More Next Blog»
Create Blog Sign In
The Cabbages of Doom A miscellany of musings from a science geek, would-be author and occasional creator/supporter of open-source bioinformatics software. Stuff I do, stuff I like... Because the Internet has a better memory than I do.
ABOUT ME
THURSDAY, 7 JUNE 2012
THE CABBAGES OF DOOM
How to root a phylogenetic tree
Richard Edwards Follow
110
View my complete profile PAGES
Home The Cabbages of Doom Mystic Mog and the Exploding Tortoise The Organisation of Really Contrived Acronyms
Teaching phylogenetics, it is clear that one of the things that causes a surprising amount of confusion is rooting the tree - defining the position on the tree of the (hypothetical) ancestor. Here, then, is my basic introduction to rooting a phylogenetic tree and why it is important. Unless you are modelling recombination or Horizontal Transfer, a phylogenetics is explicitly based on a model of a single common ancestral lineage that splits over time into multiple lineages. For species, these splits are speciation events. For molecules (e.g. genes or protein sequences), these splits can also be duplication events. But how do you know where that common ancestral lineage is? DISCLAIMER
With respect to rooting a phylogenetic tree, there are three main strategies that are routinely employed. In approximate order of confidence in the ancestry, these are: (1) No rooting (leave the tree unrooted), (2) Midpoint rooting, and (3) Outgroup (not outlier!) rooting.
Any unsourced opinions on this site are my own. I sometimes get things wrong and will be happy to amend my position in the light of new information.
Unrooted. I'll start with the unrooted tree because most methods produce an unrooted tree. Note that, although phylogenetics as a general approach assumes there's a common ancestor somewhere, many of the actual methods for constructing trees from data make no direction/ancestry assumptions. (The obvious exception is UPGMA, which is not used that much for serious phylogenetics.)
CC-BY-SA
MapTime Blog Molecular Evolution Glossary (X)HTML ASCII Codes Mac Links and Shortcuts KINDLE FICTION
Leaving the tree unrooted is also the easiest because it essentially involves doing nothing! In the figures below, the left-hand image shows the unrooted tree. The key thing here is that there is no assumption about ancestry and therefore no statement about the direction of evolution. If you trust the approximate branch lengths, it is still possible to say things about the topology, such as A and B are closer to each other than they are to C and D (with an important caveat covered below), but you cannot make any direct inferences about the common ancestor. Whilst easier, therefore, you are limited in terms of analysis and interpretation.
The Cabbages of Doom £1.19 Shop now
RESEARCHERID
MY WEB PRESENCE
This kind of representation is best used in situations where you have three or more well-defined clades (such as different members of a gene family) that radiated a long time ago over a relatively short period, such that the placement of the root and the order of branching is not known. You might still be able to say something with confidence about some of the individual radiations but you avoid making unsupported claims about the precise history and relationships of those clades. (Another option here is to "collapse" the root into a multifurcation (one-to-many split) but I will not deal with that here.)
The Cabbages of Doom Blog (text only) by Richard Edwards is licensed under a Creative Commons AttributionShareAlike 4.0 International License (Note: images and sidebar context may be subject to different re-use conditions.) SEARCH THIS BLOG Search
FEATURED POST
Bioinformatics is just like bench science and should be treated as such A bad workman blames his tools. A bad life scientist blames bioinformatics. OK, so that’s a little unfair but so is the level of criticism l...
The alternative when the actual root placement is unknown, is to use midpoint rooting:
Personal Homepage Picasa albums Twitter Google+ Lulu author spotlight Amazon author page
BLOG ARCHIVE
Kindle Edition
2017 (4)
Work homepage
2016 (15)
Edwards Lab SeqSuite and SLiMSuite
2015 (69)
LinkedIn
2014 (55)
ResearchGate
2013 (136)
Google Scholar
t 2012 (213)
ResearcherID
December (17)
NCBI Bibliography
November (12)
Microsoft Academic Research
October (20) September (11)
Biostar Profile
August (31) DARTH TATER
Celebrating Irish Jedi ALLTRIALS CAMPAIGN
July (22)
Midpoint Rooting. As its name suggests, Midpoint rooting attempts to root the tree in its middle point. It does this by calculating all of the tip-to-tip distances and selecting the longest - A to E in the tree above. The root is then placed exactly halfway between these two tips. If the tree is behaving and the rates of evolution are pretty constant throughout, this point should represent the ancestral point. It is therefore useful in situations where the actual root is not known but the assumption of a reasonably constant "clock-like" rate of evolution is quite sound. The other situation it generally works well for is when a tree is fairly balanced with some closely-related clades separated by a long branch in the middle - if midpoint rooting places the root far away from any nodes, it is less likely to be wrong (i.e. moving it a little due to rate discrepancies would not make any difference).
