19 Works

Data from: Disentangling density-dependent dynamics using full annual cycle models and Bayesian model weight updating

Orin J. Robinson, Conor P. McGowan & Patrick K. Devers
Density dependence regulates populations of many species across all taxonomic groups. Understanding density dependence is vital for predicting the effects of climate, habitat loss and/or management actions on wild populations. Migratory species likely experience seasonal changes in the relative influence of density dependence on population processes such as survival and recruitment throughout the annual cycle. These effects must be accounted for when characterizing migratory populations via population models. To evaluate effects of density on seasonal...

Data from: Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life

Chris A. Hamilton, Alan R. Lemmon, Emily Moriarty Lemmon & Jason E. Bond
Background: Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and...

Data from: Resolving Cypriniformes relationships using an anchored enrichment approach

Carla C. Stout, Milton Tan, Alan R. Lemmon, Emily Moriarty Lemmon & Jonathan W. Armbruster
Background: Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average...

Data from: Habitat- and season-specific temperatures affect phenotypic development of hatchling lizards

Phillip R. Pearson & Daniel A. Warner
Embryonic environments influence phenotypic development, but relatively few experiments have explored the effects of natural environmental variation. We incubated eggs of the lizard Anolis sagrei under conditions that mimicked natural spatial and temporal thermal variation to determine their effects on offspring morphology and performance. Incubation temperatures mimicked two microhabitats (open, shade) at two different times of the incubation season (April, July). Egg survival, incubation duration and offspring size were influenced by interactions between habitat- and...

Data from: Phylogenomics of Lophotrochozoa with consideration of systematic error

Kevin M. Kocot, Torsten H. Struck, Julia Merkel, Damien S. Waits, Christiane Todt, Pamela M. Brannock, David A. Weese, Johanna T. Cannon, Leonid L. Moroz, Bernhard Lieb & Kenneth M. Halanych
Phylogenomic studies have improved understanding of deep metazoan phylogeny and show promise for resolving incongruences among analyses based on limited numbers of loci. One region of the animal tree that has been especially difficult to resolve, even with phylogenomic approaches, is relationships within Lophotrochozoa (the animal clade that includes molluscs, annelids, and flatworms among others). Lack of resolution in phylogenomic analyses could be due to insufficient phylogenetic signal, limitations in taxon and/or gene sampling, or...

Data from: Geographic structure in the Southern Ocean circumpolar brittle star Ophionotus victoriae (Ophiuridae) revealed from mtDNA and single nucleotide polymorphism data

Matthew P. Galaska, Chester J. Sands, Scott R. Santos, Andrew R. Mahon & Kenneth M. Halanych
Marine systems have traditionally been thought of as “open” with few barriers to gene flow. In particular, many marine organisms in the Southern Ocean purportedly possess circumpolar distributions that have rarely been well verified. Here, we use the highly abundant and endemic Southern Ocean brittle star Ophionotus victoriae to examine genetic structure and determine whether barriers to gene flow have existed around the Antarctic continent. Ophionotus victoriae possesses feeding planktotrophic larvae with presumed high dispersal...

Data from: Spider phylogenomics: untangling the spider tree of life

Jason Bond, Nicole L. Garrison, Juanita Rodriguez, Ingi Agnarsson, Jonathan A. Coddington, Charles E. Griswold, Christopher A. Hamilton, Marshal Hedin, Kevin Kocot, Joel M. Ledford & Jason E. Bond
Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes...

Data from: Plasma dipeptidyl peptidase IV activity and measures of body composition in apparently healthy people

Heidi A. Kluess, Leslie E. Neidert, Katherine S. Wainright, Chen Zheng & Jeganathan Ramesh Babu
Aim: Based on its regulatory action on glucagon-like peptide 1, dipeptidyl peptidase IV (DPP-IV) has increasingly been linked to Type 2 diabetes. However, there is no evidence as to how this normal modulatory enzyme leads to pathology. It is thought that DPP-IV is affected by the development of obesity, which is a common precursor to Type 2 diabetes. Little is known about the relationship between DPP-IV activity in plasma and specific body composition measures. Main...

