55 Works

Data from: Antagonistic relationships between intron content and codon usage bias of genes in three mosquito species: functional and evolutionary implications

Susanta K. Behura, Brajendra K. Singh & David W. Severson
Genome biology of mosquitoes holds potential in developing knowledge-based control strategies against vector-borne diseases such as malaria, dengue, West Nile Virus and others. Although the genomes of three major vector mosquitoes have been sequenced, attempts to elucidate the relationship between intron and codon usage bias across species in phylogenetic contexts are limited. In this study, we investigated the relationship between intron content and codon bias of orthologous genes among three vector mosquito species. We found...

Data from: Evidence for a recent horizontal transmission and spatial spread of Wolbachia from endemic Rhagoletis cerasi (Diptera: Tephritidae) to invasive Rhagoletis cingulata in Europe

Hannes Schuler, Coralie Bertheau, Scott P. Egan, Jeffrey L. Feder, Markus Riegler, Birgit C. Schlick-Steiner, Florian M. Steiner, Jes Johannesen, Peter Kern, Katalin Tuba, Ferenc Lakatos, Kirsten Köppler, Wolfgang Arthofer & Christian Stauffer
The widespread occurrence of Wolbachia in arthropods and nematodes suggests that this intracellular, maternally inherited endosymbiont has the ability to cross species boundaries. However, direct evidence for such a horizontal transmission of Wolbachia in nature is scarce. Here, we compare the well-characterized Wolbachia infection of the European cherry fruit fly, Rhagoletis cerasi, with that of the North American eastern cherry fruit fly, Rhagoletis cingulata, recently introduced to Europe. Molecular genetic analysis of Wolbachia based on...

Data from: Ecological adaptation and reproductive isolation in sympatry: genetic and phenotypic evidence for native host races of Rhagoletis pomonella

Thomas H. Q. Powell, Andrew A. Forbes, Glen R. Hood & Jeffrey L. Feder
Ecological speciation-with-gene-flow may be an important mode of diversification for phytophagous insects. The recent shift of Rhagoletis pomonella from its native host downy hawthorn (Crataegus mollis) to introduced apple (Malus domestica) in the northeastern United States is a classic example of sympatric host race formation. Here, we test whether R. pomonella has similarly formed host races on four native Crataegus species in the southern United States: western mayhaw (C. opaca), blueberry hawthorn (C. brachyacantha), southern...

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: Environmental DNA (eDNA) detects the invasive rusty crayfish (Orconectes rusticus) at low abundances

Matthew M. Dougherty, Eric R. Larson, Mark A. Renshaw, Crysta A. Gantz, Scott P. Egan, Daniel M. Erickson & David M. Lodge
Early detection is invaluable for the cost-effective control and eradication of invasive species, yet many traditional sampling techniques are ineffective at the low population abundances found at the onset of the invasion process. Environmental DNA (eDNA) is a promising and sensitive tool for early detection of some invasive species, but its efficacy has not yet been evaluated for many taxonomic groups and habitat types. We evaluated the ability of eDNA to detect the invasive rusty...

Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella

Meredith M. Doellman, Gregory J. Ragland, Glen R. Hood, Peter J. Meyers, Scott P. Egan, Thomas H.Q. Powell, Peter Lazorchak, Mary M. Glover, Cheyenne Tait, Hannes Schuler, Daniel A. Hahn, Stewart H. Berlocher, James J. Smith, Patrik Nosil, Jeffrey L. Feder, Daniel Hahn, Stewart Berlocher, Peter Meyers, Scott Egan, Jeffrey Feder, Glen Hood, Thomas Powell & Gregory Ragland
A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a...

Data from: Evolution of invasive traits in nonindigenous species: increased survival and faster growth in invasive populations of rusty crayfish (Orconectes rusticus)

Lindsey W. Sargent & David M. Lodge
The importance of evolution in enhancing the invasiveness of species is not well understood, especially in animals. To evaluate evolution in crayfish invasions, we tested for differences in growth rate, survival, and response to predators between native and invaded range populations of rusty crayfish (Orconectes rusticus). We hypothesized that low conspecific densities during introductions into lakes would select for increased investment in growth and reproduction in invasive populations. We reared crayfish from both ranges in...

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...

