275 Works

Seismogenesis at Hikurangi Integrated Research Experiment (SHIRE) onshore seismic acquisition field report

Katie Jacobs, Stuart A Henrys, D Okaya, H Van Avendonk, Jenny Black, Dan H. N. Barker, Sapthala C Karalliyadda, E Kurashimo, Wanda R. Stratford, M Savage, R Sullivan, Zane R. Bruce & L Hughes
This report documents the acquisition and archiving of a major controlled source and passive seismic imaging project, the Seismogenesis Hikurangi Integrated Research Experiment (SHIRE). The SHIRE project aims to identify and quantify factors controlling the long-term evolution of the Hikurangi margin and the mode of slip along the subduction megathrust. The components of the data volume were acquired in two phases; between October 2017 – April 2018 (SHIRE I) and February–March 2019 (SHIRE II). The...

A Positive Spin on a Negative Narrative: How the Media Portrays Fraternities and What Fraternities Can Do About It

Zachary Taylor, Jennifer Zamora, Arianne McArdle & Mario Villa

Data from: Heritable differences in fitness-related traits among populations of the mustard hill coral, Porites astreoides

Carly D. Kenkel, Samantha P. Setta & Mikhail V. Matz
A population’s potential for rapid evolutionary adaptation can be estimated from the amount of genetic variation in fitness-related traits. Inshore populations of the mustard hill coral (Porites astreoides) have been shown to be more tolerant to thermal stress than offshore populations, but it is unclear whether this difference is due to long-term physiological acclimatization or genetic adaptation. Here, we evaluated variation in growth rate and survival among 38 families of juvenile recruits of P. astreoides...

Data from: Matrix context and patch quality jointly determine diversity in a landscape-scale experiment

Robert A. Deans & David R. Chalcraft
The biodiversity of a habitat patch is predicted to be driven in part by interactions between patch quality and landscape context (i.e., type of regional matrix), but these interactions are rarely explored experimentally. Understanding the interaction between patch quality and matrix context can provide insight into the kind of dynamics that best describe a metacommunity and help predict how the diversity of a patch will respond to environmental change at different scales. We conducted a...

Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)

Oscar M. Vargas, Edgardo M. Ortiz & Beryl B. Simpson
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the...

Data from: Genome reduction and microbe-host interactions drive adaptation of a sulfur-oxidizing bacterium associated with a cold seep sponge

Ren-Mao Tian, Weipeng Zhang, Lin Cai, Yue-Him Wong, Wei Ding & Pei-Yuan Qian
As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored “differential coverage binning” method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed “Gsub”) may represent a...

Data from: Best practices for justifying fossil calibrations

James F. Parham, Philip C. J. Donoghue, Christopher J. Bell, Tyler D. Calway, Jason J. Head, Patricia A. Holroyd, Jun G. Inoue, Randall B. Irmis, Walter G. Joyce, Daniel T. Ksepka, José S. L. Patané, Nathan D. Smith, James E. Tarver, Marcel Van Tuinen, Ziheng Yang, Kenneth D. Angielczyk, Jenny M. Greenwood, Christy A. Hipsley, Jacobs Louis, Peter J. Makovicky, Johannes Müller, Krister T. Smith, Jessica M. Theodor, Rachel C. M. Warnock, Michael J. Benton … & Louis Jacobs
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule; with replacement rates established (calibrated) using inaccurate paleontological age estimates...

Data from: Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: performance and a comparison with AFLP-derived distances

Alexander S. Mikheyev, Tanya Vo, Brian Wee, Michael C. Singer & Camille Parmesan
BACKGROUND: The isolation of microsatellite markers remains laborious and expensive. For some taxa, such as Lepidoptera, development of microsatellite markers has been particularly difficult, as many markers appear to be located in repetitive DNA and have nearly identical flanking regions. We attempted to circumvent this problem by bioinformatic mining of microsatellite sequences from a de novo-sequenced transcriptome of a butterfly (Euphydryas editha). PRINCIPAL FINDINGS: By searching the assembled sequence data for perfect microsatellite repeats we...

Data from: Geographic determinants of gene flow in two sister species of tropical Andean frogs

Carlos E. Guarnizo & David C. Cannatella
Complex interactions between topographic heterogeneity, climatic and environmental gradients, and thermal niche conservatism are commonly assumed to indicate the degree of biotic diversification in montane regions. Our aim was to investigate factors that disrupt gene flow between populations and to determine if there is evidence of downslope asymmetric migration in highland frogs with wide elevational ranges and thermal niches. We determined the role of putative impediments to gene flow (as measured by least-cost path (LCP)...