Data from: Ecosystem carbon density and allocation across a chronosequence of longleaf pine forests

Lisa J. Samuelson, Thomas A. Stokes, John R. Butnor, Kurt H. Johnsen, Carlos A. Gonzalez-Benecke, Timothy A. Martin, , Pete H. Anderson, Michael R. Ramirez, John C. Lewis & Wendell P. Cropper
Forests can partially offset greenhouse gas emissions and contribute to climate change mitigation, mainly through increases in live biomass. We quantified carbon (C) density in 20 managed longleaf pine (Pinus palustris Mill.) forests ranging in age from five to 118 years located across the southeastern USA and estimated above and belowground C trajectories. Ecosystem C stock (all pools including soil C) and aboveground live tree C increased nonlinearly with stand age and the modeled asymptotic...

Data from: Kin effects on energy allocation in group-living ground squirrels

Vincent A. Viblanc, Claire Saraux, Jan O. Murie & F. Stephen Dobson
The social environment has potent effects on individual phenotype and fitness in group-living species. We asked whether the presence of kin might act on energy allocation, a central aspect of life-history variation. Using a 22-year data set on reproductive and somatic allocations in Columbian ground squirrels (Urocitellus columbianus), we tested the effects of co-breeding and non-breeding kin on the fitness and energy allocation balance between reproduction and personal body condition of individual females. Greater numbers...

Data from: Beak color dynamically signals changes in fasting status and parasite loads in king penguins

Quentin Schull, F. Stephen Dobson, Antoine Stier, Jean-Patrice Robin, Pierre Bize & Vincent A. Viblanc
Dynamic ornamental signals that vary over minutes, hours or weeks can yield continuous information on individual condition (e.g., energy reserves or immune status), and may therefore be under strong social and/or sexual selection. In vertebrates, the coloration of the integument is often viewed as a dynamic ornament, which in birds can be apparent in the beak. King penguins (Aptenodytes patagonicus) are monomorphic seabirds that possess conspicuous yellow–orange (YO) and ultraviolet (UV) beak spots that are...

Data from: Metabarcoding reveals environmental factors influencing spatio-temporal variation in pelagic micro-eukaryotes

Pamela M. Brannock, Alice C. Ortmann, Anthony G. Moss & Kenneth M. Halanych
Marine environments harbour a vast diversity of micro-eukaryotic organisms (protists and other small eukaryotes) that play important roles in structuring marine ecosystems. However, micro-eukaryote diversity is not well understood. Likewise, knowledge is limited regarding micro-eukaryote spatial and seasonal distribution, especially over long temporal scales. Given the importance of this group for mobilizing energy from lower trophic levels near the base of the food chain to larger organisms, assessing community stability, diversity and resilience is important...

Data from: Here and there, but not everywhere: repeated loss of uncoupling protein 1 in amniotes

Suzanne McGaugh & Tonia S. Schwartz
Endothermy is an evolutionary innovation in eutherian mammals and birds. In eutherian mammals, UCP1 is a key protein in adaptive nonshivering thermogenesis (NST). Although ucp1 arose early in the vertebrate lineage, the loss of ucp1 was previously documented in several reptile species (including birds). Here we determine that ucp1 was lost at the base of the reptile lineage, as we fail to find ucp1 in every major reptile lineage. Furthermore, though UCP1 plays a key...

Data from: The evolution of annelids reveals two adaptive routes to the interstitial realm

Torsten Hugo Struck, Anja Golombek, Anne Weigert, Franziska Anni Franke, Wilfried Westheide, Günter Purschke, Christoph Bleidorn & Kenneth Michael Halanych
Many animals permanently inhabit the marine interstitium, the space between sand grains [ 1, 2 ]. Different evolutionary scenarios may explain the existence of interstitial animals [ 3, 4 ]. These scenarios include (1) that the interstitial realm is the ancestral habitat of bilaterians [ 5, 6 ], (2) that interstitial taxa evolved from larger ancestors by miniaturization, or (3) progenesis [ 3 ]. The first view mirrors the former hypothesis that interstitial annelids, called...

