User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/03/31

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Comparative Phylogenetics
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 * style="background-color: #F2F2F2" align="center"|  |Main project page


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Labrid Paper Outline
Biology Letters format, 2500 words, 2 figures.
 * Title: Phylogenetic Evidence for Multiple Morphological Niches in Coral Reef Fish
 * Summary (< 200 words)
 * We present phylogenetic evidence for two distinct evolutionary optima in the fin morphology of Labrid Fish.
 * Keywords: Evolution, Phylogenetics, Comparative Methods, Labrids, Multiple Niches
 * Introduction
 * Labrid Fin Morphology
 * Is clustering in Trait space evidence of Selection or Phylogenetic Inertia?
 * Material and Methods
 * as in this entry
 * Results
 * Evidence for and significance of the two-peak model
 * Figures
 * possibly fin morphology and data in single panel? Maybe bootstraps as well?
 * Discussion
 * 1) Understanding multiple niches within current methodology
 * 2) Novel methodology to approach this in a phylogenetic context
 * 3) Future questions
 * Acknowledgements
 * References

R Package -- To Do

 * Should move example scripts into a demo directory
 * Should wrap as an R package
 * Need function to automate the analysis of bootstrap data and recommend the right number of peaks
 * Need prototype stochastic partition and stochastic reconstruction

F1000 reviews
Constable, H. et al., 2010. VertNet: a new model for biodiversity data sharing. PLoS biology, 8(2), e1000309. Available at: http://www.ncbi.nlm.nih.gov/pubmed/20169109. Must read

Summary: Authors describe VertNet, a cloud-computing resource for vertibrate biodiversity data. Data is publicly accessible can be user annotated while remaining contributor-mediated, retaining primacy and expertise of the orignal contributor.

Opinion: Scientists have long argued for the importance of openly accessible, standardized and georeferenced biodiversity data. This work represents a significant accomplishment in overcoming technological, sociological, and idiosynchratic barriers to make this a reality.

Cadotte, M.W. et al., 2010. Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecology Letters, 13(1), 96-105. Available at: http://blackwell-synergy.com/doi/abs/10.1111/j.1461-0248.2009.01405.x. Recommended

Summary: Existing phylogenetic diversity metrics do not account for relative abundance.

Opinion: This work represents a significant improvement on existing approaches of phylogenetic diversity which are commonly used to evaluate species conservation value.

Ziebarth, N.L., Abbott, K.C. & Ives, A.R., 2010. Weak population regulation in ecological time series. Ecology letters, 13(1), 21-31. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19849710. Recommended

Summary: Authors evaluate two large data collections of population dynamics to find that many long time series express only weak regulation using autoregressive moving average (ARMA) models. The variation of the stationary distribution relative to the variation in the moving average component is taken as the measure of population regulation (1 if strong, much larger under weaker regulation).

Opinion: An intriguing paper that brings extensive analysis to a long-standing and fundamental question in population biology. These methods deserve further exploration for their ability to detect strong regulation, as it should be possible to establish confidence intervals on this estimate.

Mendeley

 * Can I get an rss feed of articles I've recently added to my Mendeley collection? Two-way cite-u-like integration?  To explore later

Libraries for stochastic simulation

 * with various levels of course graining, different tau-leaping methods, sdes, etc. Will have to explore more at some point, should see if Arkin's group uses any either.  See:
 * SynBioSS
 * Cain
 * Came across more tau-leaping methods for spatial dynamics and  another how to do tau-leaping when timescales vary widely (stiff dynamics).
 * Mario has some interesting entries on Gillespie methods as well.

Other

 * Interesting post
 * neat github collaboration map might be worth learning more about this kind of visualization.


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