97 Works

Data from: Range-wide distribution of genetic diversity in the North American tree Juglans cinerea: a product of range shifts, not ecological marginality or recent population decline

Sean M Hoban, Daniel S Borkowski, Sunshine L Brosi, Tim S McCleary, Laura M Thompson, Jason S McLachlan, Marie A Pereira, Scott E Schlarbaum & Jeanne Romero-Severson
The spatial distribution of genetic diversity is a product of recent and historical ecological processes, as well as anthropogenic activities. A current challenge in population and conservation genetics is to disentangle the relative effects of these processes, as a first step in predicting population response to future environmental change. In this investigation we compare the influence of contemporary population decline, contemporary ecological marginality, and postglacial range shifts. Using classical model comparison procedures and Bayesian methods,...

Data from: Behavioral evidence for fruit odor discrimination and sympatric host races of Rhagoletis pomonella flies in the western United States

Charles E. Linn, Wee L. Yee, Sheina B. Sim, Dong H. Cha, Thomas Powell, Robert B. Goughnour & Jeffrey L. Feder
The recent shift of Rhagoletis pomonella (Diptera: Tephritidae) from its native host downy hawthorn, Crataegus mollis, to introduced domesticated apple, Malus domestica, in the eastern U.S. is a model for sympatric host race formation. However, the fly is also present in the western U.S., where it may have been introduced via infested apples within the last 60 years. In addition to apple, R. pomonella also infests two hawthorns in the West, one the native black...

Data from: Genetic divergence along the speciation continuum: the transition from host race to species in Rhagoletis (Diptera: Tephritdae)

Thomas H. Q. Powell, Glen R. Hood, Mason O. Murphy, Jeffrey S. Heilveil, Stewart H. Berlocher, Partrik Nosil, Jeffrey L. Feder & Patrik Nosil
Studies of related populations varying in their degrees of reproductive isolation can provide insights into speciation. Here, the transition from partially isolated host races to more fully separated sibling species is investigated by comparing patterns of genetic differentiation between recently evolved (∼150 generations) apple and ancestral hawthorn-infesting populations of Rhagoletis pomonella to their sister taxon, the undescribed flowering dogwood fly attacking Cornus florida. No fixed or diagnostic private alleles differentiating the three populations were found...

Data from: Mate choice strategies in a spatially-explicit model environment

Giordano B.S. Ferreira, Matthias Scheutz, Sunny K. Boyd & Giordano B. S. Ferreira
Decisions about the choice of a mate can greatly impact both individual fitness and selection processes. We developed a novel agent-based model to investigate two common mate choice rules that may be used by female gray treefrogs (Hyla versicolor). In this model environment, female agents using the minimum-threshold strategy found higher quality mates and traveled shorter distances on average, compared with female agents using the best-of-n strategy. Females using the minimum-threshold strategy, however, incur significant...

Elucidating mechanisms of invasion success: effects of parasite removal on growth and survival rates of invasive and native frogs

Elizabeth Roznik, Kerri Surbaugh, Natalia Cano & Jason Rohr
1. Identifying the mechanisms underlying biological invasions can inform the management of invasive species. The enemy release hypothesis (ERH) suggests that invasive species have a competitive advantage in their introduced range because they leave behind many of their predators and parasites from their native range, allowing them to shift resources from defenses to growth, reproduction, and dispersal. Many studies have demonstrated that invasive species have fewer parasites than their native counterparts, but few studies have...

Data from: Quantification of mesocosm fish and amphibian species diversity via eDNA metabarcoding

Nathan T. Evans, Brett P. Olds, Cameron R. Turner, Mark A. Renshaw, Yiyuan Li, Christopher L. Jerde, Andrew R. Mahon, Michael E. Pfrender, Gary A. Lamberti & David M. Lodge
Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis...

