10 Works

Data from: Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years

Devon L. Johnstone, Michael F. O'Connell, Friso P. Palstra & Daniel E. Ruzzante
We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out-migrating smolt and post-spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (Nb)...

Data from: Genetic diversity and differentiation in a wide ranging anadromous fish, American shad (Alosa sapidissima), is correlated with latitude

Daniel J. Hasselman, Daniel Ricard & Paul Bentzen
Studies that span entire species ranges can provide insight into the relative roles of historical contingency and contemporary factors that influence population structure and can reveal patterns of genetic variation that might otherwise go undetected. American shad is a wide ranging anadromous clupeid fish that exhibits variation in demographic histories and reproductive strategies (both semelparity and iteroparity) and provides a unique perspective on the evolutionary processes that govern the genetic architecture of anadromous fishes. Using...

Data from: Telling the whole story in a 10,000-genome world

Robert G. Beiko
BACKGROUND: Genome sequencing has revolutionized our view of the relationships among genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT). Phylogenomic techniques have been used to construct purported trees of microbial life. Although such trees are easily interpreted and allow the use of a subset of genomes as "proxies" for the full set, LGT and other phenomena impact the positioning of different groups in genome trees, confounding and potentially invalidating attempts to...

Data from: Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux

Erin A. Lynch, Morgan G. I. Langille, Aaron Darling, Elizabeth G. Wilbanks, Caitlin Haltiner, Katie S. Y. Shao, Michael O. Starr, Clotilde Teiling, Timothy T. Harkins, Robert A. Edwards, Jonathan A. Eisen & Marc T. Facciotti
We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ~20√ócoverage and assembled to an average of 50 contigs...

Data from: Genetic and phenotypic differentiation among Galaxias maculatus populations in a Patagonian postglacial lake system

Cecilia Carrea, Juan P. Barriga, Victor E. Cussac & Daniel E. Ruzzante
Understanding the influence of landscape features on population differentiation is fundamental to evolutionary biology studies. We examined spatial patterns of genetic and phenotypic variability among Galaxias maculatus populations in a complex of four postglacial lakes in northwestern Patagonia differing in size and connectivity among them. A hierarchical Bayesian analysis grouped the individuals collected from 11 localities into 3 genetic clusters, first defining the populations of the two large lakes and separating the two small lakes...

Data from: Imprints from genetic drift and mutation imply relative divergence times across marine transition zones in a pan-European small pelagic fish (Sprattus sprattus)

Morten T. Limborg, Reinhold Hanel, Paul V. Debes, Anna-Karin Ring, Costas S. Tsigenopoulos, Dorte Bekkevold & Carl Andre
Geographic distributions of most temperate marine fishes are affected by post-glacial recolonisation events which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of European sprat (Sprattus sprattus L.) by combining inference from both mtDNA and microsatellite genetic markers throughout the species distribution. We compared effects from genetic drift and mutation for both genetic markers in shaping genetic differentiation across four transition zones. Microsatellite markers revealed...

Data from: A unified anatomy ontology of the vertebrate skeletal system

Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke, Matthew K. Vickaryous, Monte Westerfield & Paula M. Mabee
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate...

Data from: Migratory constraints on yolk precursors limit yolk androgen deposition and underlie a brood reduction strategy in rockhopper penguins

Glenn T. Crossin, Maud Poisbleau, Laurent Demongin, Olivier Chastel, Tony D. Williams, Marcel Eens & Petra Quillfeldt
Hormonally mediated maternal effects link maternal phenotype and environmental conditions to offspring phenotype. The production of lipid-rich maternal yolk precursors may provide a mechanism by which lipophilic steroid hormones can be transported to developing yolks, thus predicting a positive correlation between yolk precursors in mothers and androgen levels in eggs. Using rockhopper penguins (Eudyptes chrysocome), which produce a two-egg clutch characterized by extreme egg-size dimorphism, reversed hatching asynchrony and brood-reduction, we examined correlations between circulating...

Data from: Correlated evolution of mating system and floral display traits in flowering plants and its implications for the distribution of mating system variation

Carol Goodwillie, Risa D. Sargent, Susan Kalisz, Richard H. Ree, David A. Moeller, Mario Vallejo-Marin, Christopher G. Eckert, Alice A. Winn, Elizabeth Elle, Monica A. Geber & Mark O. Johnston
Reduced allocation to structures for pollinator attraction is predicted in selfing species. We explored the association between outcrossing and floral display in a broad sample of angiosperms. We used the demonstrated relationship to test for bias against selfing species in the outcrossing rate distribution, the shape of which has relevance for the stability of mixed mating. Relationships between outcrossing rate, flower size, flower number and floral display, measured as the product of flower size and...

Data from: Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux

Erin A. Lynch, Morgan G. I. Langille, Aaron Darling, Elizabeth G. Wilbanks, Caitlin Haltiner, Katie S. Y. Shao, Michael O. Starr, Clotilde Teiling, Timothy T. Harkins, Robert A. Edwards, Jonathan A. Eisen, Marc T. Facciotti & Lennart Randau
We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ~20√ócoverage and assembled to an average of 50 contigs...

Registration Year

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  • Dalhousie University
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  • Simon Fraser University
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  • San Diego State University
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  • French National Centre for Scientific Research
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  • University of California, Davis
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  • Max Planck Institute for Ornithology
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  • National Evolutionary Synthesis Center
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  • University of South Dakota
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  • University of Antwerp
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  • Oregon Health & Science University
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