26 Works

Data from: Nonlinear dynamics forecasting of obstructive sleep apnea onsets

Trung Q. Le & Satish T. S. Bukkapatnam
Recent advances in sensor technologies and predictive analytics are fueling the growth in point-of-care (POC) therapies for obstructive sleep apnea (OSA) and other sleep disorders. The effectiveness of POC therapies can be enhanced by providing personalized and real-time prediction of OSA episode onsets. Previous attempts at OSA prediction are limited to capturing the nonlinear, nonstationary dynamics of the underlying physiological processes. This paper reports an investigation into heart rate dynamics aiming to predict in real...

Data from: Independent origins of resistance or susceptibility of parasitic wasps to a defensive symbiont

Mariana Mateos, Lauryn Winter, Caitlyn Winter, Victor M. Higareda-Alvear, Esperanza Martinez-Romero & Jialei Xie
Insect microbe associations are diverse, widespread, and influential. Among the fitness effects of microbes on their hosts, defense against natural enemies is increasingly recognized as ubiquitous, particularly among those associations involving heritable, yet facultative, bacteria. Protective mutualisms generate complex ecological and co-evolutionary dynamics that are only beginning to be elucidated. These depend in part on the degree to which symbiont-mediated protection exhibits specificity to one or more members of the natural enemy community. Recent findings...

Data from: A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci

Christopher M. Hollenbeck, David S. Portnoy & John R. Gold
Estimation of contemporary effective population size (Ne) from linkage disequilibrium (LD) between unlinked pairs of genetic markers has become an important tool in the field of population and conservation genetics. If data pertaining to physical linkage or genomic position are available for genetic markers, estimates of recombination rate between loci can be combined with LD data to estimate contemporary Ne at various times in the past. We extend the well-known, LD-based method of estimating contemporary...

Data from: Multi-locus sequence data reveal a new species of coral reef goby (Teleostei: Gobiidae: Eviota), and evidence of Pliocene vicariance across the Coral Triangle

Luke Tornabene, Samantha Valdez, Mark V. Erdmann & Frank L. Pezold
Here, multi-locus sequence data are coupled with observations of live colouration to recognize a new species, Eviota punyit from the Coral Triangle, Indian Ocean and Red Sea. Relaxed molecular clock divergence time estimation indicates a Pliocene origin for the new species, and the current distribution of the new species and its sister species Eviota sebreei supports a scenario of vicariance across the Indo-Pacific Barrier, followed by subsequent range expansion and overlap in the Coral Triangle....

Data from: 3D sorghum reconstructions from depth images identify QTL regulating shoot architecture

Ryan F. McCormick, Sandra K. Truong & John E. Mullet
Dissecting the genetic basis of complex traits is aided by frequent and nondestructive measurements. Advances in range imaging technologies enable the rapid acquisition of three-dimensional (3D) data from an imaged scene. A depth camera was used to acquire images of sorghum (Sorghum bicolor), an important grain, forage, and bioenergy crop, at multiple developmental time points from a greenhouse-grown recombinant inbred line population. A semiautomated software pipeline was developed and used to generate segmented, 3D plant...

Data from: Unmanned aerial vehicles for high-throughput phenotyping and agronomic research

Yeyin Shi, John Alex Thomasson, Seth C. Murray, Nicholas Ace Pugh, William L. Rooney, Sanaz Shafian, Nithya Rajan, Gregory Rouze, Cristine L.S. Morgan, Haly L. Neely, Aman Rana, Muthu V. Bagavathiannan, James Henrichson, Ezekiel Bowden, John Valasek, Jeff Olsenholler, Michael P. Bishop, Ryan Sheridan, Eric B. Putman, Sorin Popescu, Travis Burks, Dale Cope, Amir Ibrahim, Billy F. McCutchen, David D. Baltensperger … & James Henrickson
Advances in automation and data science have led agriculturists to seek real-time, high-quality, high-volume crop data to accelerate crop improvement through breeding and to optimize agronomic practices. Breeders have recently gained massive data-collection capability in genome sequencing of plants. Faster phenotypic trait data collection and analysis relative to genetic data leads to faster and better selections in crop improvement. Furthermore, faster and higher-resolution crop data collection leads to greater capability for scientists and growers to...

