54 Works

Data from: Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system

Gary Voelker, Rauri C. K. Bowie & John Klicka
The evolution of migration in birds has fascinated biologists for centuries. In this study, we performed phylogenetic-based analyses of Catharus thrushes, a model genus in the study of avian migration, and their close relatives. For these analyses, we used both mitochondrial and nuclear genes, and the resulting phylogenies were used to trace migratory traits and biogeographic patterns. Our results provide the first robust assessment of relationships within Catharus and relatives and indicate that both mitochondrial...

Data from: Parallel evolution of local adaptation and reproductive isolation in the face of gene flow

Roger K. Butlin, Maria Saura, Grégory Charrier, Benjamin Jackson, Carl André, Armando Caballero, Jerry A. Coyne, Juan Galindo, John W. Grahame, Johann Hollander, Petri Kemppainen, Mónica Martínez-Fernández, Marina Panova, Humberto Quesada, Kerstin Johannesson, Emilio Rolán-Alvarez & Johan Hollander
Parallel evolution of similar phenotypes provides strong evidence for the operation of natural selection. Where these phenotypes contribute to reproductive isolation, they further support a role for divergent, habitat-associated selection in speciation. However, the observation of pairs of divergent ecotypes currently occupying contrasting habitats in distinct geographical regions is not sufficient to infer parallel origins. Here we show striking parallel phenotypic divergence between populations of the rocky-shore gastropod, Littorina saxatilis, occupying contrasting habitats exposed to...

Data from: Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei:Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusion

Alex Dornburg, Jon A. Moore, Rachel Webster, Dan L. Warren, Matthew C. Brandley, Teresa L. Iglesias, Peter C. Wainwright & Thomas J. Near
Squirrelfishes and soldierfishes (Holocentridae) are among the most conspicuous species in the nocturnal reef fish community. However, there is no clear consensus regarding their evolutionary relationships, which is reflected in a complicated taxonomic history. We collected DNA sequence data from multiple single copy nuclear genes and one mitochondrial gene sampled from over fifty percent of the recognized holocentrid species and infer the first species-level phylogeny of the Holocentridae. Our results strongly support the monophyly of...

Data from: Diversification and gene flow in nascent lineages of island and mainland North American tree squirrels (Tamiasciurus)

Andreas S. Chavez, George James Kenagy, Sean P. Maher, Brian S. Arbogast & G. J. Kenagy
Pleistocene climate cycles and glaciations had profound impacts on taxon diversification in the Boreal Forest Biome. Using population genetic analyses with multilocus data we examined diversification, isolation, and hybridization in two sibling species of tree squirrels (Tamiasciurus douglasii and T. hudsonicus) with special attention to the geographically and genetically enigmatic population of T. hudsonicus on Vancouver Island, Canada. The two species differentiated only about 500,000 years ago, in the late Pleistocene. The island population is...

Data from: Next-generation sequencing for molecular ecology: a caveat regarding pooled samples

Eric C. Anderson, Hans J. Skaug & Daniel J. Barshis
We develop a model based on the Dirichlet-compound multinomial distribution (CMD) and Ewens sampling formula to predict the fraction of SNP loci that will appear fixed for alternate alleles between two pooled samples drawn from the same underlying population. We apply this model to next-generation sequencing (NGS) data from Baltic Sea herring recently published by (Corander et al., , Molecular Ecology, 2931–2940), and show that there are many more fixed loci than expected in the...

Data from: Evolutionary origins and diversification of proteobacterial mutualists

Joel L. Sachs, Ryan G. Skophammer, Nidhanjali Bansal, Jason E. Stajich, N. Bansal, R. G. Skophammer & J. E. Stajich
Mutualistic bacteria infect most eukaryotic species in nearly every biome. Nonetheless, two dilemmas remain unresolved about bacterial–eukaryote mutualisms: how do mutualist phenotypes originate in bacterial lineages and to what degree do mutualists traits drive or hinder bacterial diversification? Here, we reconstructed the phylogeny of the hyperdiverse phylum Proteobacteria to investigate the origins and evolutionary diversification of mutualistic bacterial phenotypes. Our ancestral state reconstructions (ASRs) inferred a range of 34–39 independent origins of mutualist phenotypes in...

