132 Works

Data from: Evolution of stickleback in 50 years on earthquake-uplifted islands

Emily A. Lescak, Susan L. Bassham, Julian Catchen, Ofer Gelmond, Mary L. Sherbick, Frank A. Von Hippel & William A. Cresko
How rapidly can animal populations in the wild evolve when faced with sudden environmental shifts? Uplift during the 1964 Great Alaska Earthquake abruptly created freshwater ponds on multiple islands in Prince William Sound and the Gulf of Alaska. In the short time since the earthquake, the phenotypes of resident freshwater threespine stickleback fish on at least three of these islands have changed dramatically from their oceanic ancestors. To test the hypothesis that these freshwater populations...

Data from: Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower

Sean Stankowski, James M. Sobel & Matthew A. Streisfeld
A major goal of speciation research is to reveal the genomic signatures that accompany the speciation process. Genome scans are routinely used to explore genome-wide variation and identify highly differentiated loci that may contribute to ecological divergence, but they do not incorporate spatial, phenotypic or environmental data that might enhance outlier detection. Geographic cline analysis provides a potential framework for integrating diverse forms of data in a spatially explicit framework, but has not been used...

Data from: MycoDB, a global database of plant response to mycorrhizal fungi

V. Bala Chaudhary, Megan A. Rúa, Anita Antoninka, James D. Bever, Jeffery Cannon, Ashley Craig, Jessica Duchicela, Alicia Frame, Monique Gardes, Catherine Gehring, Michelle Ha, Miranda Hart, Jacob Hopkins, Baoming Ji, Nancy Collins Johnson, Wittaya Kaonongbua, Justine Karst, Roger T. Koide, Louis J. Lamit, James Meadow, Brook G. Milligan, John C. Moore, , Bridget Piculell, Blake Ramsby … & Jason D. Hoeksema
Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi...

Data from: Environmentally induced changes in correlated responses to selection reveal variable pleiotropy across a complex genetic network

Kristin L. Sikkink, Rose M. Reynolds, William A. Cresko & Patrick C. Phillips
Selection in novel environments can lead to a coordinated evolutionary response across a suite of characters. Environmental conditions can also potentially induce changes in the genetic architecture of complex traits, which in turn could alter the pattern of the multivariate response to selection. We describe a factorial selection experiment using the nematode Caenorhabditis remanei in which two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three different environmental conditions. The pattern of...

Data from: \"De novo assembly transcriptome for the rostrum dace (Leuciscus burdigalensis, Cyprinidae: fish) naturally infected by a copepod ectoparasite\" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

Olivier Rey, Géraldine Loot, Olivier Bouchez, Simon Blanchet, Maria Jose Ruiz-Lopez, Nelson Ting, Paul D. Etter, Eric A. Johnson, Tony L. Goldberg, Colin A. Chapman, James H. Jones, Patrick A. Omeja & William M. Switzer
The emergence of pathogens represents substantial threats to public health, livestock, domesticated animals, and biodiversity. How wild populations respond to emerging pathogens has generated a lot of interest in the last two decades. With the recent advent of high-throughput sequencing technologies it is now possible to develop large transcriptomic resources for non-model organisms, hence allowing new research avenues on the immune responses of hosts from a large taxonomic spectra. We here focused on a wild...

Data from: Genetic variation for outcrossing among Caenorhabditis elegans isolates

Henrique Teotonio, Diogo Manoel & Patrick C. Phillips
The evolution of breeding systems results from the existence of genetic variation and selective forces favoring different outcrossing rates. In this study we determine the extent of genetic variation for characters directly related to outcrossing, such as male frequency, male mating ability, and male reproductive success, in several wild isolates of the nematode Caenorhabditis elegans. This species is characterized by an androdioecious breeding system in which males occur with hermaphrodites that can either self-fertilize or...

Data from: Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora

Natalie L. Rosser, Luke Thomas, Sean Stankowski, Zoe T. Richards, W. Jason Kennington & Michael S. Johnson
Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC. Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it...

