8 Works

Data from: SNP discovery in wild and domesticated populations of blue catfish, Ictalurus furcatus, using genotyping-by-sequencing and subsequent SNP validation

Chao Li, Geoff Waldbieser, Brian Bosworth, Benjamin H. Beck, Wilawan Thongda & Eric Peatman
Blue catfish, Ictalurus furcatus, are valued in the United States as a trophy fishery for their capacity to reach large sizes, sometimes exceeding 45 kg. Additionally, blue catfish × channel catfish (I. punctatus) hybrid food fish production has recently increased the demand for blue catfish broodstock. However, there has been little study of the genetic impacts and interaction of farmed, introduced and stocked populations of blue catfish. We utilized genotyping-by-sequencing (GBS) to capture and genotype...

Data from: Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution

Jason E. Bond, Nicole L. Garrison, Chris A. Hamilton, Rebecca L. Godwin, Marshal Hedin & Ingi Agnarsson
Spiders represent an ancient predatory lineage known for their extraordinary biomaterials, including venoms and silks. These adaptations make spiders key arthropod predators in most terrestrial ecosystems. Despite ecological, biomedical, and biomaterial importance, relationships among major spider lineages remain unresolved or poorly supported. Current working hypotheses for a spider “backbone” phylogeny are largely based on morphological evidence, as most molecular markers currently employed are generally inadequate for resolving deeper-level relationships. We present here a phylogenomic analysis...

Data from: Phylogenomic resolution of the Hemichordate and Echinoderm clade

Johanna T. Cannon, Kevin M. Kocot, Damien S. Waits, David A. Weese, Billie J. Swalla, Scott R. Santos & Kenneth M. Halanych
Ambulacraria, comprising Hemichordata and Echinodermata, is closely related to Chordata, making it integral to understanding chordate origins and polarizing chordate molecular and morphological characters. Unfortunately, relationships within Hemichordata and Echinodermata have remained unresolved, compromising our ability to extrapolate findings from the most closely related molecular and developmental models outside of Chordata (e.g., the acorn worms Saccoglossus kowalevskii and Ptychodera flava and the sea urchin Strongylocentrotus purpuratus). To resolve long-standing phylogenetic issues within Ambulacraria, we sequenced...

Data from: Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees

Michael D. Crisp, Nate B. Hardy & Lyn G. Cook
Background: Estimating divergence times in phylogenies using a molecular clock depends on accurate modeling of nucleotide substitution rates in DNA sequences. Rate heterogeneity among lineages is likely to affect estimates, especially in lineages with long stems and short crowns (“broom” clades) and no internal calibration. We evaluate the performance of the random local clocks model (RLC) and the more routinely employed uncorrelated lognormal relaxed clock model (UCLN) in situations in which a significant rate shift...

Data from: \"Transcriptomic resources for five shrimp (Crustacea: Atyidae and Alpheidae) species from the anchialine ecosystem\" in Genomic Resources Notes accepted 1 June 2014 to 31 July 2014

Justin C. Havird & Scott R. Santos
Antecaridina_lauensis_transcriptomeFile containing contigs in FASTA format from Antecaridina lauensis assembled de novo using Trinity.Antecaridina_lauensis_TRI_1_20_2014_NORM.fastaAntecaridina_lauensis_bedAntecaridina lauensis .bed file containing information for putative ORFs as called by the program TransDecoderAntecaridina_lauensis_TRI_1_20_2014_NORM.fasta.transdecoder.bedAntecaridina_lauensis_cdsAntecaridina lauensis .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoderAntecaridina_lauensis_TRI_1_20_2014_NORM.fasta.transdecoder.cdsAntecaridina_lauensis_gffAntecaridina lauensis .gff file containing mapping information for the putative ORFs as called by the program TransDecoderAntecaridina_lauensis_TRI_1_20_2014_NORM.fasta.transdecoder.gff3Antecaridina_lauensis_pepAntecaridina lauensis .pep file containing amino acid sequences for putative ORFs as called...

Data from: Response of non-grassland avian guilds to adjacent herbaceous field buffers: testing hypotheses about configuration of targeted conservation practices in agricultural landscapes

Samuel K. Riffell, Adrian P. Monroe, James A. Martin, Kristine O. Evans, , Mark D. Smith & Loren W. Burger
1. A substantial part of the world's land base is dominated by agriculture, and forest habitat often consists of discrete patches of forest and linear woody corridors. These natural components provide habitat for some forest birds, but make conservation of these species difficult. In-field practices applied outside forest patches, such as specific juxtapositions of herbaceous field buffers adjacent to forest habitat, could increase avian diversity contributions of existing forest without creation of additional forest habitat....

Data from: \"Genome-wide microsatellite marker development from next-generation sequencing of two non-model bat species impacted by wind turbine mortality: Lasiurus borealis and L. cinereus (Vespertilionidae)\" in Genomic Resources Notes accepted 1 October 2013 to 30 November 2013

Stephen R. Keller, Regina Trott, Cortney Pylant, David N. Nelson & Scott R. Santos
Tree-roosting bats in the genus Lasiurus are widespread, migratory species that have not been well characterized for population genetic diversity and structure due to a lack of genetic resources. Generating genetic resources in Lasiurus is made pressing by the need for conservation genetic assessments of demographic trends in this genus, which comprise a large percentage of bat mortalities at wind turbine sites across North America. We report on marker development from whole-genome Illumina sequencing of...

Data from: Specialization and generalization in the diversification of phytophagous insects: tests of the musical chairs and oscillation hypotheses

Nate B. Hardy & Sarah P. Otto
Evolutionary biologists have often assumed that ecological generalism comes at the expense of less intense exploitation of specific resources and that this trade-off will promote the evolution of ecologically specialized daughter species. Using a phylogenetic comparative approach with butterflies as a model system, we test hypotheses that incorporate changes in niche breadth and location into explanations of the taxonomic diversification of insect herbivores. Specifically, we compare the oscillation hypothesis, where speciation is driven by host-plant...

Registration Year

  • 2014

Resource Types

  • Dataset


  • Auburn University
  • University of Queensland
  • University of Washington
  • University of Vermont
  • Australian National University
  • United States Department of Agriculture
  • San Diego State University
  • University of British Columbia
  • Mississippi State University
  • University of Maryland, College Park