99 Works

Data from: Feeding ecology underlies the evolution of cichlid jaw mobility

Christopher M. Martinez, Matthew David McGee, Samuel Robert Borstein, Peter C Wainwright, Matthew D. McGee, Samuel R. Borstein & Peter C. Wainwright
The fish feeding apparatus is among the most diverse functional systems in vertebrates. While morphological and mechanical variation of feeding systems are well studied, we know far less about the diversity of the motions that they produce. We explored patterns of feeding movements in African cichlids from Lakes Malawi and Tanganyika, asking whether the degree of kinesis is associated with dietary habits of species. We used geometric morphometrics to measure feeding kinesis as trajectories of...

Data from: Adaptive radiation in labrid fishes: a central role for functional innovations during 65 My of relentless diversification

Edward D. Burress & Peter C. Wainwright
Early burst patterns of diversification have become closely linked with concepts of adaptive radiation, reflecting interest in the role of ecological opportunity in modulating diversification. But, this model has not been widely explored on coral reefs, where biodiversity is exceptional, but many lineages have high dispersal capabilities and a pan-tropical distribution. We analyze adaptive radiation in labrid fishes, arguably the most ecologically dominant and diverse radiation of fishes on coral reefs. We test for time-dependent...

Data from: Phenotypic integration between claw and toepad traits promotes microhabitat specialization in the Anolis adaptive radiation

Michael L Yuan, Marvalee H Wake, Ian J Wang, Michael L. Yuan, Marvalee H. Wake & Ian J. Wang
The performance of an organism in its environment frequently depends more on its composite phenotype than on individual phenotypic traits. Thus, understanding environmental adaptation requires investigating patterns of covariation across functionally-related traits. The replicated adaptive radiations of Greater Antillean Anolis lizards are characterized by ecological and morphological convergence, thus providing an opportunity to examine the role of multiple phenotypes in microhabitat adaptation. Here, we examine integrated claw and toepad morphological evolution in relation to habitat...

Data from: Modelling the functional link between movement, feeding activity and condition in a marine predator

Enrico Pirotta, Lisa K. Schwarz, Daniel P. Costa, Patrick W. Robinson, Leslie New, Daniel P Costa, Patrick W Robinson & Lisa K Schwarz
The ability to quantify animals’ feeding activity and the resulting changes in their body condition as they move in the environment is fundamental to our understanding of a population’s ecology. We use satellite tracking data from northern elephant seals (Mirounga angustirostris), paired with simultaneous diving information, to develop a Bayesian state-space model that concurrently estimates an individual’s location, feeding activity, and changes in condition. The model identifies important foraging areas and times, the relative amount...

Data from: Patterns of transposable element variation and clinality in Drosophila

Jeffrey R. Adrion, David J. Begun & Matthew W. Hahn
Natural populations often exist in spatially diverse environments and may experience variation in the strength and targets of natural selection across their ranges. Drosophila provides an excellent opportunity to study the effects of spatially varying selection in natural populations, as both D. melanogaster and D. simulans live across a wide range of environments in North America. Here, we characterize patterns of variation in transposable elements (TEs) from six populations of D. melanogaster and nine populations...

Data from: Increased evolutionary rates and conserved transcriptional response following allopolyploidisation in brown algae

Filipe Sousa, João Neiva, Neusa Martins, Rita Jacinto, Laura Anderson, Peter T. Raimondi, Ester A. Serrao & Gareth A. Pearson
Genome mergers between independently evolving lineages, via allopolyploidy, can potentially lead to instantaneous sympatric speciation. However, little is known about the consequences of allopolyploidy and the resultant “genome shock” on genome evolution and expression beyond the plant and fungal branches of the Tree of Life. The aim of this study was to compare substitution rates and gene expression patterns in two allopolyploid brown algae (Phaeophyceae, Heterokonta) and their progenitors in the genus Pelvetiopsis N.L. Gardner...

Data from: Apparent inbreeding preference despite inbreeding depression in the American crow

Andrea K. Townsend, Conor C. Taff, Melissa L. Jones, Katherine H. Getman, Sarah S. Wheeler, Mitch G. Hinton & Ryane M. Logsdon
Although matings between relatives can have negative effects on offspring fitness, apparent inbreeding preference has been reported in a growing number of systems, including those with documented inbreeding depression. Here, we examined evidence for inbreeding depression and inbreeding preference in two populations (Clinton, New York and Davis, California, USA) of the cooperatively breeding American crow (Corvus brachyrhynchos). We then compared observed inbreeding strategies with theoretical expectations for optimal, adaptive levels of inbreeding, given the inclusive...