Data from: Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

Joshua G. Dunn, Catherine K. Foo, Nicolette G. Belletier, Elizabeth R. Gavis, Jonathan S. Weissman, Nicolette G Belletier, Elizabeth R Gavis, Joshua G Dunn, Catherine K Foo & Jonathan S Weissman
Ribosomes can read through stop codons in a regulated manner, elongating rather than terminating the nascent peptide. Stop codon readthrough is essential to diverse viruses, and phylogenetically predicted to occur in a few hundred genes in Drosophila melanogaster, but the importance of regulated readthrough in eukaryotes remains largely unexplored. Here, we present a ribosome profiling assay (deep sequencing of ribosome-protected mRNA fragments) for Drosophila melanogaster, and provide the first genome-wide experimental analysis of readthrough. Readthrough...

Data from: Combining genetic and demographic information to prioritize conservation efforts for anadromous alewife and blueback herring

Eric P. Palkovacs, Daniel J. Hasselman, Emily E. Argo, Stephen R. Gephard, Karin E. Limburg, David M. Post, Thomas F. Schultz & Theodore V. Willis
A major challenge in conservation biology is the need to broadly prioritize conservation efforts when demographic data are limited. One method to address this challenge is to use population genetic data to define groups of populations linked by migration and then use demographic information from monitored populations to draw inferences about the status of unmonitored populations within those groups. We applied this method to anadromous alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis), species for...

Data from: Phylogenomics resolves evolutionary relationships among ants, bees, and wasps

Brian R. Johnson, Marek L. Borowiec, Joanna C. Chiu, Ernest K. Lee, Joel Atallah & Philip S. Ward
Eusocial behavior has arisen in few animal groups, most notably in the aculeate Hymenoptera, a clade comprising ants, bees, and stinging wasps. Phylogeny is crucial to understanding the evolution of the salient features of these insects, including eusociality. Yet the phylogenetic relationships among the major lineages of aculeate Hymenoptera remain contentious. We address this problem here by generating and analyzing genomic data for a representative series of taxa. We obtain a single well-resolved and strongly...

Data from: Large-scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead (Oncorhynchus mykiss)

Alicia Abadía-Cardoso, Eric C. Anderson, Devon E. Pearse, John Carlos Garza & John Carlos Garza
Understanding life history traits is an important first step in formulating effective conservation and management strategies. The use of artificial propagation and supplementation as such a strategy can have numerous effects on the supplemented natural populations and minimizing life history divergence is crucial in minimizing these effects. Here, we use single nucleotide polymorphism (SNP) genotypes for large-scale parentage analysis and pedigree reconstruction in a hatchery population of steelhead, the anadromous form of rainbow trout. Nearly...

Data from: Limits to behavioral evolution: the quantitative genetics of a complex trait under directional selection

Vincent Careau, Matthew E. Wolak, Patrick A. Carter, Garland Jr., Theodore & Theodore Garland
Replicated selection experiments provide a powerful way to study how “multiple adaptive solutions” may lead to differences in the quantitative-genetic architecture of selected traits and whether this may translate into differences in the timing at which evolutionary limits are reached. We analyze data from 31 generations (n = 17,988) of selection on voluntary wheel running in house mice. The rate of initial response, timing of selection limit, and height of the plateau varied significantly between...

Data from: Increased accuracy of species lists developed for alpine lakes using morphology and cytochrome oxidase I for identification of specimens

Kristy Deiner, Roland A. Knapp, Daniel M. Boiano & Bernie May
The first step in many community ecology studies is to produce a species list from a sample of individuals. Community ecologists now have two viable ways of producing a species list: morphological and barcode identification. In this study, we compared the taxonomic resolution gained by a combined use of both methods and tested whether a change in taxonomic resolution significantly impacted richness estimates for benthic macroinvertebrates sampled from ten lakes in Sequoia National Park, USA....