t June (28) Turning to the Dark Side Congratulations, Globe-Town! Putting photos on Picasa with an iPad MapTime: visualising Deep Time using Google Maps Natural Selection: a mechanism, a theory AND a fac... Monday... Coming soon... Virus Paper
The main problem with midpoint rooting is that it is very susceptible to large deviations from a constant evolutionary rate, especially if these are not "balanced", i.e. they only occur on one side of the actual root. The other time midpoint rooting tends to go wrong is when it places the root in amongst a rather dense set of short branches, where quite small deviations will place the root on another branch. For these reasons, whenever possible, outgroup rooting is generally the method of choice.
Cakes! (And nematode cookies!) Well done, Flying Fish and L-Katz! When it comes to writing, it's more of an oPad tha... The Cabbages of Doom has its first review! Life's too short to drink bad wines Pigeon Chess: not just debunking Creationist lies ...
TOTAL PAGEVIEWS
Manga cats
5 7 4 1 7 5
Artstudio: like being a kid again (It's great!) The Cabbages of Doom: now only 99p!
BLOGOSPHERE
Let's go fly a kite...
Atheist Ethicist
Even wasps can be cute
Pragmatic Causation
Who does Microsoft Academic Research think you are...
50 minutes ago
Why Evolution Is True
Postdoc position available: one week to go before ...
Wednesday: Hili dialogue
Intelligently designed ignorance gets a boost in K...
3 hours ago
University of Southampton's Noticeboard
How to root a phylogenetic tree
Major Boost for Jazz in the South
Why Evolution Is True
A Molecular Evolution Glossary
What is a gene?
8 hours ago
Afrotheria Artstudio-style
XKCD Violin Plots 15 hours ago
BrettTerpstra.com Web Excursions for March 13, 2018 21 hours ago
Trello Blog Using Multiple Trello Boards for a SuperFlexible Workflow 1 day ago
The Contemplative Mammoth Women in the interim: thoughts on International Women’s Day, 2018 4 days ago
The Tree of Life Frustrated by YAMMMMs: Yet another mostly male microbiome meeting 5 days ago
Ensembl Blog Getting to know us: Jon from HAVANA 5 days ago
Robinince's Blog and she said “Well, I don’t think you’re a fishmonger. I think you’ve done a plop in the wrong lavatory.” – Happy Birthday, Rik 1 week ago
Student-induced hypermutation
Outgroup Rooting. Unlike midpoint rooting, in which features of the tree itself specify the root, in outgroup rooting existing knowledge is utilised to place the root in the right place. This is done by using an "Outgroup" - a species or molecule that is known to be more distantly related than everything else in the tree. In the example above, kangaroo is used to outgroup root the tree, as it is known that marsupial mammals diverged from the ancestral lineage of all placental mammals. This tree emphasises the point made above about evolutionary rates - the midpoint root was wrong because the rodent lineages (mouse, rat and their ancestor) are evolving faster than the rest of the tree, probably due to relatively short generation times. (This pattern is often seen with real trees.) This can sometimes be obvious if deleting one of the nodes used to midpoint root the tree changes the position of the root: for a perfect clock-like tree, it should make no difference (as long as you do not delete the outgroup). This will not always work, though - in the example above, it would not make a difference, for example. Why does the root matter? There are a couple of reasons why correct rooting is important. The first just comes down to interpretation and understanding - it would be wrong to get too obsessive about the superficial differences between the three trees in the above figure - they are all essentially the same tree (same topology) and the differences are all down to rooting. The second is more important and comes down to the direction of evolution and conclusions about relatedness. If you want to infer anything about ancestry, you obviously need to have the right root. From the midpoint rooted mammalian tree above, it might not be obvious that placental mammals form a Monophyletic clade. Coming back to my earlier caveat when interpreting an unrooted tree, you might determine that the kangaroo, lemur and human were all more closely related to each other than to the mouse and rat. In terms of pure sequence divergence (on which the tree was built) this might be right but, in evolutionary terms, it is wrong: all placental mammals are equally distant from kangaroos due to the shared common ancestor.
coelsblog
Related post: How to read a phylogenetic tree.