Data from: Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty

Michael J. Landis, William A. Freyman & Bruce G. Baldwin
The Hawaiian silversword alliance (Asteraceae) is an iconic adaptive radiation. However, like many island plant lineages, no fossils have been assigned to the clade. As a result, the clade's age and diversification rate are not known precisely, making it difficult to test biogeographic hypotheses about the radiation. Without fossils, paleogeographically structured biogeographic processes may inform species divergence times; for example, an island must first exist for a clade to radiate upon it. We date the...

Data from: Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise

Evelyn L. Jensen, Danielle L. Edwards, Ryan C. Garrick, Joshua M. Miller, James P. Gibbs, Linda J. Cayot, Washington Tapia, Aldalgisa Caccone, Michael A. Russello & Adalgisa Caccone
Population genetic theory related to the consequences of rapid population decline is well-developed, but there are very few empirical studies where sampling was conducted before and after a known bottleneck event. Such knowledge is of particular importance for species restoration, given links between genetic diversity and the probability of long-term persistence. To directly evaluate the relationship between current genetic diversity and past demographic events, we collected genome-wide single nucleotide polymorphism data from pre-bottleneck historical (c.1906)...

Data from: Genome-wide assessment of diversity and divergence among extant Galápagos giant tortoise species

Joshua M. Miller, Maud C. Quinzin, Danielle L. Edwards, Deren A.R. Eaton, Evelyn L. Jensen, Michael A. Russello, James P. Gibbs, Washington Tapia, Danny Rueda, Adalgisa Caccone, James P Gibbs, Joshua M Miller, Maud C Quinzin, Deren A R Eaton, Danielle L Edwards, Evelyn L Jensen & Michael A Russello
Genome-wide assessments allow for fuller characterization of genetic diversity, finer-scale population delineation, and better detection of demographically significant units to guide conservation compared to those based on “traditional” markers. Galapagos giant tortoises (Chelonoidis spp.) have long provided a case study for how evolutionary genetics may be applied to advance species conservation. Ongoing efforts to bolster tortoise populations, which have declined by 90%, have been informed by analyses of mitochondrial DNA sequence and microsatellite genotypic data,...

Data from: Ecological correlates of the spatial co-occurrence of sympatric mammalian carnivores worldwide

Courtney L. Davis, Lindsey N. Rich, Zach J. Farris, Marcella J. Kelly, Mario S. Di Bitetti, Yamil Di Blanco, Sebastian Albanesi, Mohammad S. Farhadinia, Navid Gholikhani, Sandra Hamel, Bart J. Harmsen, Claudia Wultsch, Mamadou D. Kane, Quinton Martins, Asia J. Murphy, Robin Steenweg, S. Sunarto, Atieh Taktehrani, Kanchan Thapa, Jody M. Tucker, Jesse Whittington, Febri A. Widodo, Nigel G. Yoccoz, David A.W. Miller & Yamil Di Blanco
The composition of local mammalian carnivore communities has far-reaching effects on terrestrial ecosystems worldwide. To better understand how carnivore communities are structured, we analyzed camera trap data for 108,087 trap days across 12 countries spanning 5 continents. We estimate local probabilities of co-occurrence among 768 species pairs from the order Carnivora and evaluate how shared ecological traits correlated with probabilities of co-occurrence. Within individual study areas, species pairs co-occurred more frequently than expected at random....

Data from: Eyes wide shut: the impact of dim-light vision on neural investment in marine teleosts

Teresa L. Iglesias, Alex Dornburg, Dan L. Warren, Peter C. Wainwright, Lars Schmitz & Evan P. Economo
Understanding how organismal design evolves in response to environmental challenges is a central goal of evolutionary biology. In particular, assessing the extent to which environmental requirements drive general design features among distantly related groups is a major research question. The visual system is a critical sensory apparatus that evolves in response to changing light regimes. In vertebrates, the optic tectum is the primary visual processing center of the brain, and yet it is unclear how,...

Data from: Dobzhansky-Muller incompatibilities, dominance drive, and sex-chromosome introgression at secondary contact zones: a simulation study

Luca Sciuchetti, Christophe Dufresnes, Elisa Cavoto, Alan Brelsford & Nicolas Perrin
Dobzhansky-Muller (DM) incompatibilities involving sex chromosomes have been proposed to account for Haldane’s rule (lowered fitness among hybrid offspring of the heterogametic sex) as well as Darwin’s corollary (asymmetric fitness costs with respect to the direction of the cross). We performed simulation studies of a hybrid zone to investigate the effects of different types of DM incompatibilities on cline widths and positions of sex-linked markers. From our simulations, X-Y incompatibilities generate steep clines for both...

