Reconstructing evolutionary trees

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Ilkay

Maximum clade credibility consensus tree

Maximum clade credibility consensus tree

Bayesian MCMC inference (Phylogenetic]

Fortunato and Mace 2009: in future to draw on Bayesian MCMC inference, reviewed in Huelsenbeck et al. 2001; and Holder and Lewis 2003)

Huelsenbeck, J. P., F. Renquist, R. Nielsen, J. P. Pollack. 2001. Bayesian Inference of Phylogeny and its Impact on Evolutionary Biology. Science 294[5550]:2310-2314.

Holder, M., P. O. Lewis. 2003. Phylogenetic Estimation: Traditional and Bayesian Approaches. Nature Reviews Genetics 4(4):275-284.

Paup: Phylogenetic Analysis Using Parsimony

http://paup.csit.fsu.edu/about.html Manual: 1993 302 pages long. Seemingly free at this time but obsolete.

Nostratic

http://tuvalu.santafe.edu/~johnson/articles.nostratic.html
http://en.wikipedia.org/wiki/File:Nostratic_tree.svg
http://en.wikipedia.org/wiki/Dené–Caucasian_languages

Other

- david.maddison@science.oregonstate.edu. Phone: (541) 737-2834 - Wayne P. Maddison wmaddisn@interchange.ubc.ca Office phone: 604-822-1545

