48 Works

Data from: Variance in reproductive success is driven by environmental factors not mating system in Bonytail

Megan J. Osborne, Alyssa V. Sanchez, Thomas E. Dowling & Thomas F. Turner
Studying the reproductive ecology of aggregate broadcast spawning fishes is difficult because it generally is not feasible to sample all potential parents and unambiguously assign their offspring. We used molecular‐based parentage analysis to gain insights into the reproductive ecology of the endangered Bonytail, and to evaluate whether protected off‐channel habitats could be used as an alternative to hatchery production. By genotyping adults and offspring stocked (n = 4130) into two experimental backwaters across three years,...

Dataset: Growth of Ta2SnO6 Films, a Candidate Wide-Band-Gap p‐Type Oxide

Matthew Barone, Michael mfoody, Yaoqiao HU, Jiaxin Sun, Bailey Frye, S. Sameera Perera, Biwas Subedi, Hanjong Paik, Jonathan Hollin, Myoungho Jeong, Kiyoung Lee, Charles Winter, Nikolas Podraza, Kyeongjae Cho, Adam Hock & Darrell Schlom
Raw data cited by "Growth of Ta2SnO6 Films, a Candidate Wide-Band-Gap p-Type Oxide" https://doi.org/10.1021/acs.jpcc.1c10382

Enhancing U.S. Surveillance of Laboratory Confirmed SARS-CoV-2, Influenza, and other Respiratory Viruses through a Network of Emergency Departments

Jeffrey Kline
This emergency department (ED) surveillance network comprises 24 nodes represented by site investigators at hospital systems in 21 states and the District of Columbia. This work is funded by a contract from the Centers for Disease Control with Wayne State as the prime. The goal of the network is to identify patients who present with acute respiratory illness (e.g. cough or fever). The network report demographic data, vaccination status as identified in the medical record,...

Wild at heart: programs to diminish negative ecological and evolutionary effects of conservation hatcheries

Megan Osborne, Thomas Dowling, Thomas Turner & Kim Scribner
Hatchery programs are critical for conservation and management of many imperiled fishes. Most traditional aquaculture programs negatively affect ecological performance, genetic, and phenotypic diversity of hatchery-origin fish compared with wild counterparts. Here, we synthesize outcomes of three conservation programs aimed at enhancing ‘wildness’. Each program focuses on a different species: lake sturgeon, razorback sucker, and Rio Grande silvery minnow. These species differ in key life history traits including size and age at sexual maturity, reproductive...

Do Synthesis Centers Synthesize? A Semantic Analysis of Topical Diversity in Research

Edward Hackett, Erin Leahy, John Parker, Ismael Rafols, Stephanie Hampton, Ugo Corte, Diego Chavarro, John Drake, Bart Penders, Laura Sheble, Niki Vermeulen & Todd Vision
Synthesis centers are a form of scientific organization that catalyzes and supports research that integrates diverse theories, methods and data across spatial or temporal scales to increase the generality, parsimony, applicability, or empirical soundness of scientific explanations. Synthesis working groups are a distinctive form of scientific collaboration that produce consequential, high-impact publications. But no one has asked if synthesis working groups synthesize: are their publications substantially more diverse than others, and if so, in what...

2018 Update to “A risk assesment of potential Great Lakes aquatic invaders”

El Lower, Nicholas Boucher, Peter Alsip, Alisha Davidson & Rochelle A. Sturtevant
NOAA Technical Memorandum GLERL ; 169b

Data from: Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas

Kaisa Thorell, Koji Yahara, Elvire Berthenet, Daniel J. Lawson, Jane Mikhail, Ikuko Kato, Alfonso Mendez, Cosmeri Rizzato, María Mercedes Bravo, Rumiko Suzuki, Yoshio Yamaoka, Javier Torres, Samuel K. Sheppard & Daniel Falush
For the last 500 years, the Americas have been a melting pot both for genetically diverse humans and for the pathogenic and commensal organisms associated with them. One such organism is the stomach-dwelling bacterium Helicobacter pylori, which is highly prevalent in Latin America where it is a major current public health challenge because of its strong association with gastric cancer. By analyzing the genome sequence of H. pylori isolated in North, Central and South America,...