Data from: The role of inbreeding depression and mating system in the evolution of heterostyly

Jennifer J. Weber, Stephen G. Weller, Ann K. Sakai, Olga V. Tsyusko, Travis C. Glenn, Cesar A. Dominguez, Francisco E. Molina-Freaner, Juan Fornoni, Mike Tran, Nhu Nguyen, Karen Nguyen, Lien-Khuong Tran, Greg Joice & Ellen Harding
We investigated the role of morph-based differences in the expression of inbreeding depression in loss of the mid-styled morph from populations of tristylous Oxalis alpina as proposed by theoretical analyses. The extent of self-compatibility of reproductive morphs, the degree of self-fertilization, and the magnitude of inbreeding depression were investigated in three populations of O. alpina differing in their tristylous incompatibility relationships. All three populations exhibited significant inbreeding depression. In two populations with highly modified tristylous...

Data from: Kin recognition affects plant communication and defence

Richard Karban, Kaori Shiojiri, Satomi Ishizaki, William C. Wetzel, Richard Y. Evans, S. Ishizaki, K. Shiojiri, R. Y. Evans, R. Karban & W. C. Wetzel
The ability of many animals to recognize kin has allowed them to evolve diverse cooperative behaviours; such ability is less well studied for plants. Many plants, including Artemisia tridentata, have been found to respond to volatile cues emitted by experimentally wounded neighbours to increase levels of resistance to herbivory. We report that this communication was more effective among A. tridentata plants that were more closely related based on microsatellite markers. Plants in the field that...

Data from: The biomechanical basis of evolutionary change in a territorial display

Terry J. Ord, David C. Collar & Thomas J. Sanger
1. Few studies have examined how the anatomy of an animal signal contributes to, or limits, the evolution of signal differentiation among closely related species. 2. In Anolis lizards, adult males extend a large, conspicuous dewlap as part of a territorial advertisement display. Males of species from the island of Jamaica rely on the rapid extension of the dewlap to facilitate display detection by territorial neighbours and conspecific females. Males of other species on the...

Data from: Sociality influences cultural complexity

Michael Muthukrishna, Ben W. Shulman, Vlad Vasilescu, Joseph Henrich, J. Henrich, V. Vasilescu & B. W. Shulman
Archaeological and ethnohistorical evidence suggests a link between a population's size and structure, and the diversity or sophistication of its toolkits or technologies. Addressing these patterns, several evolutionary models predict that both the size and social interconnectedness of populations can contribute to the complexity of its cultural repertoire. Some models also predict that a sudden loss of sociality or of population will result in subsequent losses of useful skills/technologies. Here, we test these predictions with...

Data from: Ecological novelty by hybridization: experimental evidence for increased thermal tolerance by transgressive segregation in Tigriopus californicus

Ricardo J. Pereira, Felipe Sousa Barreto, Ronald S. Burton & Felipe S. Barreto
Early generations of hybrids can express both genetic incompatibilities and phenotypic novelty. Insights into whether these conflicting interactions between intrinsic and extrinsic selection persist after a few generations of recombination require experimental studies. To address this question, we use interpopulation crosses and recombinant inbred lines (RILs) of the copepod Tigriopus californicus, and focus on two traits that are relevant for the diversification of this species: survivorship during development and tolerance to thermal stress. Experimental crosses...

Data from: Structural, compositional and trait differences between native and non-native dominated grassland patches

Nicole A. Molinari & Carla M. D'Antonio
1. Non-native species with growth forms that are different from the native flora may alter the physical structure of the area they invade, thereby changing the resources available to resident species. This in turn can select for species with traits suited for the new growing environment. 2. We used adjacent uninvaded and invaded grassland patches to evaluate whether the shift in dominance from a native perennial bunchgrass, Nassella pulchra, to the early season, non-native annual...

Data from: The effect of Wolbachia on the lifetime reproductive success of its insect host in the field

Michal Segoli, Richard Stouthamer, Corinne M. Stouthamer, Paul Rugman-Jones, Jay A. Rosenheim, M. Segoli, C. M. Stouthamer, J. A. Rosenheim, R. Stouthamer & P. Rugman-Jones
Wolbachia is a widespread endosymbiont that induces dramatic manipulations of its host's reproduction. Although there has been substantial progress in the developing theory for Wolbachia–host interactions and in measuring the effects of Wolbachia on host fitness in the laboratory, there is a widely recognized need to quantify the effects of Wolbachia on the host fitness in the field. The wasp Anagrus sophiae, an egg parasitoid of planthoppers, carries a Wolbachia strain that induces parthenogenesis, but...

