128 Works

Troubled waters: Water availability drives human-baboon encounters in a protected, semi-arid landscape

Elise N. Paietta, Chelsea J. Weibel, David A. Jansen, Raphael S. Mututua, J. Kinyua Warutere, I. Long'ida Siodi, Laurence R. Gesquiere, Vincent Obanda, Susan C. Alberts & Elizabeth A. Archie
Most animal habitats are affected by humans. While some species tolerate and even benefit from these changes, others suffer. Understanding when and how human-altered landscapes affect animal behavior, health, reproduction, and survival is essential to species management in a human-dominated world. Here we use 27 years of data on human-baboon encounters in a protected, semi-arid ecosystem in Kenya to: (i) identify spatial, environmental, and group-level predictors of baboon encounters with pastoralists; (ii) test whether human-built...

Data from: Metabolites from the fungal pathogen Batrachochytrium dendrobatidis (Bd) reduce Bd load in Cuban treefrog tadpoles

Caitlin Nordheim, Sarah Detmering, David Civitello, Pieter TJ Johnson, Jason Rohr & Taegan McMahon
Batrachochytrium dendrobatidis (Bd) has been associated with massive amphibian population declines worldwide. Wildlife vaccination campaigns have proven effective for mitigating damage from other pathogens, and there is evidence that adult frogs can acquire resistance to Bd when exposed to killed Bd zoospores and the metabolites they produced. Here, we investigated whether Cuban treefrogs tadpoles (Osteopilus septentrionalis) can gain protection from Bd through exposure to a prophylaxis treatment composed of killed zoospores or soluble Bd metabolites....

Data from: A field test for host fruit odour discrimination and avoidance behaviour for Rhagoletis pomonella flies in the western United States

Sheina B. Sim, Monte Mattsson, Jasmine L. Feder, Dong H. Cha, Wee L. Yee, Robert B. Goughnour, Charles E. Linn & Jeffrey L. Feder
Prezygotic isolation due to habitat choice is important to many models of speciation-with-gene-flow. Habitat choice is usually thought to occur through positive preferences of organisms for particular environments. However, avoidance of non-natal environments may also play a role in choice and have repercussions for postzygotic isolation that preference does not. The recent host shift of Rhagoletis pomonella (Diptera: Tephritidae) from downy hawthorn, Crataegus mollis, to introduced apple, Malus domestica, in the eastern U.S. is a...

Data from: Postglacial climate changes and rise of three ecotypes of harbor porpoises, Phocoena phocoena, in western Palearctic waters

Michaël C. Fontaine, Kathleen Roland, Isabelle Calves, Frederic Austerlitz, Friso P. Palstra, Krystal A. Tolley, Sean Ryan, Marisa Ferreira, Thierry Jauniaux, Angela Llavona, Bayram Öztürk, Ayaka A. Öztürk, Vincent Ridoux, Emer Rogan, Ursula Siebert, Marina Sequeira, Gísli A. Vikingsson, Asunción Borrell, Johan R. Michaux & Alex Aguilar
Despite no obvious barriers to gene flow in the marine realm, environmental variation and ecological specializations can lead to genetic differentiation in highly mobile predators. Here, we investigated the genetic structure of the harbor porpoise over the entire species distribution range in western Palearctic waters. Combined analyses of ten microsatellite loci and a 5,085 bases-pairs portion of the mitochondrial genome revealed the existence of three ecotypes, equally divergent at the mitochondrial genome, distributed in the...

Data from: Extensive introgression in a malaria vector species complex revealed by phylogenomics

Michael C. Fontaine, James B. Pease, Aaron Steele, Robert M. Waterhouse, Daniel E. Neafsey, Igor V. Sharakhov, Xiofang Jiang, Andrew B. Hall, Flaminia Catteruccia, Evdoxia Kakani, Sarah N. Mitchell, Yi-Chieh Wu, Hilary A. Smith, R. Rebecca Love, Mara K. Lawniczak, Michel A. Slotman, Scott J. Emrich, Matthew W. Hahn & Nora J. Besansky
Introgressive hybridization is now recognized as a widespread phenomenon, but its role in evolution remains contested. Here we use newly available reference genome assemblies to investigate phylogenetic relationships and introgression in a medically important group of Afrotropical mosquito sibling species. We have identified the correct species branching order to resolve a contentious phylogeny, and show that lineages leading to the principal vectors of human malaria were among the first to split. Pervasive autosomal introgression between...

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: 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: 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: The making of a pest: insights from the evolution of chemosensory receptor families in a pestiferous and invasive fly, Drosophila suzukii

Paul V. Hickner, Chissa L. Rivaldi, Cole M. Johnson, Madhura Siddappaji, Gregory J. Raster & Zainulabeuddin Syed
Background: Drosophila suzukii differs from other melanogaster group members in their proclivity for laying eggs in fresh fruit rather than in fermenting fruits. Olfaction and gustation play a critical role during insect niche formation, and these senses are largely mediated by two important receptor families: olfactory and gustatory receptors (Ors and Grs). Earlier work from our laboratory has revealed how the olfactory landscape of D. suzukii is dominated by volatiles derived from its unique niche....

Data from: Suitability of Laurentian Great Lakes for invasive species based on global species distribution models and local habitat

Andrew M. Kramer, Gust Annis, Marion E. Wittmann, William L. Chadderton, Edward S. Rutherford, David M. Lodge, Lacey Mason, Dmitry Beletsky, Catherine Riseng & John M. Drake
Efficient management and prevention of species invasions requires accurate prediction of where species of concern can arrive and persist. Species distribution models provide one way to identify potentially suitable habitat by developing the relationship between climate variables and species occurrence data. However, these models when applied to freshwater invasions are complicated by two factors. The first is that the range expansions that typically occur as part of the invasion process violate standard species distribution model...