Data from: Interbirth intervals in wild baboons: environmental predictors and hormonal correlates

Laurence R. Gesquiere, Jeanne Altmann, Elizabeth A. Archie & Susan C. Alberts
Objectives: Interbirth intervals (IBIs) are a key metric of female reproductive success; understanding how they are regulated by environmental, social, and demographic factors can provide insight into sources of variance in female fitness. Materials and Methods: Using 36 years of reproductive data on 490 IBIs for 160 wild female baboons, we identified sources of variance in the duration of IBIs and of their component phases: postpartum amenorrhea (PPA), sexual cycling, and pregnancy. We also examined...

Data from: Costs of reproduction in a long-lived female primate: injury risk and wound healing

Elizabeth A. Archie, Jeanne Altmann & Susan C. Alberts
Reproduction is a notoriously costly phase of life, exposing individuals to injury, infectious disease, and energetic tradeoffs. The strength of these costs should be influenced by life history strategies, and in long-lived species, females may be selected to mitigate costs of reproduction because life span is such an important component of their reproductive success. Here we report evidence for two costs of reproduction that may influence survival in wild female baboons— injury risk and delayed...

Data from: The hitchhiker's guide to Europe: the infection dynamics of an ongoing Wolbachia invasion and mitochondrial selective sweep in Rhagoletis cerasi

Hannes Schuler, Kirsten Koeppler, Sabine Daxböck-Horvath, Bilal Rasool, Susanne Krumboeck, Dietmar Schwarz, Thomas Hoffmeister, Birgit Schlick-Steiner, Florian Steiner, Arndt Telschow, Christian Stauffer, Wolfgang Arthofer, Markus Riegler, Birgit C. Schlick-Steiner, Florian M. Steiner & Thomas S. Hoffmeister
Wolbachia is a maternally inherited and ubiquitous endosymbiont of insects. It can hijack host reproduction by manipulations such as cytoplasmic incompatibility (CI) to enhance vertical transmission. Horizontal transmission of Wolbachia can also result in the colonization of new mitochondrial lineages. In this study, we present a 15-year-long survey of Wolbachia in the cherry fruit fly Rhagoletis cerasi across Europe and the spatiotemporal distribution of two prevalent strains, wCer1 and wCer2, and associated mitochondrial haplotypes in...

Data from: Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

Scott P. Egan, Gregory J. Ragland, Lauren Assour, Thomas H. Q. Powell, Glen R. Hood, Scott Emrich, Patrik Nosil, Jeffrey L. Feder & Thomas H.Q. Powell
Theory predicts that speciation-with-gene-flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome-wide impacts of host-associated selection between hawthorn and apple...

Data from: Conditional fetal and infant killing by male baboons

Matthew N. Zipple, Jackson H. Grady, Jacob B. Gordon, Lydia D. Chow, Elizabeth A. Archie, Jeanne Altmann & Susan C. Alberts
Sexually selected feticide—the death of infants in utero as a result of male behaviour—has only rarely been described or analysed, although it is presumed to be favoured by the same selective pressures that favour sexually selected infanticide. To test this hypothesis, we measured the frequency of feticide and infanticide by male baboons of the Amboseli basin in Kenya, and examined which characteristics of a male and his environment made him more likely to commit feticide...

Data from: Limited genetic evidence for host plant-related differentiation in the Western cherry fruit fly Rhagoletis indifferens (Diptera: Tephritidae)

Gilbert Saint Jean, Glen R. Hood, Scott P. Egan, Thomas H.Q. Powell, Hannes Schuler, Meredith M. Doellman, Mary M. Glover, James J. Smith, Wee L. Yee, Robert B. Goughnour, Howard M.A. Thistlewood, Sheri A. Maxwell, Nusha Keyghobadi, Juan Rull, Martin Aluja, Jeffrey L. Feder & Thomas H. Q. Powell
The shift of the fruit fly Rhagoletis pomonella (Walsh) in the mid-1800s from downy hawthorn, Crataegus mollis (Torrey & Asa Gray) Scheele, to introduced domesticated apple, Malus domestica (Borkhausen), in the eastern USA is a model for ecological divergence with gene flow. A similar system may exist in the northwestern USA and British Columbia, Canada, where Rhagoletis indifferens Curran (Diptera: Tephritidae) attacks the native bitter cherry Prunus emarginata (Douglas ex Hooker) Eaton (Rosaceae). Populations of...