Data from: Reliability and construct validity of the Psychopathic Personality Inventory-Revised in a Swedish non-criminal sample: a multimethod approach including psychophysiological correlates of empathy for pain

Karolina Sörman, Gustav Nilsonne, Katarina Howner, Sandra Tamm, Shilan Caman, Hui-Xin Wang, Martin Ingvar, John F. Edens, Petter Gustavsson, Scott O. Lilienfeld, Predrag Petrovic, Håkan Fischer & Marianne Kristiansson
Cross-cultural investigation of psychopathy measures is important for clarifying the nomological network surrounding the psychopathy construct. The Psychopathic Personality Inventory-Revised (PPI-R) is one of the most extensively researched self-report measures of psychopathic traits in adults. To date however, it has been examined primarily in North American criminal or student samples. To address this gap in the literature, we examined PPI-R’s reliability, construct validity and factor structure in non-criminal individuals (N = 227) in Sweden, using...

Data from: Population genomics reveals multiple drivers of population differentiation in a sex-role-reversed pipefish

Sarah P. Flanagan, Emily Rose & Adam G. Jones
A major goal of molecular ecology is to identify the causes of genetic and phenotypic differentiation among populations. Population genomics is suitably poised to tackle these key questions by diagnosing the evolutionary mechanisms driving divergence in nature. Here, we set out to investigate the evolutionary processes underlying population differentiation in the Gulf pipefish, Syngnathus scovelli. We sampled approximately 50 fish from each of 12 populations distributed from the Gulf coast of Texas to the Atlantic...

Data from: Genetic differences in the response to landscape fragmentation by a habitat generalist, the bobcat, and a habitat specialist, the ocelot

Jan E. Janecka, Michael E. Tewes, Imogene A. Davis, Aaron M. Haines, Arturo Caso, Terry L. Blankenship & Rodney L. Honeycutt
The ecology of a species strongly influences genetic variation and population structure. This interaction has important conservation implications because taxa with low dispersal capability and inability to use different habitats are more susceptible to anthropogenic stressors. Ocelots (Leopardus pardalisalbescens) and bobcats (Lynx rufus texensis) are sympatric in Texas and northeastern Mexico; however, their ecology and conservation status are markedly different. We used 10 microsatellite loci and a 397-bp segment of the mitochondrial control region to...

Data from: Identifying signatures of sexual selection using genomewide selection components analysis

Sarah P. Flanagan & Adam G. Jones
Sexual selection must affect the genome for it to have an evolutionary impact, yet signatures of selection remain elusive. Here we use an individual-based model to investigate the utility of genome-wide selection components analysis, which compares allele frequencies of individuals at different life history stages within a single population to detect selection without requiring a priori knowledge of traits under selection. We modeled a diploid, sexually reproducing population and introduced strong mate choice on a...

Data from: The lek mating system of the worm pipefish (Nerophis lumbriciformis): a molecular maternity analysis and test of the phenotype-linked fertility hypothesis

Nuno M. Monteiro, Diana Carneiro, Agostinho Antunes, Nuno Queiroz, Maria N. Vieira & Adam G. Jones
The origin and maintenance of mating preferences continues to be an important and controversial topic in sexual selection research. Leks and lek-like mating systems, where individuals gather in particular spots for the sole purpose of mate choice, are particularly puzzling, because the strong directional selection imposed by mate choice should erode genetic variation among competing individuals and negate any benefit for the choosing sex. Here, we take advantage of the lek-like mating system of the...

Data from: The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

Alvaro Martinez Barrio, Sangeet Lamichhaney, Guangyi Fan, Nima Rafati, Mats Pettersson, He Zhang, Jacques Dainat, Diana Ekman, Marc Höppner, Patric Jern, Marcel Martin, Björn Nystedt, Xin Liu, Wenbin Chen, Xinming Liang, Chengcheng Shi, Yuanyuan Fu, Kailong Ma, Xiao Zhan, Chungang Feng, Ulla Gustafson, Carl-Johan Rubin, Markus Sällman Almén, Martina Blass, Michele Casini … & Leif Andersson
Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of...

Data from: Constrained body shape among highly genetically divergent allopatric lineages of the supralittoral isopod Ligia occidentalis (Oniscidea)

Carlos A. Santamaria, Mariana Mateos, Thomas J. DeWitt & Luis A. Hurtado
Multiple highly divergent lineages have been identified within Ligia occidentalis sensu lato, a rocky supralittoral isopod distributed along a ~3000 km latitudinal gradient that encompasses several proposed marine biogeographic provinces and ecoregions in the eastern Pacific. Highly divergent lineages have nonoverlapping geographic distributions, with distributional limits that generally correspond with sharp environmental changes. Crossbreeding experiments suggest postmating reproductive barriers exist among some of them, and surveys of mitochondrial and nuclear gene markers do not show...

