Addition of a Message Board to the blog

This is a short post just to point out that there is now a Message Board on this blog, where people can post community information, such as jobs and scholarships, as well as any other requests or information. The link is at the upper-right of the blog pages.

To post a message to the Board, send an email to: Leo van Iersel.

Blog posts and formal publications

One possible use of blog posts is as first drafts of ideas that might make their appearance in a refereed publication at a later date. Thus, many of my blog posts have appeared in one form or another in my recent publications. Here I have listed the ones that I can remember using, just in case anyone wants a citable reference for the information in these posts.

A. Morrison DA (2013) Phylogenetic networks are fundamentally different from other kinds of biological networks. In W.J. Zhang (ed.) Network Biology: Theories, Methods and Applications (Nova Science Publishers, New York) pp. 23-68.

    9 Biological versus phylogenetic networks
  13 Network measures and phylogenetic networks
  23 An explanation of graph types
  25 Networks and bootstraps as tree-support criteria
  34 Networks of affinity rather than genealogy
  36 Networks of genealogy
  53 Are mathematical constraints biologically realistic?
  54 Some odd network definitions and terms
  63 Human races, networks and fuzzy clusters
  69 Is this the first network from conflicting datasets?
  70 Why do we still use trees for the Neandertal genealogy?
  72 Networks and most recent common ancestors
  74 Open questions about evolutionary networks, part 1
  75 Open questions about evolutionary networks, part 2
  76 Open questions about evolutionary networks, part 3
  88 When is there support for a large phylogeny?
  90 Explanation of the names for phylogenetic networks
  94 Phylogenetic position of turtles: a network view
  99 How networks differ from bootstrapped trees
107 We should present bayesian phylogenetic analyses using networks
115 Is there a philosophy of phylogenetic networks?

B. Morrison DA (2014) Phylogenetic networks — a new form of multivariate data summary for data mining and exploratory data analysis. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery 4: in press.

  29 Network analysis of scotch whiskies
  50 Phylogenetic network of the FIFA World Cup
  61 How to interpret splits graphs
101 Distortions and artifacts in Principal Components Analysis analysis of genome data
103 Networks can outperform PCA ordinations in phylogenetic analysis
114 Network analysis of Genesis 1:3
119 Network of ancient Thai bronze Buddha images
134 A network analysis of Simon and Garfunkel
159 Networks and human inter-population variation
172 The acoustics of the Sydney Opera House

C. Morrison DA (2014) Next generation sequencing and phylogenetic networks. EMBnet.journal: Bioinformatics in Action 20: e760.

191 Next Generation Sequencing and phylogenetic networks

D. Morrison DA (2014) Phylogenetic networks: a review of methods to display evolutionary history. Annual Research and Review in Biology 4: 1518-1543.

    2 The first phylogenetic network (1755)
  21 The second phylogenetic network (1766)
  34 Networks of affinity rather than genealogy
  36 Networks of genealogy
  67 Metaphors for evolutionary relationships
  89 Relationship trees drawn like real trees
168 Who first used the term "phylogenetic network"?
182 Affinity networks updated
183 Reticulation patterns and processes in phylogenetic networks
187 What are evolutionary networks currently used for?

E. Morrison DA (2014) Rooted phylogenetic networks for exploratory data analysis. Advances in Research 2: 145-152.

  43 Rooted networks for exploratory data analysis

F. Morrison DA (2014) Is the Tree of Life the best metaphor, model or heuristic for phylogenetics? Systematic Biology 63: 628-638.

  23 An explanation of graph types
  34 Networks of affinity rather than genealogy
  36 Networks of genealogy
  58 Who published the first phylogenetic tree?
  89 Relationship trees drawn like real trees
143 Resistance to network thinking
144 Destroying the Tree of Life?
147 Should phylogenetic modelling proceed from simple to complex or vice versa?
171 Conflicting placental roots: network or tree?
182 Affinity networks updated

Blogs about phylogenetics

I have occasionally been asked about what blogs currently exist in phylogenetics, because there seem to be very few. There are blogs in related areas, such as phyloinformatics, evolutionary biology, and systematics, but very few blogs dedicated primarily to phylogenetics (not just occasionally mentioning it).

Below is a list of the current and former blogs that I know about. In each case I have provided basic information taken from the blog itself. Please let me know about any suitable blogs that have been missed. [Updated 15 October 2014]

Current General Blogs

The Genealogical World of Phylogenetic Networks

Biology, computational science, and networks in phylogenetic analysis. This blog is about the use of networks in phylogenetic analysis, as a replacement for (or an adjunct to) the usual use of trees. This topic has received considerable attention in the biological literature, not least in microbiology (where horizontal gene transfer is often considered to be rampant) and botany (where hybridization has always been considered to be common). It has also received increasing attention in the computational sciences.

Contributors: David Morrison, Steven Kelk, Leo van Iersel, Mike Charleston, Jesper Jansson
Started: 25 February 2012


TreeThinkers

TreeThinkers is a blog devoted to phylogenetic and phylogeny-based inference. We aim to use it as a place to discuss recent research and methods; to ask and answer questions; and serve as a general resource for news and trivia in phylogenetics. Although the blog is associated with the Bodega workshop, we welcome posts and participation from the entire phylogenetics community.

