10 Works

Data from: Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)

Matthew Lance Niemiller, Benjamin Minault Fitzpatrick, Premal Shah, Lars Schmitz & Thomas J. Near
The genetic mechanisms underlying regressive evolution—the degeneration or loss of a derived trait—are largely unknown, particularly for complex structures such as eyes in cave organisms. In several eyeless animals, the visual photoreceptor rhodopsin appeared to retain functional amino-acid sequences. Hypotheses to explain apparent maintenance of function include weak selection for retention of light-sensing abilities and its pleiotropic roles in circadian rhythms and thermotaxis. In contrast, we show that there has been repeated loss of functional...

Data from: Effects of climatic and geological processes during the Pleistocene on the evolutionary history of the northern cavefish, Amblyopsis spelaea (Teleostei: Amblyopsidae)

Matthew Lance Niemiller, James R. McCandless, Robert Graham Reynolds, James Caddle, Thomas J. Near, Christopher R. Tillquist, William D. Pearson & Benjamin Minault Fitzpatrick
Climatic and geological processes associated with glaciation cycles during the Pleistocene have been implicated in influencing patterns of genetic variation and promoting speciation of temperate flora and fauna. However, determining the factors promoting divergence and speciation is often difficult in many groups because of our limited understanding of potential vicariant barriers and connectivity between populations. Pleistocene glacial cycles are thought to have significantly influenced the distribution and diversity of subterranean invertebrates; however, impacts on subterranean...

Data from: Unraveling the determinants of insular body size shifts

Craig R. McClain, Paul A. P. Durst, Alison G. Boyer & Clinton D. Francis
The island rule, a pattern of size shifts on islands, is an oft-cited but little understood phenomenon of evolutionary biology. Here we explore the evolutionary mechanisms behind the rule in 184 mammal species, testing climatic, ecological, and phylogenetic hypotheses in a robust quantitative framework. Our findings confirm the importance of species’ ecological traits in determining both the strength and the direction of body size changes on islands. Although the island rule pattern appears relatively weak...

Data from: A parametric method for assessing diversification rate variation in phylogenetic trees

Premal Shah, Benjamin Minault Fitzpatrick & James Andrew Fordyce
Phylogenetic hypotheses are frequently used to examine variation in rates of diversification across the history of a group. Patterns of diversification-rate variation can be used to infer underlying ecological and evolutionary processes responsible for patterns of cladogenesis. Most existing methods examine rate variation through time. Methods for examining differences in diversification among groups are more limited. Here we present a new method, parametric rate comparison (PRC), that explicitly compares diversification rates among lineages in a...

Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

Arlin Stoltzfus, Brian O'Meara, Jamie Whitacre, Ross Mounce, Emily L. Gillespie, Sudhir Kumar, Dan F. Rosauer & Rutger A. Vos
BACKGROUND: Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote data sharing reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing phylogenetic trees and associated data in a way that promotes re-use. RESULTS: Here we summarize...

Data from: Human impacted landscapes facilitate hybridization between a native and an introduced tree

Sean M. Hoban, Tim S. McCleary, Scott E. Schlarbaum, Sandra L. Anagnostakis & Jeanne Romero-Severson
Spatial and temporal dynamics of hybridization, in particular the influence of local environmental conditions, are well studied for sympatric species but less is known for native-introduced systems, especially for long-lived species. We used microsatellite and chloroplast DNA markers to characterize the influence of anthropogenic landscapes on the extent, direction, and spatial distribution of hybridization between a native North American tree Juglans cinerea (butternut) and an introduced tree Juglans ailantifolia (Japanese walnut) for 1363 trees at...

Data from: The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss

Richard E. Lenski, Erik R. Zinser & James Jeffrey Morris
Reductive genomic evolution is common in endosymbiotic bacteria, where it is driven by genetic drift. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococcus and Pelagibacter, and in these cases the reduction appears to be driven by natural selection rather than drift. The loss of certain genes in free-living organisms may leave them dependent on co-occurring microbes for the lost metabolic functions. We present the...

Data from: Mitochondrial genome primers for Lake Malawi cichlids

C. Darrin Hulsey, Hugo Alamillo, Benjamin P. Keck & Brian C. O'Meara
Resolving the evolutionary history of rapidly diversifying lineages like the Lake Malawi Cichlid Flock demands powerful phylogenetic tools. Although this clade of over 500 species of fish likely diversified in less than two million years, the availability of extensive sequence data sets, such as complete mitochondrial genomes, could help resolve evolutionary patterns in this group. Using a large number of newly developed primers, we generated whole mitochondrial genome sequences for 14 Lake Malawi cichlids. We...

Data from: Morphometric investigation of the Pentremites fauna from the Glen Dean Formation, Kentucky

James W. Atwood & Colin D. Sumrall
New techniques involving three-dimensional (3D) data collection and landmark analysis provide an opportunity to make breakthroughs in understanding blastoid morphology. This pilot study examines four species (Pentremites pyriformis, P. tulipiformis, P. fredericki n. sp., and P. meganae n. sp.), using 3D morphological variation and geometric morphometrics to discriminate between species. All specimens were collected from a single shale unit within the Upper Mississippian Glen Dean Formation near Hopkinsville, Kentucky. A 3D laser scanner was used...

Data from: Specificity, rank preference and the colonization of a non-native host plant by the Melissa blue butterfly

Matthew L. Forister, Cynthia F. Scholl, Josh P. Jahner, Joseph S. Wilson, James A. Fordyce, Zach Gompert, Divya R. Narala, C. Alex Buerkle & Chris C. Nice
Animals often express behavioral preferences for different types of food or other resources, and these preferences can evolve or shift following association with novel food types. Shifts in preference can involve at least two phenomena: a change in rank preference or a change in specificity. The former corresponds to a change in the order in which hosts are preferred, while a shift in specificity can be an increase in the tendency to utilize multiple hosts....

Registration Year

  • 2012

Resource Types

  • Dataset


  • University of Tennessee at Knoxville
  • Yale University
  • National Evolutionary Synthesis Center
  • University of Bath
  • University of Pennsylvania
  • National Museum of Natural History
  • University of Notre Dame
  • Scripps College
  • Duke University
  • University of Wyoming