  • Maddison, W.P. 2010. Mesquite installation for MacOS X [Online]. Website last modified in 2010 (accessed on August 18, 2011) Available at http://mesquiteproject.org/mesquite/download/installationMacOS.html
  • Maddison, W.P. & D.R. Maddison. 2010. Mesquite: a modular system for evolutionary analysis [Online]. Website last modified on October 3, 2010 (accessed on August 18, 2011) Available at http://mesquiteproject.org/mesquite/mesquite.html
  • Maddison, W.P. & D.R. Maddison. 2010a. Mesquite download page [Online]. Website last modified in 2010 (accessed on August 18, 2011) Available at http://mesquiteproject.org/mesquite/download/download.html
  • Maddison, W.P. & D.R. Maddison. 2010b. How to cite Mesquite? [Online]. Website last modified in 2010 (accessed on August 18, 2011) Available at http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/publication.html#howToCite
  • Maddison, W.P. & D.R. Maddison. 2010c. Mesquite Manual: Installation [Online]. Website last modified in 2010 (accessed on August 18, 2011) Available at http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/installation/installation.html
  • R Phylogenetics, especially Comparative -
  • R.G.FitzJohn, Maddison, WP, Otto SP. 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst Biol. 2009 Dec;58(6):595-611. doi: 10.1093/sysbio/syp067 Abstract: Species traits may influence rates of speciation and extinction, affecting both the patterns of diversification among lineages and the distribution of traits among species. Existing likelihood approaches for detecting differential diversification require complete phylogenies; that is, every extant species must be present in a well-resolved phylogeny. We developed 2 likelihood methods that can be used to infer the effect of a trait on speciation and extinction without complete phylogenetic information, generalizing the recent binary-state speciation and extinction method. Our approaches can be used where a phylogeny can be reasonably assumed to be a random sample of extant species or where all extant species are included but some are assigned only to terminal unresolved clades. We explored the effects of decreasing phylogenetic resolution on the ability of our approach to detect differential diversification within a Bayesian framework using simulated phylogenies. Differential diversification caused by an asymmetry in speciation rates was nearly as well detected with only 50% of extant species phylogenetically resolved as with complete phylogenetic knowledge. We demonstrate our unresolved clade method with an analysis of sexual dimorphism and diversification in shorebirds (Charadriiformes). Our methods allow for the direct estimation of the effect of a trait on speciation and extinction rates using incompletely resolved phylogenies.
  • see also corHMM - and Mark Pagel
http://cran.r-project.org/web/packages/ape/index.html ape: Analyses of Phylogenetics and Evolution
http://cran.r-project.org/web/packages/geiger/index.html geiger: Analysis of evolutionary diversification
http://cran.r-project.org/web/packages/phylobase/index.html phylobase: Base package for phylogenetic structures and comparative data
http://cran.r-project.org/web/packages/phytools/index.html phytools: Phylogenetic Tools for comparative biology (and other things)
https://stat.ethz.ch/pipermail/r-sig-phylo/2012-July/002194.html Pagel lambda, delta, kappa parameters
http://www.evolution.reading.ac.uk/BayesTraits.html 2013 Pagel BayesTraitsV2Manual(Beta).pdf The program is run from the command prompt (Windows) or terminal (OS X and Linux) not by double clicking
http://www.evolution.reading.ac.uk Printable BayesTraitsV2Manual(Beta).pdf
http://www.evolution.rdg.ac.uk/Files/ContinuousManual.pdf 14 pp Printable ContinuousManual. Continuous is a computer program that implements a generalised least squares (GLS) model for the across-species analysis of comparative data. The method is described in two papers (Pagel 1997 and 1999). … The application program can be used to
Screen Shot 2013-12-05 at 12.40.19 PM.png
  • Mark Pagel 1997. Inferring evolutionary processes from phylogenies. Zoologica Scripta (Journal of the Royal Swedish Academy) 25th Anniversary Special Issue on Phylogenetics and Systematics, 26(4), 331-348. Abstract: Evolutionary processes shape the regular trends of evolution and are responsible for the diversity and distribution of contemporary species. They include correlated evolutionary change and trajectories of trait evolution, convergent and parallel evolution, differential rates of evolution, speciation and extinction, the order and direction of change in characters, and the nature of the evolutionary process itself—does change accumulate gradually, episodically, or in punctuational bursts. Phylogenies, in combination with information on species, contain the imprint of these historical evolutionary processes. By applying comparative methods based upon statistical models of evolution to well resolved phylogenies, it is possible to infer the historical evolutionary processes that must have existed in the past, given the patterns of diversity seen in the present. I describe a set of maximum likelihood statistical methods for inferring such processes. The methods estimate parameters of statistical models for inferring correlated evolutionary change in continuously varying characters, for detecting correlated evolution in discrete characters, for estimating rates of evolution, and for investigating the nature of the evolutionary process itself. They also anticipate the wealth of information becoming available to biological scientists from genetic studies that pin down relationships among organisms with unprecedented accuracy.
  • Mark Pagel 1999. Inferring the historical patterns of biological evolution. Nature 401, 877-884. Abstract: Phylogenetic trees describe the pattern of descent amongst a group of species. With the rapid accumulation of DNA sequence data, more and more phylogenies are being constructed based upon sequence comparisons. The combination of these phylogenies with powerful new statistical approaches for the analysis of biological evolution is challenging widely held beliefs about the history and evolution of life on Earth.
  • meet with johnh@biomail.ucsd.edu School of Computational Science pdf Syst. Biol 2002;51:673-688.
  • The TinyURL for this site is http://tinyurl.com/2drohu
  • http://www.google.com/search?client=safari&rls=en&q=beast+phylogeography&ie=UTF-8&oe=UTF-8 BEAST phylogeography
http://www.kuleuven.be/aidslab/phylogeography/tutorial/spread_tutorial.html

MCMC phylogenetic trees

MrBayes John P. Huelsenbeck at UCSD

  • 2008 but intended for DNA: http://webpages.icav.up.pt/PTDC/BIA-BEC/104097/2008/23.pdf - John P. Huelsenbeck
  • The CIPRES Science Gateway V. 3.1 Wayne Pfeiffer - Mark Miller - Terri Schwartz (Liebowicz-Schwara) The CIPRES Science Gateway V. 3.1 is a public resource for inference of large phylogenetic trees. It is designed to provide all researchers with access to large computational resources of the NSF TeraGrid through a simple browser interface. The CIPRES Science Gateway provides new hybrid parallel versions of RAxML (7.2.7) and MrBayes (3.1.2), as well as parallel GARLI (1.0) code to insure the fastest possible run times for submitted jobs. Through a collaboration with Alexandros Stamatakis and Wayne Pfeiffer, we now offer the fastest hybrid versions of RAxML [pdf] and MrBayes [pdf] currently available.
MrBayes on the CIPRES Science Gateway.

