39 Works

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...

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...

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,...

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: 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: 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: 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: 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: 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...

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...

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: 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...

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

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...

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...

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...

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...

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: Leaf size in three generations of a dioecious tropical tree, Ocotea tenera (Lauraceae): sexual dimorphism and changes with age

Nathaniel T. Wheelwright, Jordan Sinclair, Cris Hochwender, Frederic Janzen, Fredric J. Janzen & Jordan P. Sinclair
PREMISE OF THE STUDY: In dioecious species, selection should favor different leaf sizes in males and females whenever the sexes experience distinct environments or constraints, such as different costs of reproduction. We took advantage of a long-term experimental study of Ocotea tenera (Lauraceae), a dioecious understory tree in Monteverde, Costa Rica, to explore leaf size differences between genders and age classes across generations. METHODS: We measured leaf size in adult trees in a natural population,...

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,...

Data from: Characterization of breast tumors using diffusion kurtosis imaging (DKI)

Dongmei Wu, Guanwu Li, Junxiang Zhang, Shixing Chang, Jiani Hu & Yongming Dai
Aim: The aim of this study was to investigate and evaluate the role of magnetic resonance (MR) diffusion kurtosis imaging (DKI) in characterizing breast lesions. Materials and Methods: One hundred and twenty-four lesions in 103 patients (mean age: 57±14 years) were evaluated by MR DKI performed with 7 b-values of 0, 250, 500, 750, 1,000, 1,500, 2,000 s/mm2 and dynamic contrast-enhanced (DCE) MR imaging. Breast lesions were histologically characterized and DKI related parameters—mean diffusivity (MD)...

Data from: Interactive effects of productivity and predation on zooplankton diversity

Mitra Asgari & Christopher F. Steiner
Recent studies suggest the necessity of understanding the interactive effects of predation and productivity on species coexistence and prey diversity. Models predict that coexistence of prey species with different competitive abilities can be achieved if inferior resource competitors are less susceptible to predation and if productivity and/or predation pressure are at intermediate levels. Hence, predator effects on prey diversity are predicted to be highly context dependent: enhancing diversity from low to intermediate levels of productivity...

Data from: Trophoblast survival signaling during human placentation requires HSP70 activation of MMP2-mediated HBEGF shedding

Chandni V. Jain, Philip Jessmon, Charbel T. Barrak, Alan D. Bolnick, Brian A. Kilburn, Michael Hertz & D. Randall Armant
Survival of trophoblast cells in the low oxygen environment of human placentation requires metalloproteinase-mediated shedding of HBEGF and downstream signaling. A matrix metalloproteinase (MMP) antibody array and quantitative RT-PCR revealed upregulation of MMP2 post-transcriptionally in human first trimester HTR-8/SVneo trophoblast cells and placental villous explants exposed to 2% O2. Specific MMP inhibitors established the requirement for MMP2 in HBEGF shedding and upregulation. Because α-amanitin inhibited the upregulation of HBEGF, differentially expressed genes were identified by...

Data from: A robust and tunable mitotic oscillator in artificial cells

Ye Guan, Zhengda Li, Shiyuan Wang, Patrick M Barnes, Xuwen Liu, Haotian Xu, Minjun Jin, Allen P Liu & Qiong Yang
Single-cell analysis is pivotal to deciphering complex phenomena like heterogeneity, bistability, and asynchronous oscillations, where a population ensemble cannot represent individual behaviors. Bulk cell-free systems, despite having unique advantages of manipulation and characterization of biochemical networks, lack the essential single-cell information to understand a class of out-of-steady-state dynamics including cell cycles. Here, by encapsulating Xenopus egg extracts in water-in-oil microemulsions, we developed artificial cells that are adjustable in sizes and periods, sustain mitotic oscillations for...

Temporal isolation between sympatric host plants cascades across multiple trophic levels of host-associated insects

Linyi Zhang, Glen Hood, James Ott & Scott Egan
Phenological differences between host plants can promote temporal isolation among host-associated populations of insects with life cycles tightly coupled to plant phenology. Divergence in the timing of spring budbreak between two sympatric sister oak species has been shown to promote temporal isolation between host plants and their host-associated populations of a cynipid gall wasp. Here we examined the generality of this mechanism by testing the hypothesis of cascading temporal isolation for five additional gall-formers and...

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