17 Works

Data from: Best practices for justifying fossil calibrations

James F. Parham, Philip C. J. Donoghue, Christopher J. Bell, Tyler D. Calway, Jason J. Head, Patricia A. Holroyd, Jun G. Inoue, Randall B. Irmis, Walter G. Joyce, Daniel T. Ksepka, José S. L. Patané, Nathan D. Smith, James E. Tarver, Marcel Van Tuinen, Ziheng Yang, Kenneth D. Angielczyk, Jenny M. Greenwood, Christy A. Hipsley, Jacobs Louis, Peter J. Makovicky, Johannes Müller, Krister T. Smith, Jessica M. Theodor, Rachel C. M. Warnock, Michael J. Benton … & Louis Jacobs
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule; with replacement rates established (calibrated) using inaccurate paleontological age estimates...

Data from: Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

Holly M. Bik, Way Sung, Paul De Ley, James G. Baldwin, Jyotsna Sharma, Axayácatl Rocha-Olivares & W. Kelley Thomas
Microbial eukaryotes (nematodes, protists, fungi, etc., loosely referred to as meiofauna) are ubiquitous in marine sediments and likely play pivotal roles in maintaining ecosystem function. Although the deep-sea benthos represents one of the world’s largest habitats, we lack a firm understanding of the biodiversity and community interactions amongst meiobenthic organisms in this ecosystem. Within this vast environment key questions concerning the historical genetic structure of species remain a mystery, yet have profound implications for our...

Data from: Poison frog colors are honest signals of toxicity, particularly for bird predators

Martine E. Maan & Molly E. Cummings
Antipredator defenses and warning signals typically evolve in concert. However, the extensive variation across taxa in both these components of predator deterrence, and the relationship between them, are poorly understood. Here we test whether there is a predictive relationship between visual conspicuousness and toxicity levels across 10 populations of the color polymorphic strawberry poison frog, Dendrobates pumilio. Using a mouse-based toxicity assay, we find extreme variation in toxicity between frog populations. This variation is significantly...

Data from: Effects of founding genetic variation on adaptation to a novel resource

Deepa Agashe, Jay J Falk & Daniel I Bolnick
Population genetic theory predicts that adaptation in novel environments is enhanced by genetic variation for fitness. However, theory also predicts that under strong selection, demographic stochasticity can drive populations to extinction before they can adapt. We exposed wheat-adapted populations of the flour beetle (Tribolium castaneum) to a novel suboptimal corn resource, to test the effects of founding genetic variation on population decline and subsequent extinction or adaptation. As previously reported, genetically diverse populations were less...

Data from: Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm

Amanda J Waters, Irina Makarevitch, Steve R Eichten, Ruth A Swanson-Wagner, Cheng-Ting Yeh, Wayne Xu, Patrick S Schnable, Matthew W Vaughn, Mary Gehring & Nathan M Springer
Imprinting describes the differential expression of alleles based upon their parent of origin. Deep sequencing of RNAs from maize endosperm and embryo tissue 14 days after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm including 54 maternally expressed...

Data from: Quantifying historical trends in the completeness of the fossil record and the contributing factors: an example using Aves

Daniel T. Ksepka & Clint A. Boyd
Improvements in the perceived completeness of the fossil record may be driven both by new discoveries and by reinterpretation of known fossils, but disentangling the relative effects of these processes can be difficult. Here, we propose a new methodology for evaluating historical trends in the perceived completeness of the fossil record, demonstrate its implementation using the freely available software ASCC (version 4.0.0), and present an example using crown-group birds (Aves). Dates of discovery and recognition...

Data from: Can reinforcement complete speciation?

Claudia Bank, Joachim Hermisson & Mark Kirkpatrick
Hybridization is common in nature, even between "good" species. This observation poses the question of why reinforcement is not always successful in leading to the evolution of complete reproductive isolation. To study this question, we developed a new "quasi-linkage disequilibrium" (QLD) approximation to obtain the first analytic results for the evolution of modifiers that increase mate discrimination against hybrids and heterospecifics. When such modifiers have small effects, they evolve more readily under a one-allele than...

Data from: Molecular signatures of selection on reproductive character displacement of flower color in Phlox drummondii

Robin Hopkins, Donald A. Levin & Mark D Rausher
Character displacement, which arises when species diverge in sympatry to decrease competition for resources or reproductive interference, has been observed in a wide variety of plants and animals. A classic example of reproductive character displacement, presumed to be caused by reinforcing selection, is flower-color variation in the native Texas wildflower Phlox drummondii. Here we use population genetic analyses to investigate molecular signatures of selection on flower-color variation in this species. First, we quantify patterns of...

Data from: SATé-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees

Kevin Liu, Tandy J. Warnow, Mark T. Holder, Serita M. Nelesen, Jiaye Yu, Alexandros P. Stamatakis & C. Randal Linder
Highly accurate estimation of phylogenetic trees for large datasets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Co-estimation of alignments and trees has been attempted, but currently only SATé estimates reasonably accurate trees and alignments for large datasets in practical time frames (Liu et al., 2009b). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I)...

