8 Works

Data from: Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × Picea engelmannii)

Sam Yeaman, Kathryn A. Hodgins, Haktan Suren, Kristin A. Nurkowski, Jason A. Holliday, Loren H. Rieseberg & Sally N. Aitken
Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change. By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we use de novo transcriptome assembly and RNA-seq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime...

Data from: Winter food limits timing of pre-alternate molt in a short-distance migratory bird

Raymond M. Danner, Russell S. Greenberg, Julie E. Danner & Jeffrey R. Walters
1. Molt is critical for fitness for many organisms for several reasons: it allows growth and maintains the function of the integument for protection, thermoregulation and communication. 2. Feather molt in birds is costly and therefore typically does not overlap with migration or reproduction. In spring, the rapid succession of pre-alternate molt, migration (if a migrant), and breeding suggests that timing of molt could constrain the initiation of breeding. A tradeoff between time spent molting...

Data from: Quantifying human mobility perturbation and resilience in Hurricane Sandy

Qi Wang & John E. Taylor
Human mobility is influenced by environmental change and natural disasters. Researchers have used trip distance distribution, radius of gyration of movements, and individuals' visited locations to understand and capture human mobility patterns and trajectories. However, our knowledge of human movements during natural disasters is limited owing to both a lack of empirical data and the low precision of available data. Here, we studied human mobility using high-resolution movement data from individuals in New York City...

Data from: Extensive introgression in a malaria vector species complex revealed by phylogenomics

Michael C. Fontaine, James B. Pease, Aaron Steele, Robert M. Waterhouse, Daniel E. Neafsey, Igor V. Sharakhov, Xiofang Jiang, Andrew B. Hall, Flaminia Catteruccia, Evdoxia Kakani, Sarah N. Mitchell, Yi-Chieh Wu, Hilary A. Smith, R. Rebecca Love, Mara K. Lawniczak, Michel A. Slotman, Scott J. Emrich, Matthew W. Hahn & Nora J. Besansky
Introgressive hybridization is now recognized as a widespread phenomenon, but its role in evolution remains contested. Here we use newly available reference genome assemblies to investigate phylogenetic relationships and introgression in a medically important group of Afrotropical mosquito sibling species. We have identified the correct species branching order to resolve a contentious phylogeny, and show that lineages leading to the principal vectors of human malaria were among the first to split. Pervasive autosomal introgression between...

Data from: Penalized Multi-Marker versus Single-Marker Regression methods for genome-wide association studies of quantitative traits

Hui Yi, Patrick Breheny, Netsanet Iman, Yongmei Liu, Ina Hoeschele & N. Imam
The data from genome-wide association studies (GWAS) in humans are still predominantly analyzed using single marker association methods. As an alternative to Single Marker Analysis (SMA), all or subsets of markers can be tested simultaneously. This approach requires a form of Penalized Regression (PR) as the number of SNPs is much larger than the sample size. Here we review PR methods in the context of GWAS, extend them to perform penalty parameter and SNP selection...

Data from: Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)

Lecong Zhou, Rajesh Bawa & Jason A. Holliday
Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed...

Data from: A tapetal ablation transgene induces stable male-sterility and slows field growth in Populus

Estefania Elorriaga, Richard Meilan, Cathleen Ma, Jeffrey S. Skinner, Elizabeth Etherington, Amy Brunner & Steven H. Strauss
The field performance of genetic containment technologies–considered important for certain uses of transgenic trees in forestry–is poorly known. We tested the efficiency of a barnase gene driven by the TA29 tapetum-dominant promoter for influencing growth rate and inducing male sterility in a field trial of transgenic hybrid poplar (Populus tremula × Populus tremuloides). When the growth of 18 transgenic insertion events with the sterility transgene were compared to non-transgenic controls after two growing seasons, they...

Data from: Noninvasive individual and species identification of jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) in Belize, Central America using cross-species microsatellites and fecal DNA

Claudia Wultsch, Lisette P. Waits & Marcella J. Kelly
There is a great need to develop efficient, noninvasive genetic sampling methods to study wild populations of multiple, co-occurring, threatened felids. This is especially important for molecular scatology studies occurring in challenging tropical environments where DNA degrades quickly and the quality of faecal samples varies greatly. We optimized 14 polymorphic microsatellite loci for jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) and assessed their utility for cross-species amplification. Additionally, we tested their reliability...

Registration Year

  • 2014
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Affiliations

  • Virginia Tech
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  • University of Notre Dame
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  • Oregon State University
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  • Monash University
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  • Indiana University Bloomington
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