Data from: Fetal genome profiling at 5 weeks of gestation after noninvasive isolation of trophoblast cells from the endocervical canal

Chandni V. Jain, Leena Kadam, Marie Van Dijk, Hamid-Reza Kohan-Ghad, Brian A. Kilburn, Craig Hartman, Vicki Mazzorana, Allerdien Visser, Michael Hertz, Alan D. Bolnick, Rani Fritz, D. Randall Armant & Sascha Drewlo
Single-gene mutations account for more than 6000 diseases, 10% of all pediatric hospital admissions, and 20% of infant deaths. Down syndrome and other aneuploidies occur in more than 0.2% of births worldwide and are on the rise because of advanced reproductive age. Birth defects of genetic origin can be diagnosed in utero after invasive extraction of fetal tissues. Noninvasive testing with circulating cell-free fetal DNA is limited by a low fetal DNA fraction. Both modalities...

Data from: Shaking the Diptera tree of life: performance analysis of nuclear and mitochondrial sequence data partitions

Jason Caravas & Markus Friedrich
The value of mitochondrial versus nuclear gene sequence data in phylogenetic analysis has received much attention without yielding definitive conclusions. Theoretical arguments and empirical data suggest a lower phylogenetic utility than equivalent nuclear gene sequences, but there are many examples of important progress made using mitochondrial sequences. We undertook a systematic performance analysis of mitochondrial and nuclear sequence partitions taken from a representative sample of dipteran species. When analysed alone, mitochondrial genes generally performed less...

Data from: Mode and tempo of sequence and floral evolution within the Anserineae

James A. Naeger & Edward M. Golenberg
The Chenopodiaceae Tribe Anserineae Dumort was proposed to include the genus Spinacia and the genus Blitum. In addition to the recent domestication of Spinacia, the tribe demonstrates extensive evolution within its floral development. We test whether the development of dioecy, monoecy, and protogyny is reflected differentially among floral developmental versus non-floral developmental genes, and whether recent domestication leaves traces in the phylogenetic relationship within the genus Spinacia. The phylogenetic predictions consistently support the sister relationship...

Trade-off between fecundity and survival generates stabilizing selection on gall size

Scott Egan, Amanda Weaver, Glen Hood & Michael Foster
Complex interactions within multi-trophic communities are fundamental to the evolution of individual species that reside within them. One common outcome of species interactions are fitness trade-offs, where traits adaptive in some circumstances are maladaptive in others. Here, we identify a fitness trade-off between fecundity and survival in the cynipid wasp Callirhytis quercusbatatoides that induces multi-chambered galls on the stem of its host plant Quercus virginiana. We first quantified this trade-off in natural populations by documenting...

Testing the potential contribution of Wolbachia to speciation when cytoplasmic incompatibility becomes associated with host‐related reproductive isolation

Daniel Bruzzese, Hannes Schuler, Thomas Wolfe, Mary Glover, Joseph Mastroni, Meredith Doellman, Cheyenne Tait, Wee Yee, Juan Rull, Martin Aluja, Glen Hood, Robert Goughnour, Christian Stauffer, Patrik Nosil, Jeffery Feder, Daniel J. Bruzzese, Thomas M. Wolfe, Mary M. Glover, Meredith M. Doellman, Wee L. Yee, Glen R. Hood & Jeffery L. Feder
Endosymbiont induced cytoplasmic incompatibility (CI) may play an important role in arthropod speciation. However, whether CI consistently becomes associated or coupled with other host-related forms of reproductive isolation (RI) to impede the transfer of endosymbionts between hybridizing populations and further the divergence process remains an open question. Here, we show varying degrees of pre- and post-mating RI exist among allopatric populations of two interbreeding cherry-infesting tephritid fruit flies (Rhagoletis cingulata and R. indifferens) across North...