“Sharing Reality” and how to persuade people
Posted by Richard Edwards at 19:01
Tags: bioinformatics, biology, education, evolution, phylogenetics, science
Society of Biology blog
7 comments:
Travelling to China to discuss Begonia biodiversity 5 weeks ago
Flying Fish Kiting Team Double Skyraker! 1 month ago
SLiMSuite Short Linear Motif discovery and analysis SLiMSuite REST server is back up 1 month ago
Sam Harris #113 — Consciousness and the Self 2 months ago
The Finch and Pea Break the Internet 3 months ago
Reply
Thanks so much! But i am still in trouble when you do outgroup rooting. If you don't know whether kangaroo is far different and this is even unknown, what should i do
cabbagesofdoom (16) cartoon (10) cats (34) chocolate (11) christmas (9) citation metrics (10) climate change (15) coffee (15) conferences (10) conservation (10) creationism (28) darwin (19) dawkins (10) dublin (11) education (29) environment (21) events
Richard Edwards
13 March 2016 at 10:31
(134) films and tv (17)
biology (16) (17) music (21)
olympics (14)
opinion (64) photos (55) phylogenetics (8) podcasts (13) politics (54)
Unknown 3 April 2016 at 22:20 Hi there, With out-group rooting don't you have the same confounding problem of differing evolutionary rates as you would with mid-point rooting? Cheers, James Reply Replies Richard Edwards
11 April 2016 at 19:05
You can do. If your phylogenetic inference method does not correctly handle rate variation, or it is too extreme, you will still have problems getting the right tree and the outgroup might be stuck in the wrong place. You can get a sense of this by looking at the bootstrap or likelihood values of the two descendant branches where the outgroup joins the rest of the tree. A particular problem is where you have very divergent taxa where the time between divergence was very small relative to the time since divergence; there is little signal to correctly resolve the branching order. Reply
Very good
MapTime
Reply
MapTime is currently unavailable
silly
society (57)
uk (27) videos (15) wildlife wine (24) woo (14) work (28)
Email address...
Submit
POPULAR POSTS THIS WEEK
How to root a phylogenetic tree Teaching phylogenetics, it is clear that one of the things that causes a surprising amount of confusion is rooting the tree - defining the ... OMICS Group Conferences - Sham or Scam? (Either way, don't go to one!) I want to preface this post by saying that it’s been one of the harder ones to decide whether to write. On the one hand, it feels a little u... Are "Happy Eggs" really happy? (And are Viva really pro-welfare?) Like many people, I am concerned by animal welfare but also rely on official organisations like the RCPA and their Freedom Food campaign: ... Mary Anning (21 May 1799 – 9 March 1847) Today’s Google Doodle is one of my favourites, celebrating the life (or 215th birthday) of Mary Anning , a paleontologist who discovered ... How to read a phylogenetic tree This week I have been preparing my last phylogenetics lectures and practical of the year. Something that is quite clear when marking student... Expanding Macbook Air disk space with SD cards I’ve had my Macbook Air for over a year now (crazy how time flies) and I still love it. The only drawback really is the limited disk space ...
1 year ago
The Royal Easter Show Last week, we went to the Royal Easter Show at Olympic Park in Sydney . I’ve never been to a county fair or such like before and, I must
Treevolution: Biology through the evolutionary lens Response to Late Mitochondrial Origin is Pure Artefact
say... Aussie vs British/Irish Fish ’n’ Chips We celebrated the start of the Australia Day long weekend by driving out to Brighton le Sands on Botany Bay for some fish and chips
1 year ago
Though small it is tasty A warm salad of smoked mackerel, paprika-roasted cauliflower and red rice
on the ... How to stop Outlook on Mac OSX replacing quotes & apostrophes with superscript numbers Since switching to a Mac, I have been experiencing an odd issue with Outlook: although in my message editor all would look well, recipients ...
