50 Works

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: 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: Habitat segregation and ecological character displacement in cryptic African malaria mosquitoes

Billy Tene Fossog, Diego Ayala, Pelayo Acevedo, Pierre Kengne, Ignacio Ngomo Abeso Mebuy, Boris Makanga, Julie Magnus, Parfait Awono-Ambene, Flobert Njiokou, Marco Pombi, Christophe Antonio-Nkondjio, Christophe Paupy, Nora J. Besansky & Carlo Costantini
Understanding how divergent selection generates adaptive phenotypic and population diversification provides a mechanistic explanation of speciation in recently separated species pairs. Toward this goal, we sought ecological gradients of divergence between the cryptic malaria vectors Anopheles coluzzii and An. gambiae, and then looked for a physiological trait that may underlie such divergence. Using a large set of occurrence records and eco-geographical information, we built a distribution model to predict the predominance of the two species...

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: 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: 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: Social affiliation matters: both same-sex and opposite-sex relationships predict survival in wild female baboons

Elizabeth A. Archie, Jenny Tung, Michael Clark, Jeanne Altmann, Susan C. Alberts, J. Tung, E. A. Archie, M. Clark, S. C. Alberts & J. Altmann
Social integration and support can have profound effects on human survival. The extent of this phenomenon in non-human animals is largely unknown, but such knowledge is important to understanding the evolution of both lifespan and sociality. Here, we report evidence that levels of affiliative social behaviour (i.e. ‘social connectedness’) with both same-sex and opposite-sex conspecifics predict adult survival in wild female baboons. In the Amboseli ecosystem in Kenya, adult female baboons that were socially connected...

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: Dissecting functional components of reproductive isolation among closely related sympatric species of the Anopheles gambiae complex

Marco Pombi, Pierre Kengne, Geoffrey Gimonneau, Billy Tene-Fossog, Diego Ayala, Colince Kamdem, Federica Santalomazza, Wamdaogo Moussa Guelbeogo, N'Falé Sagnon, Vincenzo Petrarca, Didier Fontenille, Nora J. Besansky, Christophe Antonio-Nkondjio, Roch K. Dabire, Alessandra Della Torre, Frederic Simard & Carlo Costantini
Explaining how and why reproductive isolation evolves and determining which forms of reproductive isolation have the largest impact on the process of population divergence are major goals in the study of speciation. By studying recent adaptive radiations in incompletely isolated taxa, it is possible to identify barriers involved at early divergence before other confounding barriers emerge after speciation is complete. Sibling species of the Anopheles gambiae complex offer opportunities to provide insights into speciation mechanisms....

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: Calling in sick: impacts of fever on intra-urban human mobility

T. Alex Perkins, Valerie A. Paz-Soldan, Steven T. Stoddard, Amy C. Morrison, Brett M. Forshey, Kanya C. Long, Eric S. Halsey, Tadeusz J. Kochel, John P. Elder, Uriel Kitron, Thomas W. Scott & Gonzalo M. Vazquez-Prokopec
Pathogens inflict a wide variety of disease manifestations on their hosts, yet the impacts of disease on the behaviour of infected hosts are rarely studied empirically and are seldom accounted for in mathematical models of transmission dynamics. We explored the potential impacts of one of the most common disease manifestations, fever, on a key determinant of pathogen transmission, host mobility, in residents of the Amazonian city of Iquitos, Peru. We did so by comparing two...

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: 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: Genetic hitchhiking and the dynamic buildup of genomic divergence during speciation with gene flow

Samuel Melvin Flaxman, Jeffrey L. Feder, Patrik Nosil, Samuel Melvin Flaxman, Jeffrey L. Feder, Patrik Nosil & Samuel M. Flaxman
A major issue in evolutionary biology is explaining patterns of differentiation observed in population genomic data, as divergence can be due to both direct selection on a locus and genetic hitchhiking. “Divergence hitchhiking” (DH) theory postulates that divergent selection on a locus reduces gene flow at physically linked sites, facilitating the formation of localized clusters of tightly linked, diverged loci. “Genome hitchhiking” (GH) theory emphasizes genome-wide effects of divergent selection. Past theoretical investigations of DH...

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

Benjamin K. Rosenzweig, James B. Pease, Nora J. Besansky, Matthew H. Hahn & Matthew W. 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: Experimental evidence for ecological selection on genome variation in the wild

Zachariah Gompert, Aaron A. Comeault, Timothy E. Farkas, Jeffery L. Feder, Thomas L. Parchman, Alex C. Buerkle, Patrik Nosil, Jeffrey L. Feder & C. Alex Buerkle
Understanding natural selection's effect on genetic variation is a major goal in biology, but the genome-scale consequences of contemporary selection are not well known. In a release and recapture field experiment we transplanted stick insects to native and novel host plants and directly measured allele frequency changes within a generation at 186 576 genetic loci. We observed substantial, genome-wide allele frequency changes during the experiment, most of which could be attributed to random mortality (genetic...

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: 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...

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