9 Works

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, 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: 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, C Zhang, M Miller, Z J Chen, Z Shen & S P Briggs
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: 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...

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, 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: 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: 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: 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: 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: 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...

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