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...

Data from: Divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression

Peter J. Meyers, Thomas H. Q. Powell, Kimberly K. O. Walden, Adam Shieferecke, Jeffrey L. Feder, Daniel A. Hahn, Hugh M. Robertson, Stewart H. Berlocher & Gregory J. Ragland
Duration of dormancy regulates seasonal timing in many organisms and may be modulated by day length and temperature. Though photoperiodic modulation has been well studied, temperature modulation of dormancy has received less attention. Here, we leverage genetic variation in diapause in the apple maggot fly, Rhagoletis pomonella, to test whether gene expression during winter or following spring warming regulates diapause duration. We used RNAseq to compare transcript abundance during and after simulated winter between an...

Data from: Multilocus approaches for the measurement of selection on correlated genetic loci

Zachariah Gompert, Scott P. Egan, Rowan D. H. Barrett, Jeffrey L. Feder & Patrik Nosil
The study of ecological speciation is inherently linked to the study of selection. Methods for estimating phenotypic selection within a generation based on associations between trait values and fitness (e.g. survival) of individuals are established. These methods attempt to disentangle selection acting directly on a trait from indirect selection caused by correlations with other traits via multivariate statistical approaches (i.e. inference of selection gradients). The estimation of selection on genotypic or genomic variation could also...

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: Climate-mediated hybrid zone movement revealed with genomics, museum collection and simulation modeling

Sean F. Ryan, Jillian M. Deines, J. Mark Scriber, Michael E. Pfrender, Stuart E. Jones, Scott J. Emrich & Jessica J. Hellmann
Climate-mediated changes in hybridization will dramatically alter the genetic diversity, adaptive capacity and evolutionary trajectory of interbreeding species. Our ability to predict the consequences of such changes will be key to future conservation and management decisions. Here we tested through simulations how recent warming (over a 32-year period) is affecting the geographic extent of a climate-mediated developmental threshold implicated in maintaining a butterfly hybrid zone (Papilio glaucus and Papilio canadensis; Lepidoptera: Papilionidae). These simulations predict...

Data from: Habitat explains patterns of population decline for an invasive crayfish

Eric R. Larson, Timothy A. Kreps, Brett Peters, Jody A. Peters & David M. Lodge
Invasive non-indigenous species are defined by their impacts: they substantially change native communities or ecosystems. Accordingly, invasive species might transform their habitats in ways that eventually become unfavorable to them, causing population declines or even extirpations. Here we use over 40 years of systematically collected data on the abundance of the invasive rusty crayfish Faxonius rusticus from 17 lakes in northern Wisconsin, USA to explore if population declines of this invader are related to the...

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: 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: Divergent diapause life history timing drives both allochronic speciation and reticulate hybridization in an adaptive radiation of Rhagoletis flies

Meredith Doellman, Katherine Inskeep, Thomas Powell, Stewart Berlocher, Nicholas Seifert, Glen Hood, Gregory Ragland, Peter Meyers & Jeff Feder
Divergent adaptation to new ecological opportunities can be an important factor initiating speciation. However, as niches are filled during adaptive radiations, trait divergence driving reproductive isolation between sister taxa may also result in trait convergence with more distantly related taxa, increasing the potential for reticulated gene flow across the radiation. Here, we demonstrate such a scenario in a recent adaptive radiation of Rhagoletis fruit flies, specialized on different host plants. Throughout this radiation, shifts to...

Social media and public perception as core aspect of public health: the cautionary case of @realdonaldtrump and COVID-19

Jeffrey Peterson & Agustin Fuentes
The social media milieu in which we are enmeshed has substantive impacts on our beliefs and perceptions. Recent work has established that this can play a role in influencing understanding of, and reactions to, public health information. Twitter, in particular, appears to play a substantive role in the public health information ecosystem. From July 25th, 2020 to November 15th, 2020, we collected weekly tweets related to COVID-19 keywords and assessed their networks, patterns and properties....

Circum-Arctic distribution of chemical anti-herbivore compounds arctic shrubs

Elin Lindén, Mariska Te Beest, Ilka Abreu, Thomas Moritz, Maja Sundqvist, Isabel C Barrio, Julia Boike, John Bryant, Kari Anne Bråthen, Agata Buchwal, Guillermo Bueno, Alain Cuerrier, Dagmar Egelkraut, Bruce Forbes, Martin Hallinger, Monique Heijmans, Luise Hermanutz, David S Hik, Annika Hofgaard, Milena Holmgren, Diane C Huebner, Toke Hoye, Ingibjörg Jónsdóttir, Elina Kaarlejärvi, Emilie Kissler … & Johan Olofsson
Spatial variation in plant chemical defence towards herbivores can help us understand variation in herbivore top-down control of shrubs in the Arctic and possibly also shrub responses to global warming. Less defended, non-resinous shrubs could be more influenced by herbivores than more defended, resinous shrubs. However, sparse field measurements limit our current understanding of how much of the circum-Arctic variation in defence compounds is explained by taxa or defence functional groups (resinous/non-resinous). We measured circum-Arctic...

Pyrite oxidation under carbonate buffer and its environmental implications: a case study from the Shangmanggang gold deposit, southwest China

Yanyan Wang, Xuemin Liu & Qi Li
Supplement 2

Pyrite oxidation under carbonate buffer and its environmental implications: a case study from the Shangmanggang gold deposit, southwest China

Yanyan Wang, Xuemin Liu & Qi Li
Supplement 2

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...

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