Data from: Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms

Andrew J Alverson, Robert K Jansen & Edward C Theriot
Salinity imposes a significant barrier to he distribution of many organisms, including diatoms. Diatoms are ancestrally marine, and the number of times they have independently colonized fresh waters and the physiological adaptations that facilitated these transitions remain outstanding questions in diatom evolution. The colonization of fresh waters by diatoms has been compared to ‘‘crossing the Rubicon,’’ implying that successful colonization events are rare, irreversible, and lead to substantial species diversification. To test these hypotheses, we...

Data from: Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill

Holly M. Bik, Kenneth M. Halanych, Jyotsna Sharma & W. Kelley Thomas
Benthic habitats harbour a significant (yet unexplored) diversity of microscopic eukaryote taxa, including metazoan phyla, protists, algae and fungi. These groups are thought to underpin ecosystem functioning across diverse marine environments. Coastal marine habitats in the Gulf of Mexico experienced visible, heavy impacts following the Deepwater Horizon oil spill in 2010, yet our scant knowledge of prior eukaryotic biodiversity has precluded a thorough assessment of this disturbance. Using a marker gene and morphological approach, we...

Data from: Consequences of frugivore-mediated seed dispersal for the spatial and genetic structures of a neotropical palm

Juanita Choo, Thomas E. Juenger & Beryl B. Simpson
The idiosyncratic behaviors of seed dispersers are important contributors to plant spatial associations and genetic structures. In this study, we used a combination of field, molecular, and spatial studies to examine the connections between seed dispersal and the spatial and genetic structures of a dominant neotropical palm Attalea phalerata. Field observation and genetic parentage analysis both indicated that the majority of A. phalerata seeds were dispersed locally over short-distances (< 30 m from the maternal...

Data from: Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors

Danny W. K. Ng, Changqing Zhang, Marisa Miller, Zhouxin Shen, Steven P. Briggs, Z. Jeffrey Chen & D W-K Ng
Autopolyploidy and allopolyploidy are common in many plants and some animals. Rapid changes in genomic composition and gene expression have been observed in both auto- and allopolyploids, but the effects of polyploidy on proteomic divergence are poorly understood. Here we report quantitative analysis of protein changes in leaves of Arabidopsis auto- and allotetraploids and their progenitors using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with mass spectrometry. Over 1 000 proteins analyzed, the...

Data from: The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella

Andrew J Alverson, Bank Beszteri, Matthew L Julius & Edward C Theriot
BACKGROUND: Publication of the first diatom genome, that of Thalassiosira pseudonana, established it as a model species for experimental and genomic studies of diatoms. Virtually every ensuing study has treated T. pseudonana as a marine diatom, with genomic and experimental data valued for their insights into the ecology and evolution of diatoms in the world's oceans. RESULTS: The natural distribution of T. pseudonana spans both marine and fresh waters, and phylogenetic analyses of morphological and...

Data from: Fast molecular evolution associated with high active metabolic rates in poison frogs

Juan C. Santos
Molecular evolution is simultaneously paced by mutation rate, genetic drift, and natural selection. Life history traits also affect the speed of accumulation of nucleotide changes. For instance, small body size, rapid generation time, production of reactive oxygen species, and high resting metabolic rate (RMR) are suggested to be associated with faster rates of molecular evolution. However, phylogenetic correlation analyses failed to support a relationship between RMR and molecular evolution in ectotherms. In addition, resting metabolic...

Data from: Evidence for a Late Pliocene faunal transition based on a new rodent assemblage from Oldowan locality Hadar A.L. 894, Afar Region, Ethiopia

Denné N. Reed & Denis Geraads
The time interval between 3-2 Ma marks several important transitions in human evolution, including the extinction of Australopithecus afarensis, the origin of the genus Homo, and the appearance of concentrated stone tool assemblages forming recognizable archaeological sites. The period also marks important changes in Earth's climatic history, with the onset of northern hemisphere glaciation starting sometime between 2.8-2.5 Ma and it remains an unresolved question in paleoanthropology whether or not the global climatic events influenced...

Data from: SuperFine: fast and accurate supertree estimation

M. Shel Swenson, Rahul Suri, C. Randal Linder & Tandy Warnow
Many research groups are estimating trees containing anywhere from a few thousand to hundreds of thousands of species, towards the eventual goal of the estimation of a Tree of Life, containing perhaps as many as several million leaves. These phylogenetic estimations present enormous computational challenges, and current computational methods are likely to fail to run even on datasets in the low end of this range. One approach to estimate a large species tree is to...

Registration Year

  • 2011

Resource Types

  • Dataset


  • The University of Texas at Austin
  • University of California System
  • North Carolina State University
  • University of Kansas
  • Field Museum of Natural History
  • Duke University
  • University of Groningen
  • St. Cloud State University
  • University of Minnesota
  • Heidelberg Institute for Theoretical Studies