120 Works

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: 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: 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: 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: 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: 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: 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: \"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.

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...

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...

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: 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...

Occurrence datasets, model outputs, and R script for 12 termite species used for niche modeling

Aaron Goodman, Jonah Allen, Jinna Brim, Alessa Codella, Brittney Hahn, Hassan Jojo, Zoila BondocGawa Mafla-Mills, Salka'Tuwa Bondoc Mafla, Agnes Oduro, Megan Wilson & Jessica Ware
The advent of citizen-science databases in conjunction with museum specimen locality information has exponentially increased the power and accuracy of ecological niche modeling (ENM). Increased occurrence data has provided colossal potential to understand the distributions of lesser known or endangered species, including arthropods. Although niche modeling of termites has been conducted in the context of invasive and pest species, few studies have been performed to understand the distribution of basal termite genera. Using specimen records...

Environmental correlates of phenotypic evolution in ecologically diverse Liolaemus lizards

Danielle Edwards, Luciano Avila, Lorena Martinez, & Mariana Morando
Evolutionary correlations between phenotypic and environmental traits characterize adaptive radiations. However, the lizard genus Liolaemus, one of the most ecologically diverse terrestrial vertebrate radiations on earth, has so far shown limited or mixed evidence of adaptive diversification in phenotype. Restricted use of comprehensive environmental data, incomplete taxonomic representation and not considering phylogenetic uncertainty may have led to contradictory evidence. We compiled a 26 taxon dataset for the L. gracilis species group, representing much of the...

The impact of Rhodiola Rosea on biomarkers of diabetes, inflammation, and microbiota in a leptin receptor-knockout mouse model

Robert Courville, Mahtab Jafari, Richard Van Etten, John Chaston, Jasmin Grace Juanson Arabit, Dara Kiani, Cindy Duy Nguyen, Nilamani Jena, Zhong-Ying Liu & Prasanthi Tata
Type 2 diabetes is the most prevalent endocrine disease in the world, and recently the gut microbiota have become a potential target for its management. Recent studies have illustrated that this disease may predispose individuals to certain microbiome compositions, and treatments like metformin have been shown to change gut microbiota and their associated metabolic pathways. However, given the limitations and side effects associated with pharmaceuticals currently being used for therapy of diabetes, there is a...

Morphometric correlations between dietary and reproductive traits of two brachyuran crabs, Hemigrapsus sanguineus and Aratus pisonii

Blaine Griffen
Many animals have flexible morphological traits that allow them to succeed in differing circumstances with differing diets available to them. For brachyuran crabs, claw height and gut size are diet-specific and largely reflect foraging strategies, while abdomen width reflects relative levels of fecundity. However, the link between claw size and diet has largely been documented only for primarily carnivorous crabs, while the link between diet and fecundity is strong in herbivorous crabs. We sought to...

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...

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...

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....

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...

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...

Data for a preliminary molecular phylogeny of the family Hydroptilidae (Trichoptera): exploring the combination of targeted enrichment data and legacy Sanger sequence data

Robin Thomson, Paul Frandsen & Ralph Holzenthal
The purpose of this study is to provide a proof-of-concept that the use of molecular data, particularly targeted enrichment data, and statistically supported methods of analysis can result in the construction of a stable phylogenetic framework for the microcaddisflies (Trichoptera: Hydroptilidae). Here, we use a combination of targeted enrichment data for ca. 300 nuclear protein-coding genes and legacy (Sanger-based) sequence data for the mitochondrial COI gene and partial sequence from the 28S rRNA gene.

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.

No evidence for increased fitness of offspring from multigenerational effects of parental size or natal carcass size in the burying beetle Nicrophorus marginatus

Mark Belk, Ethan Damron, Ashlee Momcilovitch & Dane Jo
Multigenerational effects (often called maternal effects) are components of the offspring phenotype that result from the parental phenotype and the parental environment as opposed to heritable genetic effects. Multigenerational effects are widespread in nature and are often studied because of their potentially important effects on offspring traits. Although multigenerational effects are commonly observed, few studies have addressed whether they affect offspring fitness. In this study we assess the effect of potential multigenerational effects of parental...

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  • Brigham Young University
  • Chinese Academy of Sciences
  • National Evolutionary Synthesis Center
  • University of Adelaide
  • Duke University
  • National Autonomous University of Mexico
  • University of South Carolina
  • University of Mississippi
  • University of Kansas
  • New Mexico State University