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: Partitioning the effects of spatial isolation, nest habitat, and individual diet in causing assortative mating within a population of threespine stickleback

Lisa Kathryn Snowberg & Daniel I. Bolnick
Assortative mating is measured as a phenotypic or genotypic correlation between mates. Although biologists typically view assortative mating in terms of mate preference for similar partners, correlations between mates can also arise from phenotypic spatial structure arising from spatial isolation or habitat preferences. Here, we test whether diet-assortative mating within an ecologically variable population of threespine stickleback results from small-scale geographic isolation or microhabitat preference. We find evidence for assortative mating in the form of...

Data from: Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

Holly M. Bik, Way Sung, Paul De Ley, James G. Baldwin, Jyotsna Sharma, Axayácatl Rocha-Olivares & W. Kelley Thomas
Microbial eukaryotes (nematodes, protists, fungi, etc., loosely referred to as meiofauna) are ubiquitous in marine sediments and likely play pivotal roles in maintaining ecosystem function. Although the deep-sea benthos represents one of the world’s largest habitats, we lack a firm understanding of the biodiversity and community interactions amongst meiobenthic organisms in this ecosystem. Within this vast environment key questions concerning the historical genetic structure of species remain a mystery, yet have profound implications for our...

Data from: Poison frog colors are honest signals of toxicity, particularly for bird predators

Martine E. Maan & Molly E. Cummings
Antipredator defenses and warning signals typically evolve in concert. However, the extensive variation across taxa in both these components of predator deterrence, and the relationship between them, are poorly understood. Here we test whether there is a predictive relationship between visual conspicuousness and toxicity levels across 10 populations of the color polymorphic strawberry poison frog, Dendrobates pumilio. Using a mouse-based toxicity assay, we find extreme variation in toxicity between frog populations. This variation is significantly...

Data from: Effects of founding genetic variation on adaptation to a novel resource

Deepa Agashe, Jay J Falk & Daniel I Bolnick
Population genetic theory predicts that adaptation in novel environments is enhanced by genetic variation for fitness. However, theory also predicts that under strong selection, demographic stochasticity can drive populations to extinction before they can adapt. We exposed wheat-adapted populations of the flour beetle (Tribolium castaneum) to a novel suboptimal corn resource, to test the effects of founding genetic variation on population decline and subsequent extinction or adaptation. As previously reported, genetically diverse populations were less...

Data from: Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm

Amanda J Waters, Irina Makarevitch, Steve R Eichten, Ruth A Swanson-Wagner, Cheng-Ting Yeh, Wayne Xu, Patrick S Schnable, Matthew W Vaughn, Mary Gehring & Nathan M Springer
Imprinting describes the differential expression of alleles based upon their parent of origin. Deep sequencing of RNAs from maize endosperm and embryo tissue 14 days after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm including 54 maternally expressed...

Data from: Multimodal cues improve prey localization under complex environmental conditions

Flor Rhebergen, Ryan C. Taylor, Michael J. Ryan, Rachel A. Page & Wouter Halfwerk
Predators often eavesdrop on sexual displays of their prey. These displays can provide multimodal cues that aid predators, but the benefits in attending to them should depend on the environmental sensory conditions under which they forage. We assessed whether bats hunting for frogs use multimodal cues to locate their prey and whether their use varies with ambient conditions. We used a robotic set-up mimicking the sexual display of a male túngara frog (Physalaemus pustulosus) to...

Data from: Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids

Erika N. Schwarz, Tracey A. Ruhlman, Jamal S. M. Sabir, Nahid H. Ajarah, Njud S. Alharbi, Abdulrahman L. Al-Malki, C. Donovan Bailey, Robert K. Jansen & Nahid H. Hajrah
To date, publicly available plastid genomes of legumes have for the most part been limited to the subfamily Papilionoideae. Here we report 13 new plastid genomes of legumes spanning all three subfamilies. The genomes representing Caesalpinioideae and Mimosoideae are highly conserved in gene content and gene order, similar to the ancestral angiosperm genome organization. Genomes within the Papilionoideae, however, have reduced sizes due to deletions in nine intergenic spacers primarily in the large single copy...