Data from: Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

Richard C. Harrington, Brant C. Faircloth, Ron I. Eytan, W. Leo Smith, Thomas J. Near, Michael E. Alfaro & Matt Friedman
Background: Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have yielded a polyphyletic or only weakly supported flatfish clade. Lack of resolution for flatfish relationships has been...

Data from: Extreme prescribed fire during drought reduces survival and density of woody resprouters

Dirac Twidwell, William E. Rogers, Carissa L. Wonkka, , Urs P. Kreuter & Charles A. Taylor
Management intervention in ecosystems with degraded environmental services requires innovative resource management strategies that go beyond conventional restoration and conservation practices. We established a unique study that experimentally targeted extreme fire conditions during drought in humid subtropical and semiarid ecoregions. In the southern Great Plains of North America, conventional restoration and conservation practices have been either historically ineffective or economically cost prohibitive at restoring grass-dominated ecosystems following conversion to resprouting shrublands. Our aim was to...

Data from: SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)

Irene Muñoz, Dora Henriques, Laura Jara, J. Spencer Johnston, Julio Chávez-Galarza, Pilar De La Rúa & M. Alice Pinto
The honeybee (Apis mellifera) has been threatened by multiple factors, including pests and pathogens, pesticides, and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A.m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify purebred A.m. mellifera colonies. Microsatellites have been preferred for identification...

Data from: Context-dependent expression of the foraging gene in field colonies of ants: the interacting roles of age, environment and task

Krista K. Ingram, Deborah M. Gordon, Daniel A. Friedman, Michael Greene, John Kahler & Swetha Peteru
Task allocation among social insect workers is an ideal framework for studying the molecular mechanisms underlying behavioural plasticity because workers of similar genotype adopt different behavioural phenotypes. Elegant laboratory studies have pioneered this effort, but field studies involving the genetic regulation of task allocation are rare. Here, we investigate the expression of the foraging gene in harvester ant workers from five age- and task-related groups in a natural population, and we experimentally test how exposure...

Data from: The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods

Mana Dembo, Davorka Radovčić, Heather M. Garvin, Myra F. Laird, Lauren Schroeder, Jill E. Scott, Juliet Brophy, Rebecca R. Ackermann, Charles M. Musiba, Darryl J. De Ruiter, Arne Ø. Mooers, Mark Collard & Chares M. Musiba
Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: “Where does H. naledi fit in the hominin evolutionary tree?” and “How old is it?” We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out...

Data from: Ancient hybridization and genomic stabilization in a swordtail fish

Molly Schumer, Rongfeng Cui, Daniel L. Powell, Gil G. Rosenthal & Peter Andolfatto
A rapidly increasing body of work is revealing that the genomes of distinct species often exhibit hybrid ancestry, presumably due to postspeciation hybridization between closely related species. Despite the growing number of documented cases, we still know relatively little about how genomes evolve and stabilize following hybridization, and to what extent hybridization is functionally relevant. Here, we examine the case of Xiphophorus nezahualcoyotl, a teleost fish whose genome exhibits significant hybrid ancestry. We show that...

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...

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: 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: Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

Victor C. Mason, Gang Li, Patrick Minx, Jurgen Schmitz, Gennady Churakov, Liliya Doronina, Amanda D. Melin, Nathaniel J. Dominy, Norman T-L. Lim, Mark S. Springer, Richard K. Wilson, Wesley C. Warren, Kristofer M. Helgen & William J. Murphy
Colugos are one of the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculo-skeletal related genes that likely underlie their nocturnal...

Data from: Decreased small mammal and on-host tick abundance in association with invasive red imported fire ants (Solenopsis invicta)

Adrian A. Castellanos, Matthew C.I. Medeiros, Gabriel L. Hamer, Mike E. Morrow, Micky D. Eubanks, Pete D. Teel, Sarah A. Hamer & Jessica E. Light
Invasive species may impact pathogen transmission by altering the distributions and interactions among native vertebrate reservoir hosts and arthropod vectors. Here, we examined the direct and indirect effects of the red imported fire ant (Solenopsis invicta) on the native tick, small mammal and pathogen community in southeast Texas. Using a replicated large-scale field manipulation study, we show that small mammals were more abundant on treatment plots where S. invicta populations were experimentally reduced. Our analysis...

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...

Registration Year

  • 2016
    26

Resource Types

  • Dataset
    26

Affiliations

  • Texas A&M University
    26
  • Yale University
    2
  • Louisiana State University
    2
  • Stockholm University
    2
  • University of Kansas
    1
  • National Museum
    1
  • North West Agriculture and Forestry University
    1
  • Fred Hutchinson Cancer Research Center
    1
  • Stanford University
    1
  • The University of Texas at Austin
    1