Interpreting and estimating phylogenies

Molecular Systematics
Hillis et al.
Sinauer Associates, Inc., 1996, 978-0878932825
Publisher website
Especially the chapter on Phylogenetic Inference by Swofford et al. pages 407-514

Troubleshooting Molecular Phylogenetic Analyses
Sanderson and Shaffer
Ann Rev Evol and Syst 2002 33:49-72
An excellent overview of how to approach phylogenetic analyses generally, with advice on how to deal with commonly-arising issues of concern

Fundamentals of Molecular Evolution
Graur and Li
Sinauer Associates, 2000, 978-0878932665
Publisher website
General, easily-accessible introduction to the topic

Inferring Phylogenies
Sinauer Associates, 2003, 978-0878931774
Publisher website
Very detailed discussion of the topic from one of the pioneers in the field. Goes into considerable mathematical details.

The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny
Marco Salemi and Anne-Mieke Vandamme (Eds)
Cambridge University Press, 2003, 978-0521803908
Publisher website

Molecular Phylogeny - Pitfalls and Progress
Moreira and Philippe
Intl Microbiol 2000 3:9-16

Phylogeny for the faint of heart: a tutorial
Trends in Genetics 2003 19:345-351

Models of molecular evolution and phylogeny.
Lio P and Goldman N
Genome Res 1998 8(12):1233-44

Phylogenetic inference using whole genomes.
Rannala B, Yang Z.
Annu Rev Genomics Hum Genet. 2008;9:217-31.
PMID: 18767964
PubMed Publisher Website
Review that covers many of the key issues associated with interpreting molecular phylogenies including paralogy and lineage sorting.

Computational Molecular Evolution
Yang, Z. (2006)
(Oxford Series in Ecology and Evolution). Oxford: Oxford University Press.
Publisher Website
Involved yet accessible textbook on models, and applications of models, in molecular evolution.

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.
Stamatakis A, Ludwig T, Meier H.
Bioinformatics. 2005 Feb 15;21(4):456-63.
PMID: 15608047
PubMed Publisher Website
Description of the RAxML, the maximum-likelihood software we use in the exercises to estimate phylogeny.

New methods for inferring population dynamics from microbial sequences.
Pérez-Losada M, Porter ML, Tazi L, Crandall KA.
Infect Genet Evol. 2007 Jan;7(1):24-43.
PMID: 16627010
PubMed PubMed Central Full Text
Reviews a wide range of different software and methodologies used in investigating population dynamics and evolutionary relationships

Rooting phylogenetic trees

Inferring the Root of a Phylogenetic Tree
John P. Huelsenbeck, Jonathan P. Bollback and Amy M. Levine
Systematic Biology 2002 51(1):32-43
Publishers website

Incomplete lineage sorting

Inferring phylogeny despite incomplete lineage sorting.
Maddison WP, Knowles LL.
Syst Biol. 2006 Feb;55(1):21-30.
PMID: 16507521
Introduction provides a clear and concise description of incomplete lineage sorting, along with citations of other articles focusing on this topic

Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers.
Carstens BC, Knowles LL.
Syst Biol. 2007 Jun;56(3):400-11.
PMID: 17520504
Describes an approach to species tree estimation that takes into account incomplete lineage sorting

Horizontal/lateral gene transfer

A set of articles presenting different perspectives on the topic

Estimation of phylogenetic inconsistencies in the three domains of life.
Soria-Carrasco V, Castresana J.
Mol Biol Evol. 2008 Nov;25(11):2319-29
PMID: 18701430

Dealing with incongruence in phylogenomic analyses.
Galtier N, Daubin V.
Philos Trans R Soc Lond B Biol Sci. 2008 Oct 7.
PMID: 18852109
Both articles above use a similar approach to investigating the extent of phylogenetic inconsistency that could be assigned to HGT in prokaryotes by comparison with the extent of phylogenetic inconsistency obtained from similar trees in eukaryotes (where no/very limited HGT is expected to occur).

Horizontal Gene Transfer - Genomes in Flux
Methods in Molecular Biology book series
Ed. Gogarten MB, Gogarten JP and Olendzenski L
Volume 532, March 2009
551 pages
Publishers website
An entire book focused on the topic - mostly from the position that there is extensive HGT

Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates.
Stanhope MJ, Lupas A, Italia MJ, Koretke KK, Volker C, Brown JR.
Nature. 2001 Jun 21;411(6840):940-4.
PMID: 11418856

Microbial genes in the human genome: lateral transfer or gene loss?
Salzberg SL, White O, Peterson J, Eisen JA.
Science. 2001 Jun 8;292(5523):1903-6.
PMID: 11358996
Both of the above articles use phylogenetic analyses to challenge initial claims of extensive bacterial to vertebrate HGT (claims based on initial drafts of the human genome).