Data from: Modeling character change heterogeneity in phylogenetic analyses of morphology through the use of priors

April M. Wright, Graeme T. Lloyd & David M. Hillis
The Mk model was developed for estimating phylogenetic trees from discrete morphological data, whether for living or fossil taxa. Like any model, the Mk model makes a number of assumptions. One assumption is that transitions between character states are symmetric (i.e., the probability of changing from 0 to 1 is the same as 1 to 0). However, some characters in a data matrix may not satisfy this assumption. Here, we test methods for relaxing this...

Data from: Genome-wide association study of Arabidopsis thaliana identifies determinants of natural variation in seed oil composition

Sandra E. Branham, Sara J. Wright, Aaron Reba & C. Randal Linder
The renewable source of highly reduced carbon provided by plant triacylglycerols (TAGs) fills an ever increasing demand for food, biodiesel, and industrial chemicals. Each of these uses requires different compositions of fatty acid proportions in seed oils. Identifying the genes responsible for variation in seed oil composition in nature provides targets for bioengineering fatty acid proportions optimized for various industrial and nutrition goals. Here, we characterized the seed oil composition of 391 world-wide, wild accessions...

Data from: Genome-wide association study in Arabidopsis thaliana of natural variation in seed oil melting point, a widespread adaptive trait in plants

Sandra E. Branham, Sara J. Wright, Aaron Reba, Ginnie D. Morrison & C. Randal Linder
Seed oil melting point is an adaptive, quantitative trait determined by the relative proportions of the fatty acids that compose the oil. Micro- and macro-evolutionary evidence suggests selection has changed the melting point of seed oils to covary with germination temperatures because of a trade-off between total energy stores and the rate of energy acquisition during germination under competition. The seed oil compositions of 391 natural accessions of Arabidopsis thaliana, grown under common-garden conditions, were...

Data from: Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback

Jesse N. Weber, Gideon S. Bradburd, Yoel E. Stuart, William E. Stutz & Daniel I. Bolnick
Genetic divergence between populations is shaped by a combination of drift, migration, and selection, yielding patterns of isolation-by-distance (IBD) and isolation-by-environment (IBE). Unfortunately, IBD and IBE may be confounded when comparing divergence across habitat boundaries. For instance, parapatric lake and stream threespine stickleback (Gasterosteus aculeatus) may have diverged due to selection against migrants (IBE), or mere spatial separation (IBD). To quantitatively partition the strength of IBE and IBD, we used recently-developed population genetic software (BEDASSLE)...

Data from: Transcriptome dynamics over a lunar month in a broadcast spawning Acroporid coral

Matthew J. Oldach, Matthew Workentine, Mikhail V. Matz, Tung-Yung Fan & Peter D. Vize
On one night per year, at a specific point in the lunar cycle, one of the most extraordinary reproductive events on the planet unfolds as hundreds of millions of broadcast spawning corals release their trillions of gametes into the waters of the tropical seas. Each species spawns on a specific night within the lunar cycle, typically from full moon to third quarter moon, and in a specific time window after sunset. This accuracy is essential...

Data from: A genomic approach for distinguishing between recent and ancient admixture as applied to cattle

Emily Jane McTavish & David M. Hillis
Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We developed a metric, scaled block size (SBS), that uses the unrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient admixture, and applied it to reconstructing admixture in cattle. Cattle are descendants of two independently domesticated lineages, taurine and indicine, that diverged 200,000 or more years ago. Several breeds have hybrid ancestry between these divergent lineages....

Data from: Long-branch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes

Teng Li, Jimeng Hua, April M. Wright, Ying Cui, Qiang Xie, Wenjun Bu & David M. Hillis
Background: Most previous studies of morphological and molecular data have consistently supported the monophyly of the true water bugs (Hemiptera: Nepomorpha). An exception is a recent study by Hua et al. (2009; BMC Evol Biol 9: 134) based on nine nepomorphan mitochondrial genomes. In the analysis of Hua et al. (2009), the water bugs in the group Pleoidea formed the sister group to a clade that consisted of Nepomorpha (the remaining true water bugs) +...

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  • The University of Texas at Austin
  • Cornell University
  • University of Kansas
  • University of California, Berkeley
  • King Abdulaziz University
  • Oregon State University
  • Smithsonian Tropical Research Institute
  • Michigan State University
  • University of California, Davis
  • Fred Hutchinson Cancer Research Center