Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The Generalized Mixed Yule Coalescent (GMYC) and the Poisson Tree Process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. 2. Here we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2,000 separate species delimitation analyses across 16 empirical datasets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. 3. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. 4. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses

Small-scale convection beneath the transverse ranges, California: Implications for interpretation of gravity anomalies

Tomographic inversion of upper mantle P wave velocity heterogeneities beneath southern California shows two prominent features: an east-west trending curtain of high velocity material (up to 3% fast) in the upper 250 km beneath the Transverse Ranges and a region of low velocity material (up to 4% slow) in the 100 km beneath the Salton Trough. These seismic velocity anomalies were interpreted as due to small scale convection in the mantle. Using this hypothesis and assuming that temperature and density anomalies are linearly related to seismic velocity anomalies through standard coefficients of proportionality, leads to inferred variations of approx. + or - 300 C and approx. + or - 0.03 g/cc

Negotiating the future under the shadow of the past: the eleventh session of the United Nations Forum on Forests and the 2015 renewal of the international arrangement on forests

Prior to the eleventh session of the United Nations Forum on Forests (UNFF) in 2015 a series of interlinked initiatives took place intended to generate new options for strengthening the international arrangement on forests. The paper analyses these initiatives and identifies the main proposals to emerge from them. It is shown that almost all these proposals were lost or weakened during the negotiation process. One reason for this, it is argued, is the consensual decision making procedures of the UNFF whereby it takes all states to say yes, and only one to say no. This empowers veto states, namely powerful and intransigent states that wish to resist change in key areas. It is also argued that international forest negotiations do not start from a blank page with ‘textual shadows’, namely precedents from inside and outside the UNFF, delimiting the possibilities available for delegates and, for some issues, leading to the perpetuation of the status quo. The result is that during the formal intergovernmental negotiations creativity is stifled with the textual outputs tending towards a politics of the lowest common denominator

Center and representations of infinitesimal Hecke algebras of sl_2

In this paper, we compute the center of the infinitesimal Hecke algebras Hz associated to sl_2 ; then using nontriviality of the center, we study representations of these algebras in the framework of the BGG category O. We also discuss central elements in infinitesimal Hecke algebras over gl(n) and sp(2n) for all n. We end by proving an analogue of the theorem of Duflo for Hz.Comment: Final form, to appear in "Communications in Algebra"; 35 pages, laTe

Genetic tracing of the epithelial lineage during mammalian kidney repair

Developing new therapeutic approaches to treat acute kidney injury requires a detailed understanding of endogenous cellular repair. Genetic fate mapping defines cellular hierarchies in vivo and we used this technique to assess a possible contribution of non-epithelial stem cells to renal repair after ischemic injury. Mice with efficient labeling of renal epithelial cells, but not non-epithelial interstitial cells, were subjected to a single cycle or sequential cycles of kidney injury and repair. No dilution of the epithelial cell fate marker was observed despite robust epithelial cell proliferation. Thus, non-tubular cells do not have the ability to migrate across the basement membrane and differentiate into epithelial cells in this model. Instead, surviving tubular epithelial cells are responsible for repair of the damaged nephron. Future studies will need to distinguish between uniform dedifferentiation and proliferation of all epithelial cells after injury versus selective expansion of an intratubular epithelial stem cell

Planetary Magnetic Dynamo Theories: A Century of Failure

For nearly a century, geoscientists who believe the earth is billions of years old have been striving to develop a successful dynamo theory to explain how the earth\u27s magnetic field might maintain itself over that long time. After reviewing analytic theories, computer simulations, and laboratory experiments, I have concluded that all those efforts have fallen short of proving the geomagnetic field could be maintained by a dynamo. To contrast with this apparent failure, I touch upon the remarkable success of creationist theories in explaining magnetic fields in our Solar system, especially the planet Mercury. This contrast supports the young Biblical age of the world, about 6,000 years

Regulation of Physician Self-Referral Arrangements: Is Prohibition the Answer Or Has Congress Operated on the Wrong Patient

Rapidly increasing health care costs have created a national crisis. Perceiving physician referral behavior as the principal cause, Congress and several state legislatures have prohibited certain referrals. This Comment analyzes the data that spawned such legislation and critiques prohibition of referrals as a solution to the crisis. The Comment asserts that the prohibition remedy is overly broad and largely ineffective. The author recommends a more farsighted solution, such as the creation of a prepaid physician compensation system. The author argues that such a system would minimize the incentive to make unnecessary referrals while simultaneously reducing the level of health care costs borne by the government

Reversals of the Earth\u27s Magnetic Field During the Genesis Flood

Strong convection in the earth\u27s core during the Deluge would rapidly reverse the magnetic field while the fossil layers were being laid down. Afterwards the field would fluctuate for several thousand years and then begin decaying steadily. This young-earth model explains the paleomagnetic and archaeomagnetic evidence better than old-earth dynamo theories do

A Biblical Basis for a Creationist Cosmology

Taking Genesis 1 and other scriptures in the most straightforward possible sense leads to several conclusions of great importance for cosmology: (1) The expanse of Genesis chapter 1 is not the earth\u27s atmosphere but interstellar space, (2) The waters above the expanse are cosmic in scale and represent a boundary for interstellar space, (3) the earth is near the center of the universe. These conclusions form the basis for a young-earth relativistic cosmology which I describe in another paper presented at this conference