The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts

Patric Vaelli, Kevin Theis, Janet Williams, James Foster, Lauren O'Connell & Heather Eisthen
Rough-skinned newts (Taricha granulosa) use tetrodotoxin (TTX) to block voltage-gated sodium (Nav) channels as a chemical defense against predation. Interestingly, newts exhibit extreme population-level variation in toxicity attributed to a coevolutionary arms race with TTX-resistant predatory snakes, but the source of TTX in newts is unknown. Here, we investigated whether symbiotic bacteria isolated from toxic newts could produce TTX. We characterized the skin-associated microbiota from a toxic and non-toxic population of newts and established pure...

Concordant patterns of morphological, stable isotope, and genetic variation in a recent ecological radiation (Salmonidae:Coregonus spp.)

Moisés Bernal, Daniel Yule, Wendylee Stott, Lori Evrard, Thomas Dowling & Trevor Krabbenhoft
Groups of sympatric taxa with low inter-specific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes (Coregonus spp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within the Coregonus artedi complex...

Data from: Vaginal host immune-microbiome interactions in a cohort of primarily African-American women who ultimately underwent spontaneous preterm birth or delivered at term

Violetta Florova & Nardhy Gomez-Lopez
Background: Recent studies suggest that alterations in the vaginal microbiome allow for the assessment of the risk for spontaneous preterm birth (PTB), the leading cause of neonatal morbidity and mortality worldwide. However, the associations between the local immune response and the vaginal microbiome are still poorly understood. Herein, we characterize the vaginal host immune-microbiome interactions in women who ultimately underwent PTB and in those who delivered at term. Methods: Vaginal fluid samples from 52 pregnant...

Asymmetric, but opposing reductions in immigrant viability and fecundity promote reproductive isolation among host-associated populations of an insect herbivore

Linyi Zhang, Glen Hood, Amy Roush, Shihan Shzu, Mattheau Comerford, James Ott & Scott Egan
Immigrant inviability can contribute to reproductive isolation (RI) during ecological speciation by reducing the survival of immigrants in non-native environments. However, studies that assess the fitness consequence of immigrants moving from native to non-native environments typically fail to explore the potential role of concomitant reductions in immigrant fecundity despite recent evidence suggesting its prominent role during local adaptation. Here, we evaluate the directionality and magnitude of both immigrant viability and fecundity to RI in a...

Data from: String phase in an artificial spin ice

Xiaoyu Zhang, Ayhan Duzgun, Yuyang Lao, Shayaan Subzwari, Nicholas Bingham, Joseph Sklenar, Hilal Saglam, Justin Ramberger, Joseph Batley, Justin Watts, Daniel Bromley, Rajesh Chopdekar, Liam O'Brien, Chris Leighton, Cristiano Nisoli & Peter Schiffer
The appearance of one-dimensional strings of local excitations represents an interesting feature of the physical behavior of strongly correlated topological quantum matter. Here we demonstrate that strings of local excitations can also describe the physics of a classical thermal system of interacting nanomagnets, the Santa Fe Ice geometry of artificial spin ice. We measure the moment configuration of the nanomagnets, both after annealing near the ferromagnetic Curie point and in a thermally dynamic state. While...

Genomic evidence for correlated trait combinations and antagonistic selection contributing to counterintuitive genetic patterns of adaptive diapause divergence in Rhagoletis flies

McCall Calvert, Meredith Doellman, Jeffrey Feder, Glenn Hood, Peter Meyers, Scott Egan, Thomas Powell, Mary Glover, Cheyenne Tait, Hannes Schuler, Stewart Berlocher, James Smith, Patrik Nosil, Dan Hahn & Gregory Ragland
Adaptation to novel environments often results in unanticipated genomic responses to selection. Here, we illustrate how multifarious, correlational selection helps explain a counterintuitive pattern of genetic divergence between the recently derived apple- and ancestral hawthorn-infesting host races of Rhagoletis pomonella (Diptera: Tephritidae). The Apple host race terminate diapause and emerge as adults earlier in the season than the hawthorn host race to coincide with the earlier fruiting phenology of their apple hosts. However, alleles at...

