Reconstructing evolutionary trees

From InterSciWiki

From bridewealth to dowry? A bayesian estimation of ancestral states of marriage transfers in Indo-European groups 2007 Human Nature 17(4): 355-376. Laura Fortunato1 Contact Information, Clare Holden1 and Ruth Mace

The TinyURL for this site is http://tinyurl.com/2drohu

Tanmoy Bhattacharya has been working with his LANL colleagues on on <Large scale computation applied to phylogenetic problems in biology and their extensions to language (and possibly cultural) evolution. Here is the subscription link to the [http://www.sciencemag.org/cgi/content/abstract/288/5472/1796 Science 9 June 2000: Vol. 288. no. 5472, pp. 1796 - 1802 DOI: 10.1126/science.288.5472.1796] article that Tanmoy discusses and that has been so widely cited.

New software for this problem has been tested by William J. Bruno and Chang-Shung Tung as reported in their LANL paper <Quantitative measurement of covariation on an evolutionary tree tested successfully on five CASP6 targets (ca. 2000). Here are the links to the key cited articles for the RIND, CoRind, and MLE programs:

Modeling residue usage in aligned protein sequences via maximum likelihood. WJ Bruno. Los Alamos National Laboratory, New Mexico 87545, USA. billb@lanl.gov free full-text pdf download
Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376.
Pollock, D.D., Taylor, W.R. and Goldman, N. (1999) Coevolving protein residues: maximum likelihood identification and relationship to structure. Journal of Molecular Biology 287:187-198. See also http://scholar.google.com/scholar?hl=en&lr=&oi=qs&q=%22coevolving+protein+residues+maximum+likelihood%22+author:d-pollock
Free full text - Molecular Biology and Evolution 17:189-197 (2000) Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction. William J. Bruno*, Nicholas D. Socci and Aaron L. Halpern, *Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico.
Related work on Neighbor Joining
Related work on protein structure: <Critical assessment of methods of protein structure prediction (CASP) - Round VII

<Doug Wallace and his colleagues utilize mitochondrial DNA to reconstruct human evolutionary trees and migration routes.

<David Haussler develops new statistical and algorithmic methods to explore the molecular evolution of the human genome, integrating cross-species comparative and high-throughput genomics data to study gene structure, function, and regulation.

[edit] Project plan

. Ask Tanmoy Bhattacharya to invite his LANL colleagues to analyze Cultural data (186 society SCCS, 1292 society EthnoAtlas) phylogeny

also Douglas Wallace's mitochondrial DNA data

. This can be compared with the language phylogeny of Tanmoy using Gell-Mann's data if permitted
. Ask Doug Wallace for the ethnographic level mitochondrial DNA phylogeny.
. Match all these data to common ethnographic level groups where possible (allowing missing data)
. Ask Doug Wallace and his colleagues how to do this for Y chromosome phylogeny
. Ask his colleagues studying migrations histories for their data
. Match all the phylogenies to splitting, dispersals, migrations.
. Estimate the genetic bottlenecks, from the bottlenecks the areas in which these occurred
. Date these "survivors of bottlenecks" areas
. Get the ice cores and other climate data and match to these dates.
. Identify the cultural and linguistic reconstructions for these bottlenecks
. Trace the lines of geographic stability, growth and population expansion, settlement expansion
. Trace the cultural and linguistic trees from these and nonbottleneck areas
. Match where possible to states, empires, city systems, and their ecological environments.

Parties directly interested in collaborating so far on these reconstructions:

Scott White

Doug White

Douglas Wallace