Data from: Mechanisms of biotic resistance across complex life cycles

M. Rius, Elaine E. Potter, John J. Stachowicz, J. David Aguirre & Marc Rius
1. Biotic resistance is the ability of communities to inhibit the establishment, spread or impact of novel species. However, the interactions that underlie biotic resistance depend heavily on the contexts in which species interact. Consequently, studies of biotic resistance that consider single processes, patches, species or life-history stages may provide an incomplete picture of the capacity for communities to resist invasion. 2. Many organisms have multiphasic life cycles, where individuals can occupy distinct niches at...

Data from: Convergent evolution in the territorial communication of a classic adaptive radiation: Caribbean Anolis lizards

Terry J. Ord, Judy A. Stamps & Jonathan B. Losos
To demonstrate adaptive convergent evolution, it must be shown that shared phenotypes have evolved independently in different lineages and that a credible selection pressure underlies adaptive evolution. There are a number of robust examples of adaptive convergence in morphology for which both these criteria have been met, but examples from animal behaviour have rarely been tested as rigorously. Adaptive convergence should be common in behaviour, especially behaviour used for communication, because the environment often shapes...

Data from: Artificial bat roosts did not accelerate forest regeneration in abandoned pastures in southern Costa Rica

J. Leighton Reid, Ellen K. Holste & Rakan A. Zahawi
Artificial roosts have been proposed as a tool for augmenting bat populations and catalyzing tropical forest regeneration. In the best case scenario, roosts would attract seed-carrying bats (Family Phyllostomidae) into degraded pastures and form nucleating patches of native vegetation. We tested this scenario by monitoring 48 artificial roosts in pastures and adjacent forest fragments in southern Costa Rica over 2 years. Half of the pasture roosts were exposed to direct sunlight and half were affixed...

Data from: Urban land use limits regional bumble bee gene flow

Shalene Jha, Claire Kremen & C. Kremen
Potential declines in native pollinator communities and increased reliance on pollinator-dependent crops have raised concerns about native pollinator conservation and dispersal across human-altered landscapes. Bumble bees are one of the the most effective native pollinators, and are often the first to be extirpated in human-altered habitats, yet little is known about how bumble bees move across fine spatial scales and what landscapes promote or limit their gene flow. In this study, we examine regional genetic...

Data from: Restricted gene flow within and between rapidly diverging neotropical plant species

Kathleen M. Kay & Yann Surget-Groba
Speciation involves the evolution of traits and genetic differences that contribute to reproductive isolation and the cessation of gene flow, and studying closely related species and divergent populations gives insight into how these phenomena proceed. Here, we document patterns of gene flow within and between two members of a rapid Neotropical species radiation, Costus pulverulentus and Costus scaber (Costaceae). These species co-occur in the tropical rainforest and share pollinators, but are reproductively isolated by a...

Data from: Spatial distribution of nests constrains the strength of sexual selection in a warbler

Conor C. Taff, Corey R. Freeman-Gallant, Peter O. Dunn, Linda A. Whittingham, C. C. Taff, P. O. Dunn & L. A. Whittingham
In socially monogamous species, extra-pair paternity may increase the strength of inter-sexual selection by allowing males with preferred phenotypes to monopolize matings. Several studies have found relationships between male signals and extra-pair mating, but many others fail to explain variation in extra-pair mating success. A greater appreciation for the role that ecological contingencies play in structuring behavioral processes may help to reconcile contradictory results. We studied extra-pair mating in a spatial context in the common...

Registration Year

  • 2013

Resource Types

  • Dataset


  • University of California System
  • Yale University
  • French National Centre for Scientific Research
  • The University of Texas at Austin
  • University of Georgia
  • French National Institute for Agricultural Research
  • Southwest Fisheries Science Center
  • University of Arizona
  • UNSW Sydney
  • University of British Columbia
  • Harvard University
  • Brown University
  • National Museum
  • University of Massachusetts Amherst
  • University of Montana