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The conflation of ignorance and knowledge in the inference of clade posteriors
Christopher P. Randle a,* and Kurt M. Pickett b
a Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77341-2116, USA ; b Department of Biology, University of Vermont, 316 Marsh Life Science Building, Burlington, VT 05404, USA
*Corresponding author.
Cladistics 26: (2009) 1-10.
Published Online: Jan 4 2010 3:13PM

ABSTRACT

The objective Bayesian approach relies on the construction of prior distributions that reflect ignorance. When topologies are considered equally probable a priori, clades cannot be. Shifting justifications have been offered for the use of uniform topological priors in Bayesian inference. These include: (i) topological priors do not inappropriately influence Bayesian inference when they are uniform; (ii) although clade priors are not uniform, their undesirable influence is negated by the likelihood function, even when data sets are small; and (iii) the influence of nonuniform clade priors is an appropriate reflection of knowledge. The first two justifications have been addressed previously: the first is false, and the second was found to be questionable. The third and most recent justification is inconsistent with the first two, and with the objective Bayesian philosophy itself. Thus, there has been no coherent justification for the use of nonflat clade priors in Bayesian phylogenetics. We discuss several solutions: (i) Bayesian inference can be abandoned in favour of other methods of phylogenetic inference; (ii) the objective Bayesian philosophy can be abandoned in favour of a subjective interpretation; (iii) the topology with the greatest posterior probability, which is also the tree of greatest marginal likelihood, can be accepted as optimal, with clade support estimated using other means; or (iv) a Bayes factor, which accounts for differences in priors among competing hypotheses, can be used to assess the weight of evidence in support of clades.
©The Willi Hennig Society, 2009.

DIGITAL OBJECT IDENTIFIER (DOI)

10.1111/j.1096-0031.2009.00301.x
http://www3.interscience.wiley.com/journal/123232287/abstract?

Preguntas de los lectores

1. ¿es posible usar como marcador evolutivo a los ARNm (solo exones) teniendo en cuenta que puede haber mucha variaciones debido al splicing alternativo?

2. ¿Conoces de otros sitios como CIPRES (http://www.phylo.org/) para analizar moderadas cantidades de secuencias?

Luis Tataje,
http://www.blogger.com/profile/07472607612141390238
Perú

Conservation Fellowships for Bolivia, Colombia, Ecuador, Mexico, and Peru

December 29, 2009

Russell E. Train Fellowships for Conservation Studies

Application Deadlines: January 31 and February 28, 2010
WWF’s Education for Nature Program is pleased to announce the availability of Russell E. Train Fellowships for students from Bolivia, Colombia, Ecuador, Kenya, Mexico, Papua New Guinea, Peru, Tanzania, and Timor Leste who are pursuing master’s and doctoral degrees in conservation-related fields.

Train Fellowships provide up to two years of support for education-related costs including tuition and fees, room and board, books, travel, and research. Applicants must be citizens or permanent residents of a participating country and must have at least two years’ experience in conservation. Applicants must have applied to, have been accepted to, or be currently enrolled in a conservation-related degree program at an accredited institution of higher education.
Applications for students from Bolivia, Colombia, Ecuador, and Peru are due by January 31, 2010.

Applications from Kenya, Mexico, Papua New Guinea, Tanzania, and Timor Leste are due by February 28, 2010.

Guidelines, applications, and application deadlines vary by country.

Further Scholarship Information and Application Train Fellowship webpage.

Read more: http://www.worldwildlife.org/science/fellowships/TrainDT/item1826.html