Entropy driven order in an array of nanomagnets

Hilal Saglam, Ayhan Duzgun, Aikaterini Kargioti, Nikhil Harle, Xiaoyu Zhang, Nicholas Bingham, Yuyang Lao, Ian Gilbert, Joseph Sklenar, Justin Watts, Justin Ramberger, Daniel Bromley, Rajesh Chopdekar, Liam O’Brien, Chris Leighton, Cristiano Nisoli & Peter Schiffer
Long-range ordering, while typically understood as a decrease in entropy, can also be driven by increasing system entropy in certain special cases. We demonstrate that artificial spin ice arrays of single-domain nanomagnets can be designed to produce entropy-driven order. We probe thermally active tetris artificial spin ice, known to have a zero point Pauli entropy, both experimentally and through simulations. We find two-dimensional magnetic ordering in one subset of the nanomagnet moments, which we demonstrate...

Data from: The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves

Ilana Janowitz Koch, Michelle M. Creek, Michael J. Thompson, Kerry A. Deere-Machemer, Jun Wang, Lionel Duarte, Gitanjali E. Gnanadesikan, Eskender L. McCoy, Liudmilla Rubbi, Daniel R. Stahler, Matteo Pellegrini, Elaine A. Ostrander, Robert K. Wayne, Janet S. Sinsheimer, Bridgett M. VonHoldt & Michelle M. Clark
The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified...

Data from: Impacts of dispersal on rapid adaptation and dynamic stability of Daphnia in fluctuating environments

Christopher F. Steiner, Richard D. Stockwell, Monica Tadros, Laith Shaman, Komal Patel & Laila Khraizat
Prior ecological research has shown that spatial processes can enhance the temporal stability of populations in fluctuating environments. Less explored is the effect of dispersal on rapid adaptation and its concomitant impact on population dynamics. For asexually reproducing populations, theory predicts that dispersal in fluctuating environments can facilitate asynchrony among clones and enhance stability by reducing temporal variability of total population abundance. This effect is predicted when clones exhibit heritable variation in environmental optima and...

Data from: Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries

Morris Goodman, Kirstin N. Sterner, M. Munirul Islam, Monica Uddin, Chet C. Sherwood, Patrick R. Hof, Zhuo-Cheng Hou, Leonard Lipovich, Hui Jia, Lawrence I. Grossman, Derek E. Wildman, M. Islam & Z. C. Hou
Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains...

Data from: Influence of introgression and geological processes on phylogenetic relationships of western North American mountain suckers (Pantosteus, Catostomidae)

Peter J. Unmack, Thomas E. Dowling, Nina J. Laitinen, Carol L. Secor, Richard L. Mayden, Dennis K. Shiozawa & Gerald R. Smith
Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western...

Data from: Evolution of longevity improves immunity in Drosophila

Daniel K. Fabian, Kathrin Garschall, Peter Klepsatel, Gonçalo Santos-Matos, Élio Sucena, Martin Kapun, Bruno Lemaitre, Robert Arking, Christian Schloetterer & Thomas Flatt
Much has been learned about the genetics of aging from studies in model organisms, but still little is known about naturally occurring alleles that contribute to variation in longevity. For example, analysis of mutants and transgenes has identified insulin signaling as a major regulator of longevity, yet whether standing variation in this pathway underlies microevolutionary changes in lifespan and correlated fitness traits remains largely unclear. Here we have analyzed the genomes of a set of...

Data from: Coevolution drives the emergence of complex traits and promotes evolvability

Luis Zaman, Justin R. Meyer, Suhas Devangam, David M. Bryson, Richard E. Lenski & Charles Ofria
The evolution of complex organismal traits is obvious as a historical fact, but the underlying causes—including the role of natural selection—are contested. Gould argued that a random walk from a necessarily simple beginning would produce the appearance of increasing complexity over time. Others contend that selection, including coevolutionary arms races, can systematically push organisms toward more complex traits. Methodological challenges have largely precluded experimental tests of these hypotheses. Using the Avida platform for digital evolution,...

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