Data from: Variation in ecophysiological traits might contribute to ecogeographic isolation and divergence between parapatric ecotypes of Mimulus aurantiacus

James M. Sobel, Sean Stankowski & Matthew A. Streisfeld
Many forms of reproductive isolation contribute to speciation, and early acting barriers may be especially important, because they have the first opportunity to limit gene flow. Ecogeographic isolation occurs when intrinsic traits of taxa contribute to disjunct geographic distributions, reducing the frequency of inter‐taxon mating. Characterizing this form of isolation requires knowledge of both the geographic arrangement of suitable habitats in nature and the identification of phenotypes involved in shaping geographic distributions. In Mimulus aurantiacus,...

Shifting Practices for a Stronger Tomorrow: Local Journalism in the Pacific Northwest (2019)

Damian Radcliffe

Data from: Minor allele frequency thresholds strongly affect population structure inference with genomic datasets

Ethan Linck & C.J. Battey
One common method of minimizing errors in large DNA sequence datasets is to drop variable sites with a minor allele frequency below some specified threshold. Though widespread, this procedure has the potential to alter downstream population genetic inferences and has received relatively little rigorous analysis. Here we use simulations and an empirical SNP dataset to demonstrate the impacts of minor allele frequency (MAF) thresholds on inference of population structure. We find that model-based inference of...

Data from: Prairie plant phenology driven more by temperature than moisture in climate manipulations across a latitudinal gradient in the Pacific Northwest, USA

Paul B. Reed, Laurel E. Pfeifer-Meister, Bitty A. Roy, Bart R. Johnson, Graham T. Bailes, Aaron A. Nelson, Peg C. Boulay, Sarah T. Hamman & Scott D. Bridgham
Plant phenology will likely shift with climate change, but how temperature and/or moisture regimes will control phenological responses is not well understood. This is particularly true in Mediterranean climate ecosystems where the warmest temperatures and greatest moisture availability are seasonally asynchronous. We examined plant phenological responses at both the population and community levels to four climate treatments (control, warming, drought, and warming plus additional precipitation) embedded within three prairies across a 520 km latitudinal Mediterranean...

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: Phylogeographic estimation and simulation of global diffusive dispersal

Stilianos Louca
The analysis of time-resolved phylogenies (timetrees) and geographic location data allows estimation of dispersal rates, for example for invasive species and infectious diseases. Many estimation methods are based on the Brownian Motion model for diffusive dispersal on a 2-dimensional plane, however the accuracy of these methods deteriorates substantially when dispersal occurs at global scales because Spherical Brownian Motion (SBM) differs from planar Brownian Motion. No statistical method exists for estimating SBM diffusion coefficients from a...

Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

Julian Catchen, Angel Amores & Susan Bassham
The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional,...

Latitudinal gradients in population growth do not reflect demographic responses to climate

Megan Peterson, Graham Bailes, Lauren Hendricks, Laurel Pfeifer-Meister, Paul Reed, Scott Bridgham, Bart Johnson, Robert Shriver, Ellen Waddle, Hannah Wroton, Daniel Doak, Bitty Roy & William Morris
Spatial gradients in population growth, such as across latitudinal or elevational gradients, are often assumed to primarily be driven by variation in climate, and are frequently used to infer species’ responses to climate change. Here, we use a novel demographic, mixed model approach to dissect the contributions of climate variables vs. other latitudinal or local site effects on spatiotemporal variation in population performance in three perennial bunchgrasses. For all three species, we find that performance...

Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

Aryn Wilder, Stephen Palumbi, David Conover & Nina Overgaard Therkildsen
The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome-wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity...

Dental measurement and diet data for mammals

Samantha Hopkins, Samantha Price & Alec Chiono
Because teeth are the most easily preserved part of the vertebrate skeleton and are particularly morphologically variable in mammals, studies of fossil mammals rely heavily on dental morphology. Dental morphology is used both for systematics and phylogeny as well as for inferences about paleoecology, diet in particular. We analyze the influence of evolutionary history on our ability to reconstruct diet from dental morphology in the mammalian order Carnivora, and we find that much of our...