Contributors: Bastien Boussau, Gideon Bradburd, Jeremy Brown, Rich Glor, Tracy Heath, David Hillis, Sebastian Höhna, Luke Mahler, Mike May, Brian Moore, Samantha Price, Peter Wainwright
Editor: Bob Thomson
Started: 2 October 2012


Open Tree of Life

The tree of life links all biodiversity through a shared evolutionary history. This project will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. Assembly of the tree will incorporate previously-published results, with strong collaborations between computational and empirical biologists to develop, test and improve methods of data synthesis. This initial tree of life will not be static; instead, we will develop tools for scientists to update and revise the tree as new data come in.

Contributors: Robin Blom, Karen Cranston, Karl Gude, Mark Holder, Rosemary Keane, Rick Ree
Started: April 8, 2012


EvoPhylo

Evolution, phylogenetics, bioinformatics, stuff.

Contributor: Dave Lunt
Started: 30 January 2008


The Bayesian Kitchen

Statistical inference and evolutionary biology. Undoubtedly, since its introduction in phylogenetics in the late 90's, Bayesian inference has become an essential part of current applied statistical work in evolutionary sciences. However, there are still many problems, computational, theoretical and even foundational. After ten years of applied Bayesian work in phylogenetics and in evolutionary genetics, I feel the need to step back and re-think the whole thing.

Contributor: Nicolas Lartillot
Started: 24 December 2013


Phylogenetics...

Musings on eukaryote evolution.

Contributor: Marko Prous
Started: 31 December 2013

Current Program Blogs

Phylogenetic Tools for Comparative Biology

This web-log chronicles the development of new tools for phylogenetic analyses in the phytools R package. Unless you are reading a very recent page of the blog, I recommend that you install the latest CRAN version of phytools (or latest beta release) before attempting to replicate any of the analyses of this site. That is because the linked functions may be archived, and very likely have been replaced by newer versions.

Contributor: Liam Revell
Started: 11 December 2010 (at Blogspot)


Osiris Phylogenetics

Accessible and reproducible phylogenetics using the Galaxy workflow system.

Contributor: Todd Oakley
Started: 7 September 2012

Beast 2: Bayesian Evolutionary Analysis by Sampling Trees

Announces the introduction of new tools for phylogenetic analyses in the Beast 2 package, as well as discussing usage issues with the current version, along with tips and tricks.

Contributor: Remco Bouckaert

Started: 18 March 2014

Blogs Currently in Limbo

Dechronization

Dechronization is authored by evolutionary biologists interested in the development and application of methods for estimating phylogeny and making phylogeny-based inferences. The goal of the blog is to provide a forum for discussion of the latest research and methods, while also providing anecdotes, tidbits of natural history, and other related information.

Contributors: Rich Glor, Luke Harmon, Brian Moore, Tom Near, Dan Rabosky, Liam Revell
Started: 29 April 2008      Last post: 6 June 2011


CYPHY - Cybertaxonomy and Phylogenetics

Mostly harmless pointing at things pertaining to cybertaxonomy and phylogenetics.

Contributor: Matt Yoder
Started: 6 November 2007      Last post: 23 February 2011


Phylogeny etc.

Meditations on phylogenetic inference.

Contributor: Bruce Rannala
Started: 6 March 2014      Last post: 6 March 2014


Fish Phylogenetics

I created this new blog to share thoughts on work from my research group on the phylogenetics and evolutionary biology of fishes. This will provide a forum to share insight about the studies that we publish, discuss important scientific aspects of fish diversity, reflect on my experiences teaching ichthyology (the study of fishes), and to comment and review contributions by other researchers.

Contributor: Tom Near
Started: 23 August 2012      Last post: 15 September 2012


Taxonomy Phylogeny

Taxonomies group organisms according to phenotype, while phylogenetic systems groups organisms according to shared evolutionary heritage.

Contributor: ???
Started: 1 January 2008      Last post: 31 December 2010


Phylogenetic Geek

A bag of info on phylogenetics.

Contributor: ???
Started: 5 August 2011      Last post: 16 September 2011

Introduction

This blog is about the use of networks in phylogenetic analysis, as a replacement for (or an adjunct to) the usual use of trees. This topic has received considerable attention in the biological literature, not least in microbiology (where horizontal gene transfer is often considered to be rampant) and botany (where hybridization has always been considered to be common). It has also received increasing attention in the computational sciences, although the dialog between the biologists and the mathematicians is not always as clear as it should be.

Networks are acknowledged to have two main uses within phylogenetics: (i) exploratory data analysis, in which conflicting data patterns are visualized and their nature and quantity assessed; and (ii) evolutionary analysis, in which the historical patterns involve not only vertical descent (parent to offspring) but also reticulations due to horizontal processes (such as HGT, hybridization, recombination, and genome fusion).

We are hoping that this blog will help the various groups involved in phyloinformatics focus on a common agenda: the widespread use of networks in phylogenetics. Blog posts might involve news, announcements, new results, commentaries on old results, unpublished (or unpublishable) opinions, or interesting tidbits of information that have no other home. No topic is necessarily excluded.

As always, opinions expressed in this blog are the author's own, and no other blogger necessarily agrees with any of them. We are keen to receive responses to the blog commentaries, and to facilitate discussion of important or interesting topics. We are hoping to have many guest posters, as well. If you would like to contribute to the blog, regularly or even irregularly, then please contact us.