9 Works

Data from: Genetic data reveal mixed-stock aggregations of gray whales in the North Pacific Ocean

Anna Brüniche-Olsen, R. Jorge Urban, Vladimir V. Vertyankin, Celine A.J. Godard-Codding, John W. Bickham & J. Andrew DeWoody
Gray whales (Eschrichtius robustus) in the Western Pacific are critically endangered whereas in the Eastern Pacific they are relatively common. Holocene environmental changes and commercial whaling reduced their numbers, but gray whales in the Eastern Pacific now outnumber their Western counterparts by more than 100-fold. Herein, we investigate the genetic diversity and population structure within the species using a panel of genic SNPs. Results indicate the gray whale gene pool is differentiated into two substocks...

Data from: Variation in coexisting birds to exploit spatial heterogeneity in small mammal activity

Quinn C. Emmering, Janice K. Kelly, Richard S. Ostfeld & Kenneth A. Schmidt
Breeding nest site selection is often the first defense against nest predation risk. To be effective, this mechanism requires site-specific spatial heterogeneity in predator abundance which produces predator-poor space, prey's ability to assess spatial heterogeneity in risk, and few or weak constraints on the ability to settle in within predator-poor space. We used a 15-year dataset on forested grids that provided extensive records of fledging success of veeries (Catharus fuscescens) and ovenbirds (Seiurus aurocapilla) in...

Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

Matthew G. Johnson, Lisa Pokorny, Steven Dodsworth, Laura R. Botigue, Robyn S. Cowan, Alison Devault, Wolf L. Eiserhardt, Niroshini Epitawalage, Félix Forest, Jan T. Kim, James Leebens-Mack, Ilia J. Leitch, Olivier Maurin, Doug Soltis, Pamela S. Soltis, Gane Ka-Shu Wong, William J. Baker & Norman Wickett
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used...

Data from: True homoplasy of retrotransposon insertions in primates

Liliya Doronina, Olga Reising, Hiram Clawson, David A. Ray & Jürgen Schmitz
How reliable are the presence/absence insertion patterns of the supposedly homoplasy-free retrotransposons, that were randomly inserted in the quasi infinite genomic space? To systematically examine this question in an up-to-date, multi-genome comparison, we screened millions of primate transposed Alu SINE elements for incidences of homoplasious precise insertions and deletions. In genome-wide analyses, we identified and manually verified nine cases of precise parallel Alu insertions of apparently identical elements at orthologous positions in two ape lineages...

Data from: Habitat selection and the value of information in heterogenous landscapes

Kenneth A. Schmidt & Francois Massol
Despite the wide usage of the term information in evolutionary ecology, there is no general treatise between fitness (i.e., density-dependent population growth) and selection of the environment sensu lato. Here we (1) initiate the building of a quantitative framework with which to examine the relationship between information use in spatially heterogeneous landscapes and density-dependent population growth, and (2) illustrate its utility by applying the framework to an existing model of breeding habitat selection. We begin...

Data from: Evaluating a handheld decision support device in pediatric intensive care settings

Tera L. Reynolds, Patricia R. DeLucia, Karen A. Esquibel, Todd Gage, Noah J. Wheeler, J. Adam Randell, James G. Stevenson & Kai Zheng
Objective: To evaluate end-user acceptance and the effect of a commercial handheld decision support device in pediatric intensive care settings. The technology, pac2, was designed to assist nurses in calculating medication dose volumes and infusion rates at the bedside. Materials and Methods: The devices, manufactured by InformMed Inc., were deployed in the pediatric and neonatal intensive care units in two health systems. This mixed methods study assessed end-user acceptance, as well as pac2’s effect on...

Data from: Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus

Heather Rose Kates, Matthew G. Johnson, Elliot M. Gardner, Nyree J.C. Zerega, Norman J. Wickett & Nyree J. C. Zerega
Premise of the study: Untapped information about allelic diversity within populations and individuals (i.e. heterozygosity) could improve phylogenetic resolution and accuracy. Many phylogenetic reconstructions ignore heterozygosity because it is difficult to assemble allele sequences and combine allelic data across unlinked loci and it is unclear how reconstruction methods accommodate variable sequences. We review the common methods of including heterozygosity in phylogenetic studies and present a novel method for assembling allele sequences from target enriched Illumina...

Data from: A latitudinal gradient in dimensionality of biodiversity

Richard D. Stevens & J. Sebastian Tello
Biodiversity is multifaceted and represents numerous dimensions expressing variation in richness and abundances of species, ecosystem functions, phylogenetic relationships, morphology, traits and interactions. Such dimensions are correlated to varying degrees and recent research has attempted to better understand behavior of such correlations. We define dimensionality of biodiversity as degree of redundancy in variation among multiple dimensions of biodiversity. One fundamental question regarding biodiversity is whether its dimensionality is spatially structured, also exhibiting geographic gradients. We...

Data from: Changing environmental gradients over forty years alter ecomorphological variation in Guadalupe Bass Micropterus treculii throughout a river basin

Jessica E. Pease, Timothy B. Grabowski, Allison A. Pease & Preston T. Bean
Understanding the degree of intraspecific variation within and among populations is a key aspect of predicting the capacity of a species to respond to anthropogenic disturbances. However, intraspecific variation is usually assessed at either limited temporal, but broad spatial scales or vice versa, which can make assessing changes in response to long-term disturbances challenging. We evaluated the relationship between the longitudinal gradient of changing flow regimes and land use/land cover patterns since 1980 and morphological...

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