Data from: Historical contingency in a multigene family facilitates adaptive evolution of toxin resistance

Joel McGlothlin, Megan Kobiela, Chris R. Feldman, Todd A. Castoe, Shana L. Geffeney, Charles T. Hanifin, Gabriela Toledo, Freek J. Vonk, Michael K. Richardson, , Michael Pfrender &
Novel adaptations must originate and function within an already established genome [ 1 ]. As a result, the ability of a species to adapt to new environmental challenges is predicted to be highly contingent on the evolutionary history of its lineage [ 2–6 ]. Despite a growing appreciation of the importance of historical contingency in the adaptive evolution of single proteins [ 7–11 ], we know surprisingly little about its role in shaping complex adaptations...

Data from: Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons

Elizabeth A. Miller, Joshua A. Livermore, Susan C. Alberts, Jenny Tung & Elizabeth A. Archie
Background: The vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend women against infectious disease. However, lactobacilli do not dominate the vaginal microbiota of any other mammal studied to date, raising key questions about the forces that shape the vaginal microbiome in non-human mammals. Results: We used Illumina sequencing of the bacterial 16S rRNA gene to investigate...

Key words related to public engagement with science by Society of Freshwater Science journals and conference sessions (1997-2019)

Ayesha S. Burdett, Katherine E. O’Reilly, Rebecca J. Bixby & Selena S. Connealy
Data set that was used to determine the frequency each of 4 key words (public engagement, education, outreach, or science communication) in the title or abstract of published papers in Freshwater Science (formerly the Journal of the North American Benthological Society) and oral presentations (talks) at the annual Society for Freshwater Science meetings from 1997 to 2019. Does not include any data on talks for 2013-2014 because they were not published during those years.

Indoor dust as a matrix for surveillance of COVID-19 outbreaks

Nicole Renninger, Nick Nastasi, Ashleigh Bope, Samuel Cochran, Sarah Haines, Neeraja Balasubrahmaniam, Katelyn Stuart, Aaron Bivins, Kyle Bibby, Natalie Hull & Karen Dannemiller
Ongoing disease surveillance is a critical tool to mitigate viral outbreaks, especially during a pandemic. Environmental monitoring has significant promise even following widespread vaccination among high-risk populations. The goal of this work is to demonstrate molecular SARS-CoV-2 monitoring in bulk floor dust and related samples as a proof-of-concept of a non-invasive environmental surveillance methodology for COVID-19 and potentially other viral diseases. Surface swab, passive sampler, and bulk floor dust samples were collected from rooms of...

Data from: Successional loss of two key food tree species best explains decline in group size of Panamanian howler monkeys (Alouatta palliata)

Katharine Milton, David W. Armitage & Wayne P. Sousa.
Negative impacts of discrete, short-term disturbances to wildlife populations are well-documented. The consequences of more gradual environmental change are less apparent and harder to study because they play out over longer periods and are often indirect in their action. Yet, they can drive the decline of wildlife populations even in seemingly pristine and currently well-protected habitats. One such environmental change is a successional shift in a community’s species composition as it regenerates from disturbance caused...

Understanding what women want: eliciting preference for delivery health facility in a rural sub-County in Kenya, a discrete choice experiment

Jackline Oluoch-Aridi, Mary Adam, Francis Wafula & Gilbert Kokwaro
Objective: To identify what women want in a delivery health facility and how they rank the attributes that influence the choice of a place of delivery. Design: A Discrete Choice Experiment was conducted to elicit rural women’s preferences for choice of delivery health facility. Data were analyzed using both a conditional logit model to evaluate relative importance of the selected attributes. A mixed multinomial model evaluated how interactions with sociodemographic variables influence the choice of...

Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis

Meredith M. Doellman, Peter J. Meyers, Gregory J. Ragland, Glen R. Hood, Scott P. Egan, Thomas H. Q. Powell, Patrik Nosil & Jeffrey L. Feder
Studies assessing the predictability of evolution typically focus on short-term adaptation within populations or the repeatability of change among lineages. A missing consideration in speciation research is to determine whether natural selection predictably transforms standing genetic variation within populations into differences between species. Here, we test whether host-related selection on diapause timing anticipates genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of Rhagoletis pomonella to their sibling species...

Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)

Meredith M. Doellman, Glen R. Hood, Jacob Gersfeld, Amanda Driscoe, Charles C.Y. Xu, Ryan N. Sheehy, Noah Holmes, Wee L. Yee & Jeffrey L. Feder
Insect pests destroy ~15% of all USA crops, resulting in losses of $15 billion annually. Thus, developing cheap, quick and reliable methods for detecting harmful species is critical to curtail insect damage and lessen economic impact. The apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), is a major invasive pest threatening the multibillion-dollar apple industry in the Pacific Northwest USA. The fly is also sympatric with a benign but morphologically similar and genetically closely related species,...

Data from: Social bonds do not mediate the relationship between early adversity and adult glucocorticoids in wild baboons

Stacy Rosenbaum, Shuxi Zeng, Fernando Campos, Laurence Gesquiere, Jeanne Altmann, Susan Alberts, Fan Li & Elizabeth Archie
In humans and other animals, harsh conditions in early life can have profound effects on adult physiology, including the stress response. This relationship may be mediated by a lack of supportive relationships in adulthood. That is, early life adversity may inhibit the formation of supportive social ties, and weak social support is itself often linked to dysregulated stress responses. Here we use prospective, longitudinal data from wild baboons in Kenya to test the links between...

Data from: Sequential divergence and the multiplicative origin of community diversity

Glen R. Hood, Andrew A. Forbes, Thomas H. Q. Powell, Scott P. Egan, Gabriela Hamerlinck, James J. Smith & Jeffrey L. Feder
Understanding how new life forms originate is a central question in biology. Population divergence is usually studied with respect to how single lineages diverge into daughter taxa. However, populations may not always differentiate in isolation; divergence of one taxon could create new niche opportunities in higher trophic levels, leading to the sequential origin of many new taxa. Here, we show that this may be occurring for three species of parasitoid wasps attacking Rhagoletis fruit flies....

Data from: Powerful methods for detecting introgressed regions from population genomic data

Benjamin K. Rosenzweig, James B. Pease, Nora J. Besansky & Matthew H. Hahn
Understanding the types and functions of genes that are able to cross species boundaries—and those that are not—is an important step in understanding the forces maintaining species as largely independent lineages across the remainder of the genome. With large next-generation sequencing data sets we are now able to ask whether introgression has occurred across the genome, and multiple methods have been proposed to detect the signature of such events. Here, we introduce a new summary...

Data from: Rapid and repeatable shifts in life-history timing of Rhagoletis pomonella (Diptera: Tephritidae) following colonization of novel host plants in the Pacific Northwestern United States

Monte Mattsson, Glen R. Hood, Jeffrey L. Feder & Luis A. Ruedas
Host shifts of phytophagous insect specialists to novel plants can result in divergent ecological adaptation, generating reproductive isolation and potentially new species. Rhagoletis pomonella fruit flies in eastern North America underwent a host shift ~160 ya from native downy hawthorn (Crataegus mollis) to introduced, domesticated apple (Malus domestica). Divergent selection on diapause phenology related to the earlier fruiting time of apples versus downy hawthorns resulted in partial allochronic reproductive isolation between the fly races. Here,...

Data from: Widespread position-specific conservation of synonymous rare codons within coding sequences

Julie L. Chaney, Aaron Steele, Rory Carmichael, Anabel Rodriguez, Alicia T. Specht, Kim Ngo, Jun Li, Scott J. Emrich, Patricia L. Clark & Scott Emrich
Synonymous rare codons are considered to be sub-optimal for gene expression because they are translated more slowly than common codons. Yet surprisingly, many protein coding sequences include large clusters of synonymous rare codons. Rare codons at the 5’ terminus of coding sequences have been shown to increase translational efficiency. Although a general functional role for synonymous rare codons farther within coding sequences has not yet been established, several recent reports have identified rare-to-common synonymous codon...

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