Horizontal gene transfer, genome innovation and evolution.
Gogarten JP, Townsend JP.
Nat Rev Microbiol. 2005 Sep;3(9):679-87.
PMID: 16138096

Horizontal gene transfer in eukaryotic evolution.
Keeling PJ, Palmer JD.
Nat Rev Genet. 2008 Aug;9(8):605-18.
PMID: 18591983
Both of the above articles are reviews of the topic written from a position that there is extensive HGT

What tangled web: barriers to rampant horizontal gene transfer.
Kurland CG.
Bioessays. 2005 Jul;27(7):741-7.
PMID: 15954096
A review from the position that the "rampant HGT" model is unlikely to be appropriate

Phylogenetic networks

SplitsTree: a network based tool for exploring evolutionary relationships in molecular data
Vincent Moulton
Chapter 12, The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny

Application of phylogenetic networks in evolutionary studies.
Huson, DH and Bryant, D
Mol Biol Evol 2006, 23(2):254-67

Simultaneous alignment and tree estimation

Bayesian coestimation of phylogeny and sequence alignment.
Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.
BMC Bioinformatics. 2005 Apr 1;6:83.
PMID: 15804354
PubMed Publisher Website

Joint Bayesian estimation of alignment and phylogeny.
Redelings BD, Suchard MA.
Syst Biol. 2005 Jun;54(3):401-18.
PMID: 16012107
PubMed Publisher Website

SATCHMO: sequence alignment and tree construction using hidden Markov models.
Edgar RC, Sjölander K.
Bioinformatics. 2003 Jul 22;19(11):1404-11.
PMID: 12874053
PubMed Publisher Website


Homology assessment and molecular sequence alignment.
Phillips AJ.
J Biomed Inform. 2006 Feb;39(1):18-33.
PMID: 16380300
PubMed Publisher Website

Interconversion between two unrelated protein folds in the lymphotactin native state.
Tuinstra RL, Peterson FC, Kutlesa S, Elgin ES, Kron MA, Volkman BF.
Proc Natl Acad Sci U S A. 2008 Apr 1;105(13):5057-62. Epub 2008 Mar 25.
PMID: 18364395
PubMed Publisher Website

Some new terms for duplicated genes.
Sharman AC.
Semin Cell Dev Biol. 1999 Oct;10(5):561-3.
PMID: 10597641
PubMed Publisher Website

Multiple sequence alignment

Multiple sequence alignment.
Edgar, R.C., and S. Batzoglou.
2006 Curr Opin Struct Biol 16:368-373.
A review of available MSA software, with recommendations on possible procedures to follow given different MSA tasks.

Multiple protein sequence alignment.
Pei, J.
2008 Curr Opin Struct Biol 18:382-386.
A more recent review of current MSA methods.

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.
Loytynoja A and Goldman N
Science 2008 320(5883):1632-5
Highlights an important source of systematic error present in many popular MSA programs.

The Rieske protein: a case study on the pitfalls of multiple sequence alignments and phylogenetic reconstruction.
Lebrun E, Santini JM, Brugna M, Ducluzeau AL, Ouchane S, Schoepp-Cothenet B, Baymann F, Nitschke W.
Mol Biol Evol. 2006 Jun;23(6):1180-91.
PMID: 16569761
PubMed Publishers Website
Structurally guided alignments reduce conflicts between trees expected to have similar/the same phylogenetic relationships.

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.
Paten B, Herrero J, Beal K, Fitzgerald S, Birney E.
Genome Res. 2008 Nov;18(11):1814-28.
PMID: 18849524
PubMed Publisher Website

Multiple sequence alignment: in pursuit of homologous DNA positions.
Kumar S, Filipski A.
Genome Res. 2007 Feb;17(2):127-35. Review.
PMID: 17272647
PubMed Publisher Website

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.
Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, Gorodkin J.
Genome Res. 2008 Feb;18(2):242-51.
PMID: 18096747
PubMed Publisher Website

Multiple sequence alignment accuracy and phylogenetic inference.
Ogdenw TH, Rosenberg MS.
Syst Biol. 2006 Apr;55(2):314-28.
PMID: 16611602
PubMed Publisher Website

PDFs to many important molecular evolution articles (including some of these) can be found here

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