MrBayes is a program for the Bayesian estimation of phylogeny --- evolutionary models for nucleotide, amino acid, restriction site (binary), and standard discrete data. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. Development history

John P. Huelsenbeck. johnh@biomail.ucsd.edu 2002.'Potential Applications and Pitfalls of Bayesian Inference of Phylogeny -pdf Syst. Biol 2002;51:673-688.

Section of Ecology, Behavior and Evolution

          Division of Biological Sciences
       University of California, San Diego

Liam Revell

Liam J. Revell, LD Mahler, PR Peres‐Neto, 2012. A new phylogenetic method for identifying exceptional phenotypic diversification. Evolution 661(1): 135-146. pdf pdf pdf

Liam J. Revell, R. Graham Reynolds. 2012. A New Bayesian Method for Fitting Evolutionary Models to Comparative Data With Intraspecific Variation. Evolutionary Biology forthcoming. Keywords:

  • Comparative method;
  • interspecific data;
  • phylogenetic tree

Abstract: Phylogenetic comparative methods that incorporate intraspecific variability are relatively new and, so far, not especially widely used in empirical studies. In the present short article we will describe a new Bayesian method for fitting evolutionary models to comparative data that incorporates intraspecific variability. This method differs from an existing likelihood-based approach in that it requires no a priori inference about species means and variances; rather it takes phenotypic values from individuals and a phylogenetic tree as input, and then samples species means and variances, along with the parameters of the evolutionary model, from their joint posterior probability distribution. One of the most novel and intriguing attributes of this approach is that jointly sampling the species means with the evolutionary model parameters means that the model and tree can influence our estimates of species mean trait values, not just the reverse. In the present implementation, we first apply this method to the most widely used evolutionary model for continuously valued phenotypic trait data (Brownian motion). However, the general approach has broad applicability, which we illustrate by also fitting the λ model, another simple model for quantitative trait evolution on a phylogeny. We test our approach via simulation and by analyzing two empirical datasets obtained from the literature. Finally, we have implemented the methods described herein in a new function for the R statistical computing environment, and this function will be distributed as part of the ‘phytools’ R library.

phytools: Phylogenetic Tools for comparative biology (and other things).
Liam J. Revell, 2012. phytools: An R package for phylogenetic comparative biology (and other things) Methods in Ecology and Evolution 3: 217-223 doi:10.1111/j.2041-210X.2011.00169.x

Emmanuel Paradis

Emmanuel Paradis Analysis of phylogenetics and evolution with R - Google Books Amazon

Paradis phylogenetic software page - obsolete

R-Sig-Phylo

AWTY

Genographic Project

Ancestry project Genographic Project

University College London

Pagel, M., Meade, A. and Barker, D. 2004. Bayesian estimation of ancestral character states on phylogenies. Systematic Biology, 53, 673-684.

http://www.evolution.reading.ac.uk/BayesTraits.html

Greenhill SJ, Currie TE, Gray RD. 2009. Does horizontal transmission invalidate cultural phylogenies? Proc Biol Sci. 2009 Jun 22;276(1665):2299-306. Epub 2009 Mar 18.

Abstract. Phylogenetic methods have recently been applied to studies of cultural evolution. However, it has been claimed that the large amount of horizontal transmission that sometimes occurs between cultural groups invalidates the use of these methods. Here, we use a natural model of linguistic evolution to simulate borrowing between languages. The results show that tree topologies constructed with Bayesian phylogenetic methods are robust to realistic levels of borrowing. Inferences about divergence dates are slightly less robust and show a tendency to underestimate dates. Our results demonstrate that realistic levels of reticulation between cultures do not invalidate a phylogenetic approach to cultural and linguistic evolution.
Rogers, D. S., Marcus W. Feldman, and P. R. Ehrlich. 2009. Inferring population histories using cultural dataProc R Soc B November 7, 2009 276:3835-3843.

