54 Works

Data from: Environmental context and contaminant biotransport by Pacific salmon interact to mediate the bioaccumulation of contaminants by stream-resident fish

Brandon S. Gerig, Dominic T. Chaloner, David J. Janetski, Ashley H. Moerke, Richard R. Rediske, James P. O'Keefe, Dilkushi A. De Alwis Pitts & Gary A. Lamberti
1.The extent to which environmental context mediates the bioaccumulation of biotransported contaminants by stream-resident organisms is poorly understood. For example, it is unclear the extent to which contaminant type, instream characteristics, or resident fish identity interact to influence the uptake of contaminants deposited by Pacific salmon (Oncorhynchus spp.) during their spawning runs. 2.To address this uncertainty, we sampled four stream-resident fish species from 13 watersheds of the Laurentian Great Lakes in locations with and without...

Data from: A century of genetic variation inferred from a persistent soil-stored seed bank

Jennifer L. Summers, Brittany Bernik, Colin J. Saunders, Jason S. McLachlan & Michael J. Blum
Stratigraphic accretion of dormant propagules in soil can result in natural archives useful for studying ecological and evolutionary responses to environmental change. Few attempts have been made, however, to use soil-stored seed banks as natural archives, in part because of concerns over non-random attrition and mixed stratification. Here we examine the persistent seed bank of Schoenoplectus americanus, a foundational brackish marsh sedge, to determine whether it can serve as a resource for reconstructing historical records...

Data from: Adaptive periodicity in the infectivity of malaria gametocytes to mosquitoes

Petra Schneider, Samuel S.C. Rund, Natasha L. Smith, Kimberley F. Prior, Aidan J. O'Donnell, Sarah E. Reece & Samuel S. C. Rund
Daily rhythms in behaviour, physiology, and molecular processes are expected to enable organisms to appropriately schedule activities according to consequences of the daily rotation of the Earth. For parasites, this includes capitalizing on periodicity in transmission opportunities and for hosts/vectors, this may select for rhythms in immune defence. We examine rhythms in the density and infectivity of transmission forms (gametocytes) of rodent malaria parasites in the host’s blood, parasite development inside mosquito vectors, and potential...

Data from: Group living and male dispersal predict the core gut microbiome in wild baboons

Laura E. Grieneisen, Josh Livermore, Susan Alberts, Jenny Tung & Elizabeth A. Archie
The mammalian gut microbiome plays a profound role in the physiology, metabolism, and overall health of its host. However, biologists have only a nascent understanding of the forces that drive inter-individual heterogeneity in gut microbial composition, especially the role of host social environment. Here we used 178 samples from 78 wild yellow baboons (Papio cynocephalus) living in two social groups to test how host social context, including group living, social interactions within groups, and transfer...

Data from: Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing

R. Rebecca Love, Aaron M. Steele, Mamadou B. Coulibaly, Sekou F. Traore, Scott J. Emrich, Michaël C. Fontaine & Nora J. Besansky
The molecular mechanisms and genetic architecture that facilitate adaptive radiation of lineages remain elusive. Polymorphic chromosomal inversions, due to their recombination-reducing effect, are proposed instruments of ecotypic differentiation. Here we study an ecologically diversifying lineage of An. gambiae, known as the Bamako chromosomal form based on its unique complement of three chromosomal inversions, to explore the impact of these inversions on ecotypic differentiation. We used pooled and individual genome sequencing of Bamako, typical (non-Bamako) An....

Data from: Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae)

Vid Bakovic, Hannes Schuler, Martin Schebeck, Jeffrey L. Feder, Christian Stauffer & Gregory J. Ragland
Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for...

Social bonds, social status, and survival in wild baboons: A tale of two sexes

Fernando Campos, Francisco Villavicencio, Elizabeth Archie, Fernando Colchero & Susan Alberts
People who are more socially integrated or have higher socioeconomic status live longer. Recent studies in nonhuman primates show striking convergences with this human pattern: female primates with more social partners, stronger social bonds, or higher dominance rank all lead longer lives. However, it remains unclear whether social environments also predict survival in male nonhuman primates, as it does in men. This gap persists because, in most primates, males disperse among social groups, resulting in...