Woody encroachment happens via intensification, not extensification, of species ranges in an African savanna

Yong Zhou, Morgan Tingley, Madelon Case, Corli Coetsee, Gregory Kiker, Rheinhardt Scholtz, Freek Venter & Carla Staver
Widespread woody encroachment is a prominent concern for savanna systems as it is often accompanied by losses in productivity and biodiversity. Extensive ecosystem-level work has advanced our understanding of its causes and consequences. However, there is still debate over whether local management can override regional and global drivers of woody encroachment, and it remains largely unknown how encroachment influences woody community assemblages. Here, we examined species-level changes in woody plant distributions and size structure from...

Single cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

Hope Healey, Susan Bassham & William Cresko
Single cell RNA sequencing (scRNAseq) is a powerful technique that continues to expand across various biological applications. However, incomplete 3’ UTR annotations can impede single cell analysis resulting in genes that are partially or completely uncounted. Performing scRNAseq with incomplete 3’ UTR annotations can hinder the identification of cell identities and gene expression patterns and lead to erroneous biological inferences. We demonstrate that performing single cell isoform sequencing (ScISOr-Seq) in tandem with scRNAseq can rapidly...

Evolutionary causes and consequences of ungulate migration

Joel Abraham, Nathan Upham, Alejandro Damian-Serrano & Brett Jesmer
Ungulate migrations are crucial for maintaining abundant populations and functional ecosystems. However, little is known about how or why migratory behavior evolved in ungulates. To investigate the evolutionary origins of ungulate migration, we employed phylogenetic path analysis using a comprehensive species-level phylogeny of mammals. We found that 95 of 207 extant ungulate species are at least partially migratory, with migratory behavior originating independently in 17 lineages. The evolution of migratory behavior is associated with reliance...

Using GBIF to Demonstrate Colonial Legacies on Biodiversity Data

Ryan S. Mohammed, Melissa Kemp, Michelle J. LeFebvre, Alexis M. Mychajliw, Grace Turner, Kelly Fowler, Michael Pateman, Maria A. Nieves-Colón, Lanya Fanovich, Siobhan B. Cooke, Liliana M. Dávalos, Scott M. Fitzpatrick, Christina M. Giovas, Myles Stokowski & Ashley A. Wrean
Biologists recognize the Caribbean archipelago as a biodiversity hotspot and employ it for their research as a “natural laboratory”, but do not always appreciate that these ecosystems are in fact palimpsests shaped by multiple human cultures over millennia. We discuss two case studies of the Caribbean’s fragmented natural history collections, the effects of differing legislation and governance by the region’s multiple nation states. We use digital natural history specimen data from GBIF to demonstrate how...

Living Languages – Lenguas Vivas – Línguas Vivas: Joining efforts towards language revitalization

Luiz A. Amaral, Gabriela Pérez Báez & Jorge Emilio Rosés Labrada

Western Juniper Woodlands climate relations meta analysis

Schyler Reis
These data are based on tree-ring data from the internation tree ring data base and PRISM climate data.

Joint coding of visual input and eye/head position in V1 of freely moving mice dataset

Philip RL Parker, Elliott TT Abe, Emmalyn SP Leonard, Dylan M Martins & Cristopher M Niell
Visual input during natural behavior is highly dependent on movements of the eyes and head, but how information about eye and head position is integrated with visual processing during free movement is unknown, since visual physiology is generally performed under head-fixation. To address this, we performed single-unit electrophysiology in V1 of freely moving mice while simultaneously measuring the mouse’s eye position, head orientation, and the visual scene from the mouse’s perspective. From these measures, we...

A conserved transcriptional fingerprint of multi-neurotransmitter neurons necessary for social behavior

Denver Ncube, Alexandra Tallafuss, Jen Serafin, Joseph Bruckner, Dylan R. Farnsworth, Adam C. Miller, Judith S. Eisen & Philip Washbourne
Abstract Background An essential determinant of a neuron’s functionality is its neurotransmitter phenotype. We previously identified a defined subpopulation of cholinergic neurons required for social orienting behavior in zebrafish. Results We transcriptionally profiled these neurons and discovered that they are capable of synthesizing both acetylcholine and GABA. We also established a constellation of transcription factors and neurotransmitter markers that can be used as a “transcriptomic fingerprint” to recognize a homologous neuronal population in another vertebrate....

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