Mace R, Holden CJ. 2005. A phylogenetic approach to cultural evolution. Trends Ecol Evol. 2005 Mar;20(3):116-21. Epub 2004 Dec 24.

Abstract. There has been a rapid increase in the use of phylogenetic methods to study the evolution of languages and culture. Languages fit a tree model of evolution well, at least in their basic vocabulary, challenging the view that blending, or admixture among neighbouring groups, was predominant in cultural history. Here, we argue that we can use language trees to test hypotheses about not only cultural history and diversification, but also bio-cultural adaptation. Phylogenetic comparative methods take account of the non-independence of cultures (Galton's problem), which can cause spurious statistical associations in comparative analyses. Advances in phylogenetic methods offer new possibilities for the analysis of cultural evolution, including estimating the rate of evolution and the direction of coevolutionary change of traits on the tree. They also enable

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

Peter Gray. Linguistic evolution and phylogenetics. (Courtesy Richard McElreath UC Davis)

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:

  1. 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
  2. Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376.
  3. 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
  4. 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.
  5. Related work on Neighbor Joining
  6. 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.

A Project plan that isn't working

  1. . 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
  1. . This can be compared with the language phylogeny of Tanmoy using Gell-Mann's data if permitted
  2. . Ask Doug Wallace for the ethnographic level mitochondrial DNA phylogeny.
  3. . Match all these data to common ethnographic level groups where possible (allowing missing data)
  4. . Ask Doug Wallace and his colleagues how to do this for Y chromosome phylogeny
  5. . Ask his colleagues studying migrations histories for their data
  6. . Match all the phylogenies to splitting, dispersals, migrations.
  7. . Estimate the genetic bottlenecks, from the bottlenecks the areas in which these occurred
  8. . Date these "survivors of bottlenecks" areas
  9. . Get the ice cores and other climate data and match to these dates.
  10. . Identify the cultural and linguistic reconstructions for these bottlenecks
  11. . Trace the lines of geographic stability, growth and population expansion, settlement expansion
  12. . Trace the cultural and linguistic trees from these and nonbottleneck areas
  13. . 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

AMNK cladistics

Phylogenetic Analysis of DNA and other data using dynamic homology

Download Current version: 4.1.2 (7 August 2009)

   * Change history

Citation

Binaries

   * WinXP (single & parallel) [download] (969 downloads)
   * Mac OS X (single & parallel) [download] (618 downloads)
   * Linux (single, x86) [download] (815 downloads)

Source code

   * Source code [download] (815 downloads)

Documentation

   * Documentation and sample datasets [download] (741 downloads)

Phylogenetic analyses of behavior support existence of culture among wild chimpanzees

Stephen J. Lycett, Mark Collard, and William C. McGrew. 2011. Phylogenetic analyses of behavior support existence of culture among wild chimpanzees. NAS November 6, 2007 vol. 104 no. 45 17588-17592.

Links

http://intersci.ss.uci.edu/wiki/index.php/Complexity_in_human_behavior (first and second paragraphs)

Ilkay Phylogenetics

Hi Doug,
Sorry to be late with my response. 
CIPReS project had a good package for phylo some years ago:  http://www.phylo.org/sub_sections/software/
I have asked how to get a hold of those documents since the links at the url seem to be missing. 
Will update you when I have more information.
Best, ilkay
These are some of the packages: http://sisyphus.eecs.berkeley.edu:8079/hudson/job/kepler/javadoc/org/cipres/kepler/package-summary.html
Are they helpful? I can dig them up if needed.
Actually, no need to dig anything up. They are still in the kepler trunk. Just search for cipres in the actor pane. Kepler Phylo Workflow
A slideshow from 2006: http://www.powershow.com/view/8ee52-MjUxM/CIPRes_in_Kepler_An_integrative_workflow_package_for_streamlining_phylogenetic_data_analyses_powerpoint_ppt_presentation
Code for the packages: https://svn.sdsc.edu/repo/CIPRES/cipres-kepler/trunk/java/org/cipres/kepler/
Best,
-ilkay