Data from: Identification of a transporter complex responsible for the cytosolic entry of nitrogen-containing-bisphosphonates

Zhou Yu, Lauren E. Surface, Chong Yon Park, Max A Horlbeck, Gregory A Wyant, Monther Abu-Remaileh, Timothy R. Peterson, David M. Sabatini, Jonathan S. Weissman, Erin K. O'Shea, Lauren E Surface, Erin K O'Shea, David M Sabatini, Jonathan S Weissman & Timothy R Peterson
Nitrogen-containing-bisphosphonates (N-BPs) are widely prescribed to treat osteoporosis and other bone-related diseases. Although previous studies established that N-BPs function by inhibiting the mevalonate pathway in osteoclasts, the mechanism by which N-BPs enter the cytosol from the extracellular space to reach their molecular target is not understood. Here we implemented a CRISPRi-mediated genome-wide screen and identified SLC37A3 (solute carrier family 37 member A3) as a gene required for the action of N-BPs in mammalian cells. We...

Data from: Habitat structure modifies microclimate: an approach for mapping fine-scale thermal refuge

Charlotte R. Milling, Janet L. Rachlow, Peter J. Olsoy, Mark A. Chappell, Timothy R. Johnson, Jennifer S. Forbey, Lisa A. Shipley & Daniel H. Thornton
1. Contemporary techniques predicting habitat suitability under climate change projections often underestimate availability of thermal refuges. Habitat structure contributes to thermal heterogeneity at a variety of spatial scales, but quantifying microclimates at organism‐relevant resolutions remains a challenge. Landscapes that appear homogeneous at large scales may offer patchily distributed thermal refuges at finer scales. 2. We quantified the relationship between vegetation structure and the thermal environment at a scale relevant to small, terrestrial animals using a...

Data from: Sympatric serpentine endemic Monardella (Lamiaceae) species maintain habitat differences despite hybridization

Kathleen M. Kay, Suzie Woolhouse, Brett A. Smith, Nathaniel S. Pope & Nishanta Rajakaruna
Ecological differentiation and genetic isolation are thought to be critical in facilitating coexistence between related species, but the relative importance of these phenomena, and the interactions between them, are not well understood. Here we examine divergence in abiotic habitat affinity and the extent of hybridization and introgression between two rare species of Monardella (Lamiaceae) that are both restricted to the same serpentine soil exposure in California. Although broadly sympatric, they are found in microhabitats that...

Data from: The evolution of diapause in Rivulus (Laimosemion)

Andrew I. Furness, David N. Reznick, Andrey Tatarenkov, John C. Avise, David N Reznick, Andrew I Furness & John C Avise
Annual killifish adapted to life in aquatic habitat that seasonally dries have evolved desiccation resistant eggs capable of undergoing diapause, developmental arrest, at specific stages during embryology. Although noted for their remarkable abilities to live at the land-water interface, species in the genus Rivulus are considered non-annual killifish exhibiting typical teleost development patterns and no embryonic diapause. Here, we combine a molecular phylogeny with embryological study to demonstrate an independent origin of mid-embryonic diapause within...

Data from: Along the speciation continuum: quantifying intrinsic and extrinsic isolating barriers across five million years of evolutionary divergence in California jewelflowers

Kyle Christie & Sharon Y. Strauss
Understanding the relative roles of intrinsic and extrinsic reproductive barriers, and their interplay within the geographic context of diverging taxa, remains an outstanding challenge in the study of speciation. We conducted a comparative analysis of reproductive isolation in California Jewelflowers (Streptanthus, s.l., Brassicaceae) by quantifying potential barriers to gene flow at multiple life history stages in 39 species pairs spanning five million years of evolutionary divergence. We quantified nine potential pre- and postzygotic barriers and...

Data from: Stream flow alone does not predict population structure of diving beetles across complex tropical landscapes

Athena Lam, Emmanuel F. A. Toussaint, Carolin Kindler, Matthew H. Van Dam, Rawati Panjaitan, George K. Roderick & Michael Balke
Recent theoretical advances have hypothesized a central role of habitat persistence on population genetic structure and resulting biodiversity patterns of freshwater organisms. Here, we address the hypothesis that lotic species, or lineages adapted to comparably geologically stable running water habitats (streams and their marginal habitats), have high levels of endemicity and phylogeographic structure due to the persistent nature of their habitat. We use a nextRAD sequencing approach to investigate the population structure and phylogeography of...

Data from: Using geometric morphometric visualizations of directional selection gradients to investigate morphological differentiation

Timothy D. Weaver & Philipp Gunz
Researchers studying extant and extinct taxa are often interested in identifying the evolutionary processes that have lead to the morphological differences among the taxa. Ideally, one could distinguish the influences of neutral evolutionary processes (genetic drift, mutation) from natural selection, and in situations for which selection is implicated, identify the targets of selection. The directional selection gradient is an effective tool for investigating evolutionary process, because it can relate form (size and shape) differences between...