2 years ago
2 years ago
restaurant (13) review
When is a Moro not a Boost? When it's an Aussie Cadbury's Mars Bar! One of the pleasures of moving to a new country is getting to grips with it's idiosyncracies, especially when the familiar gets a touch ...
Jilguero 22 February 2017 at 04:13
1 year ago
Moving House
python (9) rants (33) recipes (12)
travel (15)
Reply
Science, Reason and Critical Thinking
molecular museum
FOLLOW BY EMAIL
If you don't have any way of determining what the outgroup should be then you cannot use outgroup rooting. If the tree is looking wellbehaved, with a fairly constant rate of evolution and reasonably long ancestral branches, you can use midpoint rooting. Otherwise, it is probably safest to leave your tree unrooted. You should always work within the limits and uncertainties of your data - it is much better to say "I don't know", or "there is insufficient signal in the data to determine", than to force the issue.
1 year ago
A Tippling Philosopher
fave
(11) evolution (64)
(12) writing (20)
Replies
Electrofishing for Whales
My blog has moved!
books (34)
web (48)
Reply
XKCD: What If?
Ewan's Blog; bioinformatician at large
blogs (41)
southampton (27) sport (8) sydney (38)
Unknown 13 March 2016 at 09:14
11 months ago
1 year ago
bbc (15) beer (8) best of british (23) bioinformatics (19) biology (84)
(15)
A Branching Strategy Simpler than GitFlow: Three-Flow
Always Look on the Bright Side of Death
academia (43) animals (67) apple (15) apps (20) art (22) atheism (16) australia (49)
selection (8)
10 months ago
Absolutely No Machete Juggling
TAGS
(102) rock (9) science (190) science fiction (8)
Well explained!!Thanks
Bizzy Mum Le Toy Van Twinkle Tower Review And Budkin Competition
2007 (7)
religion (26)
pawan jayaswal 28 May 2014 at 15:26
5 months ago
9 months ago
2008 (11)
random (33)
Rationalist Association
Living in America: Part 3, The Fruited Plain
2010 (2)
medicine (19)
Reply
4 months ago
Shit You Didn't Know About Biology
2011 (90)
geekcraft (14) geeks (16) genetics (29) geology (13) google (8) hampshire (10) history (12) home (21) humanism (8) intelligent design (10) ipad (20) ireland (17)
Thanks, i found this very useful. I have been debating how important it is to root a tree when looking at phylogenetics of MLST sequences. I had composed phylogenetics on both unrooted and outgroups methods. Now that i have read this, i will be using the outgroups method so that i can put the ancestry of the different groups into perspective.
Dolichoderus, at last
7 months ago
January (11)
Marie Anne Chattaway 21 March 2013 at 21:44
MYRMECOS
New blog — Feeling engaged? — for matters relating to website metrics and social media
February (20)
life (52)
3 months ago
Keith Bradnam's Blog
March (11)
gadgets (20)
Joel Parcoeur A simple 10 step method to write an expository paper for school
April (14)
food (58) fun (16) fun with words (12) funny (34)
4 weeks ago
May (16)
Thanks for leaving a comment!
Links to this post Create a Link
Organisation of Really Contrived Acronyms
ZAZZLE STORE
IRENE - Image, Reconstruct, Erase Noise, Etc.
Newer Post
2 years ago
Subscribe to: Post Comments (Atom)
Home
Older Post
James McInerney's Science Exploratorium Origins of major archaeal clades correspond to gene acquisitions from bacteria 3 years ago
Captain Cook's Endeavour Journal
make custom gifts at Zazzle
9th to 13th July 1771 3 years ago
AMAZON FAVES
SLiMSuite & SeqSuite: opensource bioinformatics in Python New SLiMSuite Blog 3 years ago
Ants, bees & wasps Martian landscapes… or ants? 3 years ago
Mystic Mog and the Exploding Tortoise Mid-season break II 5 years ago
Arabelegans Guest blogger for grads.co.uk
AMAZON ASSOCIATE
Richard Edwards is a participant in the Amazon EU Associates Programme, an affiliate advertising programme designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.co.uk.
5 years ago
Working at the Death Star Not working at the Death Star 6 years ago
Hume's Apprentice Arizona Atheist Conquering Crafts Society for Molecular Biology and Evolution Cryptogenomicon
Picture Window theme. Theme images by lucato. Powered by Blogger.