12 Works

Data from: Pulmonary anatomy and a case of unilateral aplasia in a common snapping turtle (Chelydra serpentina): developmental perspectives on cryptodiran lungs

Emma R. Schachner, Jayc C. Sedlmayr, Renée Schott, Tyler R. Lyson, R. Kent Sanders & Markus Lambertz
The common snapping turtle (Chelydra serpentina) is a well studied and broadly distributed member of Testudines; however, very little is known concerning developmental anomalies and soft tissue pathologies of turtles and other reptiles. Here, we present an unusual case of unilateral pulmonary aplasia, asymmetrical carapacial kyphosis, and mild scoliosis in a live adult C. serpentina. The detailed three-dimensional (3D) anatomy of the respiratory system in both the pathological and normal adult C. serpentina, and a...

Data from: Phylogenomics using formalin-fixed and 100+ year old intractable natural history specimens

Sara Ruane & Christopher C. Austin
Museum specimens provide a wealth of information to biologists, but obtaining genetic data from formalin-fixed and fluid-preserved specimens remains challenging. While DNA sequences have been recovered from such specimens, most approaches are time-consuming and produce low data quality and quantity. Here we use a modified DNA extraction protocol combined with high-throughput sequencing to recover DNA from formalin-fixed and fluid-preserved snakes that were collected over a century ago and for which little or no modern genetic...

Data from: Contemporary evolution of a Lepidopteran species, Heliothis virescens, in response to modern agricultural practices

Megan L. Fritz, Alexandra M. DeYonke, Alexie Papanicolaou, Stephen Micinski, John Westbrook & Fred Gould
Adaptation to human-induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so...

Data from: Dynamics of marsh-mangrove ecotone since the mid-Holocene: a palynological study of mangrove encroachment and sea level rise in the Shark River Estuary, Florida

Qiang Yao & Kam-Biu Liu
Sea level rise and the associated inland shift of the marsh-mangrove ecotone in south Florida have raised many scientific and management concerns in recent years. Holocene paleoecological records can provide an important baseline to shed light on the long-term dynamics of vegetation changes across this ecotone in the past, which is needed to predict the future. In this study, we present palynological, X-ray fluorescence, and loss-on ignition data from four sedimentary cores recovered from a...

Data from: Genome-wide association analysis in dogs implicates 99 loci as risk variants for anterior cruciate ligament rupture

Lauren A. Baker, Brian Kirkpatrick, Guilherme J.M. Rosa, Daniel Gianola, Bruno Valente, Julia P. Sumner, Wendy Baltzer, Zhengling Hao, Emily E. Binversie, Nicola Volstad, Alexander Piazza, Susannah J. Sample, Peter Muir & Guilherme J. M. Rosa
Anterior cruciate ligament (ACL) rupture is common condition that can be devastating and life changing, particularly in young adults. A non-contact mechanism is typical. Second ACL ruptures through rupture of the contralateral ACL or rupture of a graft repair is also common. Risk of rupture is increased in females. ACL rupture is also common in dogs. Disease prevalence exceeds 5% in several dog breeds, ~100 fold higher than human beings. We provide insight into the...

Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them

Brant C. Faircloth
Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717–726, 2012; Molecular Ecology Resources, 15, 489–501, 2015). Unfortunately, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and...

Data from: Dry habitats were crucibles of domestication in the evolution of agriculture in ants

Michael G. Branstetter, Ana Ješovnik, Jeffrey Sosa-Calvo, Michael W. Lloyd, Brant C. Faircloth, Seán G. Brady & Ted R. Schultz
The evolution of ant agriculture, as practiced by the fungus-farming “attine” ants, is thought to have arisen in the wet rainforests of South America about 55-65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in South American rainforests. The “out-of-the-rainforest” hypothesis, while generally accepted, has never been tested in a phylogenetic context. It also presents a problem for explaining...

Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera

Michael G. Branstetter, John T. Longino, Philip S. Ward & Brant C. Faircloth
1. Targeted enrichment of conserved genomic regions (e.g., ultraconserved elements or UCEs) has emerged as a promising tool for inferring evolutionary history in many organismal groups. Because the UCE approach is still relatively new, much remains to be learned about how best to identify UCE loci and design baits to enrich them. 2. We test an updated UCE identification and bait design workflow for the insect order Hymenoptera, with a particular focus on ants. The...

Data from: Impact of model violations on the inference of species boundaries under the multispecies coalescent

Anthony J. Barley, Jeremy M. Brown & Robert C. Thomson
The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence, and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning...

Data from: Phylogenomics of pike cichlids (Cichlidae: Crenicichla): the rapid evolution and trophic diversification of an incipient species flock

Edward D. Burress, Fernando Alda, Alejandro Duarte, Marcelo Loureiro, Jonathan W. Armbruster & Prosanta Chakrabarty
The rapid rise of phenotypic and ecological diversity in independent lake-dwelling groups of cichlids is emblematic of the East African Great Lakes. In this study, we show that similar ecologically-based diversification has occurred in pike cichlids (Crenicichla) throughout the Uruguay River drainage of South America. We collected genomic data from nearly 500 ultraconserved element (UCEs) loci and >260,000 base pairs across 33 species, to obtain a phylogenetic hypothesis for the major species-groups and to evaluate...

Data from: Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees

Michael G. Branstetter, Bryan N. Danforth, James P. Pitts, Brant C. Faircloth, Philip S. Ward, Matthew L. Buffington, Michael W. Gates, Robert R. Kula & Seán G. Brady
The stinging wasps (Hymenoptera: Aculeata) are an extremely diverse lineage of hymenopteran insects, encompassing over 70,000 described species and a diversity of life history traits, including ectoparasitism, cleptoparasitism, predation, pollen feeding (bees [Anthophila] and Masarinae) and eusociality (social vespid wasps, ants, and some bees) [1]. The most well-studied lineages of Aculeata are the ants, which are ecologically dominant in most terrestrial ecosystems [2], and the bees, the most important lineage of angiosperm-pollinating insects [3]. Establishing...

Data from: Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis bats

, Brant C. Faircloth, Kevin A.M. Sullivan, Troy J. Kieran, Travis C. Glenn, Michael W. Vandewege, , Robert J. Baker, Richard D. Stevens, David A. Ray, Thomas E Lee, Roy N Platt & Kevin A M Sullivan
The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial...

Registration Year

  • 2017

Resource Types

  • Dataset


  • Louisiana State University of Alexandria
  • University of Utah
  • Smithsonian Institution
  • Abilene Christian University
  • Utah State University
  • University of California System
  • University of Georgia
  • Oregon State University
  • University of Hawaii at Manoa
  • University of Wisconsin-Madison