The Future of Systematics: Tree-Thinking Without the Tree

Phylogenetic trees are meant to represent the genealogical history of life and apparently derive their justification from the existence of the tree of life and the fact that evolutionary processes are tree-like. However, there are a number of problems for these assumptions. Here it is argued that once we understand the important role that phylogenetic trees play as models which contain idealizations, we can accept these criticisms and deny the reality of the tree while justifying the continued use of trees in phylogenetic theory and preserving nearly all of what defenders of trees have called “the importance of tree-thinking.

Sceloporus orcutti

Number of Pages: 2Integrative BiologyGeological Science

Restating the Original Source Exception to the False Claims Act\u27s “Public Disclosure Bar”

The False Claims Act (FCA) is the Department of Justice’s (DOJ) primary litigative tool to combat fraud under federal government programs, including as Medicare and the military. The FCA provides for triple damages and civil penalties. It also contains a unique qui tam provision, which allows a whistleblower, known as a “relator,” to file a FCA lawsuit on behalf of the government and receive a share of 15-25% in the recovery. The DOJ has recovered $20 billion under the FCA from companies cheating the government, and has paid out over$2 billion in citizen rewards. The FCA contains a “public disclosure bar,” which is triggered when the fraud allegations were in the public domain before a relator filed suit. If the bar applies, the relator must prove he meets the Act’s “original source exception” or be dismissed from the case. Due to a circuit split in interpreting the original source exception, the Supreme Court granted certiorari in Rockwell v. United States, 127 S. Ct. 1397 (2007), to determine whether the Tenth Circuit misapplied the definition of an original source. This article restates the original source exception by outlining the law and proposing a test to the Supreme Court and lower courts. This article was cited five times in an Amicus brief in the Rockwell case. The author has written another law review article for publication in the Fall of 2008, discussing the Rockwell decision and providing guidance regarding the proper application of the original source exception post-Rockwell

Systematics of the North American menhadens: molecular evolutionary reconstructions in the genus Brevoortia (Clupeiformes: Clupeidae)

Evolutionary associations among the four North American species of menhadens (Brevoortia spp.) have not been thoroughly investigated. In the present study, classifications separating the four species into small-scaled and large-scaled groups were evaluated by using DNA data, and genetic associations within these groups were explored. Specifically, data from the nuclear genome (microsatellites) and the mitochondrial genome (mtDNA sequences) were used to elicit patterns of recent and historical evolutionary associations. Nuclear DNA data indicated limited contemporary gene flow among the species, and also indicated higher relatedness within the small-scaled and large-scaled menhadens than between these groups. Mitochondrial DNA sequences of the large-scaled menhadens indicated the presence of two ancestral lineages, one of which contained members of both species. This result may indicate genetic diver-gence (reproductive isolation) followed by secondary contact (hybridization) between these species. In contrast, a single ancestral lineage indicated incomplete genetic divergence between the small-scaled menhaden. These results are discussed in the context of the biology and demographics of each species

Imaging Characterization of Current Generating Lipid-protein Membranes

Imaging Characterization of Current Generating Lipid-protein Membrane

Axiomatic opportunities and obstacles for inferring a species tree from gene trees

The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all taxa are present in every gene tree. Here, we list four apparently desirable properties that a method for estimating a species tree from gene trees could have (the strongest property states that building a species tree from input gene trees and then pruning leaves gives a tree that is the same as, or more resolved than, the tree obtained by first removing the taxa from the input trees and then building the species tree). We show that while it is technically possible to simultaneously satisfy these properties when taxon coverage is complete, they cannot all be satisfied in the more general supertree setting. In part two, we discuss a concordance-based consensus method based on Baum's `plurality clusters', and an extension to concordance supertrees.Comment: 19 pages, 2 figure

VARTOOLS: A Program for Analyzing Astronomical Time-Series Data

This paper describes the VARTOOLS program, which is an open-source command-line utility, written in C, for analyzing astronomical time-series data, especially light curves. The program provides a general-purpose set of tools for processing light curves including signal identification, filtering, light curve manipulation, time conversions, and modeling and simulating light curves. Some of the routines implemented include the Generalized Lomb-Scargle periodogram, the Box-Least Squares transit search routine, the Analysis of Variance periodogram, the Discrete Fourier Transform including the CLEAN algorithm, the Weighted Wavelet Z-Transform, light curve arithmetic, linear and non-linear optimization of analytic functions including support for Markov Chain Monte Carlo analyses with non-trivial covariances, characterizing and/or simulating time-correlated noise, and the TFA and SYSREM filtering algorithms, among others. A mechanism is also provided for incorporating a user's own compiled processing routines into the program. VARTOOLS is designed especially for batch processing of light curves, including built-in support for parallel processing, making it useful for large time-domain surveys such as searches for transiting planets. Several examples are provided to illustrate the use of the program.Comment: 83 pages, 5 figures, accepted for publication in Astronomy and Computing, code available at http://www.astro.princeton.edu/~jhartman/vartools.htm