Data from: Reconstruction of genetically identified neurons imaged by serial-section electron microscopy

Maximilian Joesch, David Mankus, Masahito Yamagata, Ali Shahbazi, Richard Shalek, Adi Suissa-Peleg, Markus Meister, Jeff W. Lichtman, Walter J. Scheirer, Joshua R. Sanes, Walter J Scheirer, Richard Schalek, Jeff W Lichtman & Joshua R Sanes
Resolving patterns of synaptic connectivity in neural circuits currently requires serial section electron microscopy. However, complete circuit reconstruction is prohibitively slow and may not be necessary for many purposes such as comparing neuronal structure and connectivity among multiple animals. Here, we present an alternative strategy, targeted reconstruction of specific neuronal types. We used viral vectors to deliver peroxidase derivatives, which catalyze production of an electron-dense tracer, to genetically identified neurons, and developed a protocol that...

Data from: Rates of genomic divergence in humans, chimpanzees and their lice

Kevin P. Johnson, Julie M. Allen, Brett P. Olds, Lawrence Mugisha, David L. Reed, Ken N. Paige, Barry R. Pittendrigh, B. P. Olds, J. M. Allen, K. N. Paige, D. L. Reed & L. Mugisha
The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their...

Data from: Theoretical models of the influence of genomic architecture on the dynamics of speciation

Samuel M. Flaxman, Aaron C. Wacholder, Jeffrey L. Feder & Patrik Nosil
A long-standing problem in evolutionary biology has been determining whether and how gradual, incremental changes at the gene level can account for rapid speciation and bursts of adaptive radiation. Using genome-scale computer simulations, we extend previous theory showing how gradual adaptive change can generate nonlinear population transitions, resulting in the rapid formation of new, reproductively isolated species. We show that these transitions occur via a mechanism rooted in a basic property of biological heredity: the...

Data from: Social networks predict gut microbiome composition in wild baboons

Jenny Tung, Luis B. Barriero, Michael B. Burns, J. C. Grenier, Josh Lynch, L. E. Grieneisen, J. Altmann, S. C. Alberts, R. Blekhman, E. A. Archie, Laura E Grieneisen, Elizabeth A Archie, Susan C Alberts, Jeanne Altmann, Luis B Barreiro, Jean-Christophe Grenier, Michael B Burns & Ran Blekhman
Social relationships have profound effects on health in humans and other primates, but the mechanisms that explain this relationship are not well understood. Using shotgun metagenomic data from wild baboons, we found that social group membership and social network relationships predicted both the taxonomic structure of the gut microbiome and the structure of genes encoded by gut microbial species. Rates of interaction directly explained variation in the gut microbiome, even after controlling for diet, kinship,...

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: Transitions between phases of genomic differentiation during stick-insect speciation

Rüdiger Riesch, Moritz Muschick, Dorothea Lindtke, Romain Villoutreix, Aaron A. Comeault, Timothy E. Farkas, Kay Lucek, Elizabeth Hellen, Víctor Soria-Carrasco, Stuart R. Dennis, Clarissa F. De Carvalho, Rebecca J. Safran, Cristina P. Sandoval, Jeff Feder, Regine Gries, Bernard J. Crespi, Gerhard Gries, Zach Gompert & Patrik Nosil
Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to...

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: 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: 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...

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: 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: 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: Stick insect genomes reveal natural selection's role in parallel speciation

Victor Soria-Carrasco, Zachariah Gompert, Aaron A. Comeault, Timothy E. Farkas, Thomas L. Parchman, J. Spencer Johnston, C. Alex Buerkle, Jeffrey L. Feder, Jens Bast, Tanja Schwander, Scott P. Egan, Bernard J. Crespi & Patrik Nosil
Natural selection can drive the repeated evolution of reproductive isolation, but the genomic basis of parallel speciation remains poorly understood. We analyzed whole-genome divergence between replicate pairs of stick insect populations that are adapted to different host plants and undergoing parallel speciation. We found thousands of modest-sized genomic regions of accentuated divergence between populations, most of which are unique to individual population pairs. We also detected parallel genomic divergence across population pairs involving an excess...

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: 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: 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: Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Eddy J. Dowle, Ryan R. Bracewell, Michael E. Pfrender, Karen E. Mock, Barbara J. Bentz & Gregory J. Ragland
Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and gene flow analyses revealed three distinct...

Data from: Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

Sean F. Ryan, Michaël C. Fontaine, J. Mark Scriber, Michael E. Pfrender, Shawn T. O'Neil & Jessica J. Hellmann
Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate...

Registration Year

  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
  • 2012

Resource Types

  • Dataset


  • Notre Dame University
  • University of Notre Dame
  • University of Sheffield
  • Rice University
  • Utah State University
  • Duke University
  • Princeton University
  • University of Florida
  • University of Nevada Reno
  • University of Colorado Boulder