Data from: Relationship between maternal environment and DNA methylation patterns of estrogen receptor alpha in wild Eastern Bluebird (Sialia sialis) nestlings: a pilot study

Alexandra B. Bentz, Aubrey E. Sirman, Haruka Wada, Kristen J. Navara & Wendy R. Hood
There is mounting evidence that, across taxa, females breeding in competitive environments tend to allocate more testosterone to their offspring prenatally and these offspring typically have more aggressive and faster-growing phenotypes. To date, no study has determined the mechanisms mediating this maternal effect's influence on offspring phenotype. However, levels of estrogen receptor alpha (ERα) gene expression are linked to differences in early growth and aggression; thus, maternal hormones may alter gene regulation, perhaps via DNA...

Data from: Reproduction does not adversely affect liver mitochondrial respiratory function but results in lipid peroxidation and increased antioxidants in house mice

Annelise V. Mowry, Andreas N. Kavazis, Aubrey E. Sirman, Wayne K. Potts & Wendy R. Hood
Reproduction is thought to come at a cost to longevity. Based on the assumption that increased energy expenditure during reproduction is associated with increased free-radical production by mitochondria, oxidative damage has been suggested to drive this trade-off. We examined the impact of reproduction on liver mitochondrial function by utilizing post-reproductive and non-reproductive house mice (Mus musculus) living under semi-natural conditions. The age-matched post-reproductive and non-reproductive groups were compared after the reproductive females returned to a...

Data from: Who let the CAT out of the bag? accurately dealing with substitutional heterogeneity in phylogenomic analyses

Nathan V. Whelan & Kenneth M. Halanych
As phylogenetic datasets have increased in size, site-heterogeneous substitution models such as CAT-F81 and CAT-GTR have been advocated in favor of other models because they purportedly suppress long-branch attraction (LBA). These models are two of the most commonly used models in phylogenomics, and they have been applied to a variety of taxa ranging from Drosophila to land plants. However, many arguments in favor of CAT models have been based on tenuous assumptions about the true...

Data from: Genetic basis for red coloration in birds

Ricardo J Lopes, James D Johnson, Matthew B Toomey, Mafalda S Ferreira, Pedro M Araújo, José Melo-Ferreira, Leif Andersson, Geoffrey E Hill, Joseph C Corbo & Miguel Carneiro
The yellow and red feather pigmentation of many bird species [1] plays pivotal roles in social signaling and mate choice [2, 3]. To produce red pigments, birds ingest yellow carotenoids and endogenously convert them into red ketocarotenoids via an oxidation reaction catalyzed by a previously unknown ketolase [4–6]. We investigated the genetic basis for red coloration in birds using whole-genome sequencing of red siskins (Spinus cucullata), common canaries (Serinus canaria), and ‘‘red factor’’ canaries, which...

Data from: SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus)

Allison J. Shultz, Allan J. Baker, Geoffrey E. Hill, Paul M. Nolan & Scott V. Edwards
Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch (Haemorhous mexicanus) using samples collected before and after a pathogen-induced selection event. Using ddRADseq, we genotyped over 18,000 SNPs across the genome in native pre-epizootic western US birds, introduced birds from Hawaii and the eastern United States, post-epizootic eastern birds, and...

Registration Year

  • 2016

Resource Types

  • Dataset


  • Auburn University
  • University of Vermont
  • University of Florida
  • Florida State University
  • University of Strasbourg
  • University of Georgia
  • University of Alberta
  • University of Minnesota
  • United States Department of Agriculture
  • Smithsonian Institution