Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

The use of fossil evidence to calibrate divergence time estimation has a long history. More recently Bayesian MCMC has become the dominant method of divergence time estimation and fossil evidence has been re-interpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting has not been carefully investigated. Here we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis

Correlations in a BEC collision: First-principles quantum dynamics with 150 000 atoms

The quantum dynamics of colliding Bose-Einstein condensates with 150 000 atoms are simulated directly from the Hamiltonian using the stochastic positive-P method. Two-body correlations between the scattered atoms and their velocity distribution are found for experimentally accessible parameters. Hanbury Brown-Twiss or thermal-like correlations are seen for copropagating atoms, while number correlations for counterpropagating atoms are even stronger than thermal correlations at short times. The coherent phase grains grow in size as the collision progresses with the onset of growth coinciding with the beginning of stimulated scattering. The method is versatile and usable for a range of cold atom systems.Comment: 4 pages, 4 figures. v2: Rewording and style changes, minor except for rewrite of background on the positive-P representation. Original research unchange

GPS and property surveying

In 2010 the Global Positioning System (GPS) developed by the United States military was the best known Global Navigation Satellite System (GNSS). Others included Russia’s GLONASS, China’s COMPASS and Europe’s GALILEO systems. Although military satellite navigation systems can be traced back to the 1960s, their civilian uses emerged in the 1980s, initially limited to navigation positioning, not property surveying. Property surveying methods have varied both between and within nations. However, GPS surveying with some supporting legislation, had, by the early years of the 21st century, sufficiently developed to meet the needs of the property sector. This chapter looks at this development, and its implications with respect to cadastral surveying

An integrated approach for predicting the fate of reintroduced populations : a thesis presented in partial fulfilment of the requirements for the degree of Masters of Science in Conservation Biology at Massey University, Palmerston North, New Zealand

I provide a comprehensive account of the fate of a reintroduced population of North Island robins (Petroica longipes) at Tawharanui Regional Park, a predator-free peninsular site in the Auckland Region. All factors affecting the success of reintroductions do so through survival, reproduction, or dispersal. I use an integrated Bayesian approach to assess the impact these factors have on population persistence. I estimated population growth by combining vital rates (survival and reproduction) using 9 years of post-release monitoring data. There was no change to estimates when informative priors that accounted for site-tosite variation were included. I determined that despite low recruitment, the population will persist under current circumstances. I then focused on what was causing low recruitment by distinguishing juvenile survival from permanent natal dispersal. Habitat fragmentation prevented juvenile dispersal out of the park, and juvenile survival was low with most mortality occurring within four months of fledging. It is low juvenile survival that is causing low recruitment, indicating the habitat quality is marginal. Despite this, current habitat quality and connectivity is sufficient to maintain a population, but there may be implications for management if connectivity is increased in the future. Finally, I assessed whether it would be sensible to harvest this population as their location makes them a convenient source for future reintroductions. I projected population dynamics 10 years into the future and examined the implications of a one-off harvest on population persistence. Whilst there was negligible chance that the population would go extinct, a harvest at any level reduced the number of females in the population throughout the 10 years, with larger harvests causing a greater reduction. My results can be used within a decision analysis framework to facilitate the decision of whether Tawharanui would be a suitable source population for future reintroductions

Generalized reduction and pure spinors

We study reduction of Dirac structures from the point of view of pure spinors. We describe explicitly the pure spinor line bundle of the reduced Dirac structure. We also obtain results on reduction of generalized Calabi-Yau structures.Comment: Revised version. To appear in Journal of Symplectic Geometry 12 (3

Theology and the culture of the sciences

This is a PDF version of an article published in New Blackfriars© 2000. The definitive version is available at www.blackwell-synergy.com.This article discusses the relationship between religion and science. It focuses on facts and values, encultured science, exploring elements of scientific culture, theology and scientism, and theology and the future of science

Gaia as science made myth: Implications for environmental ethics

This is a PDF version of an article published in Studies in Christian Ethics© 1996. The definitive version is available at http://sce.sagepub.comThis article discusses the Gaia hypothesis - the earth as a giant ecosystem. It comments on scientific models of Gaia (the interconnected model, the homeostatic process model, the cooperative evolutionary model, the ideological/technological model) and ambiguous ethical implications. The article particularly comments on the work of James Lovelock

An Exploration into the Ethics of Cloning Endangered Species

Researchers are cloning endangered species, expanding the debate on human cloning to include both the value of evolution and the question of whether ethical issues affecting endangered species should be defined in terms of human medical benefit. In this paper, the author explores these questions and others with evolutionary biologist Kathryn Rodriguez-Clark, philosopher Holmes Rolston, III, and toxicologist Don Sparling. Whether or not we are ready to formulate ethics on the subject, if we do not enter into a serious dialogue now, then we allow the question of whether to clone any species—including our own— to be decided for us