systems (sUAS or drones) may provide an effective alternative to ground surveys for rare and endangered plants....

Data on the Effects of Persuasive Message Content on Retweet Counts during Natural Hazard Events

Yajie Li, Amanda Hughes & Peter Howe
This dataset contains Twitter messages about heat hazards posted by U.S. National Weather Service accounts in 2016. The dataset also contains the retweet counts of the heat-related tweets and whether several types of persuasive message content were included in each tweet. The population and temperature for the forecast area of each sending National Weather Service account are also included.

Data from: Sympatry predicts spot pigmentation patterns and female association behavior in the livebearing fish Poeciliopsis baenschi

Andrea J. Roth-Monzón, Laura E. Scott, Ashley A. Camargo, Eliza I. Clark, Eric E. Schott & Jerald B. Johnson
In this study, we explored the possibility that differences in pigmentation patterns among populations of the fish Poeciliopsis baenschi were associated with the presence or absence of the closely related species P. turneri. If reproductive character displacement is responsible, spotting patterns in these two species should diverge in sympatry, but not allopatry. We predicted that female P. baenschi from sympatric sites should show a preference for associating with conspecifics vs. heterospecific males, but females from...

Data from: Sampling strategies for delimiting species: genes, individuals, and populations in the Liolaemus elongatus-kriegi complex (Squamata: Liolaemidae) in Andean-Patagonian South America

Mariana Morando, Luciano J. Avila & Jack W Sites
Recovery of evolutionary history and delimiting species boundaries in widely distributed, poorly-known groups requires extensive geographic sampling, but this is difficult to design a priori because evolutionary diversity is often "hidden" by an inadequate taxonomy. Large data sets are needed, and these provide unique challenges for analysis when they span intra and inter-specific levels of divergence. Protocols have been designed to combine methods of analysis for DNA sequences that exhibit both very shallow and relatively...

Data from: Testes mass in the livebearing fish Brachyrhaphis rhabdophora (Poeciliidae) varies hypoallometrically with body size but not between predation environments

Haley N. Brown, Brittany Herrod Gale, Jerald B. Johnson & Mark C. Belk
In this study, we considered potential causes of variation in testis size in the livebearing fish Brachyrhaphis rhabdophora. We evaluated variation in testes mass among individual males and among populations that occupy different selective environments. First, we predicted that small males should allocate more to testes mass than large males (i.e., hypoallometric pattern) based on a sperm competition argument. Second, based on life history theory and associated differences in mortality rates between populations that co-exist...

Data from: Residency time as an indicator of reproductive restraint in male burying beetles

Ashlee N. Smith, Mark C. Belk & J. Curtis Creighton
The cost of reproduction theory posits that there are trade-offs between current and future reproduction because resources that are allocated to current offspring cannot be used for future reproductive opportunities. Two adaptive reproductive strategies have been hypothesized to offset the costs of reproduction and maximize lifetime fitness. The terminal investment hypothesis predicts that as individuals age they will allocate more resources to current reproduction as a response to decreasing residual reproductive value. The reproductive restraint...

Data from: Decoupled responses of soil bacteria and their invertebrate consumer to warming, but not freeze-thaw cycles, in the Antarctic Dry Valleys

Matthew A. Knox, Walter S. Andriuzzi, Heather N. Buelow, Cristina Takacs-Vesbach, Byron J. Adams & Diana H. Wall
Altered temperature profiles resulting in increased warming and freeze–thaw cycle (FTC) frequency pose great ecological challenges to organisms in alpine and polar ecosystems. We performed a laboratory microcosm experiment to investigate how temperature variability affects soil bacterial cell numbers, and abundance and traits of soil microfauna (the microbivorous nematode Scottnema lindsayae) from McMurdo Dry Valleys, Antarctica. FTCs and constant freezing shifted nematode body size distribution towards large individuals, driven by higher mortality among smaller individuals....

Data from: Hybridization could be a common phenomenon within the highly diverse lizard genus Liolaemus

Melisa Olave, Luciano J. Avila, , Mariana Morando & Jack W. Sites
Hybridization is likely to occur more often between closely related taxa that have had insufficient time to diverge to the point of reproductive incompatibility; hybridization between deeply divergent lineages is rare. In squamate reptiles, hybridization has been proposed as a possible explanation for the extensive paraphyly observed in mitochondrial gene trees in several species complexes of the South American lizard genus Liolaemus. One of the best-documented cases is within the L. boulengeri and L. rothi...

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