Tag Archives: reconstruction

Fun with estimating divergence times


Estimating divergence times is notorious difficult and the field can be downright rancorous with some being accused of reading tea leaves and chicken entrails – interesting reading for personalities as much as the different scientific approaches. There are several different approaches to trying to estimate a divergence time among species, using calibration points usually anchored by fossil data. Molecular clock methods have problems sometimes producing extremely old dates that are quite hotly debated. In fungi we have a very few fossils (and their placement on the phylogeny is debated).

There are quite a few available methods for reconstructing divergence times including r8s and multidivtime which start with various types of trees and use calibration time points that are typically informed by fossil dates. The simplest approaches assume a molecular clock (rates are same across the tree) and then one only needs to calibrate the number of substitutions (or rate really) to time to determine how phylogenetic tree branch lengths map to time. The BEAST package also does phylogenetic inference and divergence time estimation (and provided the necessary analysis for exoneration of the Tripoli Six) across a sample of trees. BEAST (and MrBayes) use MCMC to sample the space of parameters and tree space to identify phylogenies and evolutionary parameters that explain the data (an alignment of sequences).

A paper from Akerborg and colleagues introduces a new approach that uses MCMC but apply a few twists, using a birth-death model that doesn’t assume a molecular clock and employing a hill-climbing algorithm instead of MCMC to find parameter optima. They use a Maximum a posterior (MAP) framework which is more computational efficient than MCMC. They couple the MAP approach with a dynamic-programming approach that separates the estimation of rates (branch length) from the estimation of times (which often require assumption of a molecular clock). While I can’t speak with much authority on the MAP approach or yet how well this compares on different datasets, it suggests a different method to tackle these problems. They authors point out one drawback with their approach is it only allows for derivation of point-estimates so statistical confidences like bootstrap support are not easily calculated through this approach. Their software, called PRIME is available here and I will be curious to see how it performs in other peoples’ hands.

Akerborg, O., Sennblad, B., Lagergren, J. (2008). Birth-death prior on phylogeny and speed dating. BMC Evolutionary Biology, 8(1), 77. DOI: 10.1186/1471-2148-8-77

Some links


I’ve been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.

Schmitt, I., Partida-Martinez, L.P., Winkler, R., Voigt, K., Einax, E., Dölz, F., Telle, S., Wöstemeyer, J., Hertweck, C. (2008). Evolution of host resistance in a toxin-producing bacterial–fungal alliance. The ISME Journal DOI: 10.1038/ismej.2008.19

LEVASSEUR, A. (2008). FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds. Fungal Genetics and Biology DOI: 10.1016/j.fgb.2008.01.004

Shivaji, S., Bhadra, B., Rao, R.S., Pradhan, S. (2008). Rhodotorula himalayensis sp. nov., a novel psychrophilic yeast isolated from Roopkund Lake of the Himalayan mountain ranges, India. Extremophiles DOI: 10.1007/s00792-008-0144-z

Evolutionary morphology of mushroom-forming fungi

Blogging about Peer-Reviewed ResearchDave Hibbett wrote a great article for Mycological Research that describes the current state of systematics and evolutionary studies of morphology in mushroom-forming Agaricomycete fungi. His article, dedicated to the late, great mycologist Orson K Miller, Jr and entitled “After the gold rush, or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century” describes the how classification and systematics has changed in the last two hundred years and macromorphology to the more than “108,000 nucleotide sequences of ‘homobasidiomycetes’, filed under 7300 unique names.”

The article contains some beautiful pictures many of which are taken from some of the eminent mycological photographers and mycologists Michael Wood and Taylor Lockwood.

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Exploring CUG codon evolution in Candida

A recent PLoS One article “A Genetic Code Alteration Is a Phenotype Diversity Generator in the Human Pathogen Candida albicans” finds some pretty dramatic changes in gene expression and phenotypes by replacing the tRNAs for CUG back to Leucine (Leu; in the standard genetic code) from their meaning of Serine (Ser) in these Candida species. The CUG codon transition in some Candida spp has been of interest since it is an example of a recent change in the genetic code and provides a comparative system to study the mechanism and genome changes of how a genetic code shift is manifested.

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