Data from: Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA

Kristy Deiner, Mark A. Renshaw, Yiyuan Li, Brett P. Olds, David M. Lodge & Michael E. Pfrender
As environmental DNA (eDNA) from macro-organisms is often assumed to be highly degraded, current eDNA assays target small DNA fragments to estimate species richness by metabarcoding. A limitation of this approach is the inherent lack of unique species-specific single-nucleotide polymorphisms available for unequivocal species identification. We designed a novel primer pair capable of amplifying whole mitochondrial genomes and evaluated it in silico for a wide range of ray-finned fishes (Class: Actinopterygii). We tested the primer...

Data from: Cast adrift on an island: introduced populations experience an altered balance between selection and drift

Eric M. O'Neill, Karen H. Beard & Michael E. Pfrender
A long-standing question in evolutionary biology is what becomes of adaptive traits when a species expands its range into novel environments. Here we report the results of a study on an adaptive colour pattern polymorphism (stripes) of the coqui frog following its introduction to Hawaii from Puerto Rico. We compared population differentiation (φ'ST and FST) for the stripes locus —which underlies this colour pattern polymorphism— with neutral microsatellite loci to test for a signature of...

Data from: Estimating species richness using environmental DNA

Brett P. Olds, Christopher L. Jerde, Mark A. Renshaw, Yiyuan Li, Nathan T. Evans, Cameron R. Turner, Kristy Deiner, Andrew R. Mahon, Michael A. Brueseke, Patrick D. Shirey, Michael E. Pfrender, David M. Lodge & Gary A. Lamberti
The foundation for any ecological study and the for effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion-based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct...

Data from: Divergent host preferences of above- and below-ground Culex pipiens (Diptera: Culicidae) and their hybrid offspring.

Megan L. Fritz, Edward D. Walker, James R. Miller, David W. Severson & Ian Dworkin
Culex pipiens form pipiens and Cx. pipiens form molestus (Diptera: Culicidae) belong to a cosmopolitan taxonomic group known as the Pipiens Assemblage. Hybridization between these forms is thought to contribute to human transmission of West Nile virus (WNV) in North America. Complementary choice and no-choice landing assays were developed to examine host acceptance by North American Cx. pipiens in the laboratory. Populations collected from above- and below-ground sites in suburban Chicago were identified as forms...

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...

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: A test of genomic modularity among life-history adaptations promoting speciation with gene flow

Gregory Ragland, Meredith M. Doellman, Peter J. Meyers, Glen R. Hood, Scott P. Egan, Thomas H. Q. Powell, Daniel A. Hahn, Patrik Nosil, Jeffrey L. Feder & Gregory J. Ragland
Speciation with gene flow may require adaptive divergence of multiple traits to generate strong ecologically based reproductive isolation. Extensive negative pleiotropy or physical linkage of genes in the wrong phase affecting these diverging traits may therefore hinder speciation, while genetic independence or “modularity” among phenotypic traits may reduce constraints and facilitate divergence. Here, we test whether the genetics underlying two components of diapause life history, initial diapause intensity and diapause termination timing, constrain differentiation between...

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...

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: Social environment influences the relationship between genotype and gene expression in wild baboons

Daniel E. Runcie, Ralph T. Wiedmann, Elizabeth A. Archie, Jeanne Altmann, Gregory A. Wray, Susan C. Alberts & Jenny Tung
Variation in the social environment can have profound effects on survival and reproduction in wild social mammals. However, we know little about the degree to which these effects are influenced by genetic differences among individuals, and conversely, the degree to which social environmental variation mediates genetic reaction norms. To better understand these relationships, we investigated the potential for dominance rank, social connectedness and group size to modify the effects of genetic variation on gene expression...

Data from: Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies

Meredith M. Doellman, Scott P. Egan, Gregory J. Ragland, Peter J. Meyers, Glen R. Hood, Thomas H.Q. Powell, Peter Lazorchak, Daniel A. Hahn, Stewart H. Berlocher, Patrik Nosil, Jeff L. Feder, Jeffrey L. Feder & Thomas H. Q. Powell
Taxa harboring high levels of standing variation may be more likely to adapt to rapid environmental shifts and experience ecological speciation. Here, we characterize geographic and host-related differentiation for 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies to infer if standing genetic variation in adult eclosion time in the ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new mutations, contributed substantially to its recent shift to earlier fruiting apple (Malus domestica). Allele frequency...

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
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: 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: 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...

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