Data from: The evolution of floral signals in relation to range overlap in a clade of California Jewelflowers (Streptanthus s.l.)

Marjorie G. Weber, N. Ivalu Cacho, Martin J. Q. Phan, Caprice Disbrow, Santiago R. Ramirez & Sharon Y. Strauss
Because of their function as reproductive signals in plants, floral traits experience distinct selective pressures related to their role in speciation, reinforcement, and prolonged coexistence with close relatives. However, few studies have investigated whether population-level processes translate into detectable signatures at the macroevolutionary scale. Here, we ask whether patterns of floral trait evolution and range overlap across a clade of California Jewelflowers reflect processes hypothesized to shape floral signal differentiation at the population level. We...

Data from: RRapid global spread of wRi-like Wolbachia across multiple Drosophila

Michael Turelli, Brandon S. Cooper, Kelly M. Richardson, Paul S. Ginsberg, Brooke Peckenpaugh, Chenling X. Antelope, Kevin J. Kim, Michael R. May, Antoine Abrieux, Derek A. Wilson, Michael J. Bronski, Brian R. Moore, Jian-Jun Gao, Michael B. Eisen, Joanna C. Chiu, William R. Conner & Ary A. Hoffmann
Maternally transmitted Wolbachia, Spiroplasma and Cardinium bacteria are common in insects, but their interspecific spread is poorly understood. Endosymbionts can spread rapidly within host species by manipulating host reproduction, as typified by the global spread of wRi Wolbachia observed in Drosophila simulans. However, because Wolbachia cannot survive outside host cells, spread between distantly related host species requires horizontal transfers that are presumably rare. Here we document spread of wRi-like Wolbachia among eight highly diverged Drosophila...

Data from: Deconstruction of a plant-arthropod community reveals influential plant traits with nonlinear effects on arthropod assemblages

Joshua G. Harrison, Casey Philbin, Zach Gompert, Glen Forister, Leonardo Hernandez, Benjamin W. Sullivan, Ian Wallace, Lyra Beltran, Craig Dodson, Jacob S. Francis, Amie Schlageter, Oren Shelef, Su'ad Yoon, Matthew L. Forister, Ian S. Wallace, Su'ad A. Yoon, Zachariah Gompert, Casey S. Philbin, Craig D. Dodson, Leonardo Hernandez-Espinoza & Glen W. Forister
1. Studies of herbivores and secondary consumer communities rarely incorporate a comprehensive characterization of primary producer trait variation, thus limiting our understanding of how plants mediate community assembly of consumers. 2. We took advantage of recent technological developments for efficient generation of phytochemical, microbial, and genomic data to characterize individual alfalfa plants (Medicago sativa; Fabaceae) growing in an old-field, semi-naturalized state for 770 traits (including 753 chemical features). Using random forest modeling, we investigated the...

Data from: Genome-wide expression reveals multiple systemic effects associated with detection of anticoagulant poisons in bobcats (Lynx rufus)

Devaughn Fraser, Alice Mouton, Laurel E.K. Serieys, Steve Cole, Scott Carver, Sue Vandewoude, Michael Lappin, Seth P.D. Riley, Robert Wayne & Laurel E. K. Serieys
Anticoagulant rodenticides (ARs) are indiscriminate toxicants that threaten non-target predatory and scavenger species through secondary poisoning. Accumulating evidence suggests that AR exposure may have disruptive sublethal consequences on individuals that can affect fitness. We evaluated AR-related effects on genome wide expression patterns in a population of bobcats in southern California. We identify differential expression of genes involved in xenobiotic metabolism, endoplasmic reticulum stress response, epithelial integrity, and both adaptive and innate immune function. Further, we...

Data from: Resolving the phylogenetic position of Darwin’s extinct ground sloth (Mylodon darwinii) using mitogenomic and nuclear exon data

Frédéric Delsuc, Melanie Kuch, Gillian C. Gibb, Jonathan Hughes, Paul Szpak, John Southon, Jacob Enk, Ana T. Duggan & Hendrik N. Poinar
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first discovered its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12,880 year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient sub-fossil, likely the result of the dry and cold conditions prevailing within...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of California System
  • Yale University
  • Harvard University
  • University of British Columbia
  • Howard Hughes Medical Institute
  • Stanford University
  • Columbia University
  • University of Michigan–Ann Arbor
  • Smithsonian Institution
  • State University of New York
  • University of Florida
  • University of Sao Paulo
  • Michigan State University
  • University of Kansas
  • University of Washington