On the limits of feathery trees

By Razib Khan | August 11, 2012 12:53 am

The NJ tree is from Genome-Wide Analysis in Brazilian Xavante Indians Reveals Low Degree of Admixture. It’s a visualization of a genetic distance matrix. Am I strange, or do these sorts of trees really leave a lot to be desired in terms of actually getting across any extra information beyond a table?

CATEGORIZED UNDER: Genetics
MORE ABOUT: phylogenetics
  • Mike

    I would MUCH rather have the tree. Of course, I am constantly looking at gene trees. To try to reflect the topology and the branch lengths for so much data would be a mess of a table.

  • http://dienekes.blogspot.com Dienekes

    Figures have their uses, it’s easier to spot a little red outlier in a background of blue, rather than going through a long list of numbers.

    But, I think there should definitely be more “numbers” to accompany the figures. Numbers can be re-analyzed, but figures usually can’t.

  • Brazen Normalcy

    Agreed. Pretty. And pretty useless. I could see such a tree having utility in a digital setting, but mainly because then you might zoom in on a branch, revealing actual data there.

  • http://sjespositoweblog.blogspot.com S.J. Esposito

    I don’t mind the tree–it’s just as useful as any other network or neighbor diagram. But you asked if it offers anything extra, and the answer is no. In fact, it offers less than a table in terms of information (as Dienekes said); but it’s a decent visual representation of a result, I think.

  • https://plus.google.com/109962494182694679780/posts Razib Khan

    #1, the issue i have is that these two dimensional representations remove some information…which is fine i think when you have a small number of branches. but it seems that too many clades are being thrown down here, and misleading people as to relationships. i’ve been mislead in the past by unrooted trees. i think people who look at these all the time don’t have a problem, but for anyone who is outside the core of the field it can give a false sense of precision.

  • http://www.astraean.com/borderwars/ Christopher@BorderWars

    I’ve written on how these trees can be deceptive especially when they are sparsely populated with data that has a strong selection bias. While most scientists are likely interested in how closely populations are related, I’ve documented a poor study which uses these trees to suggest that there’s a significant genetic split within the Border Collie breed.

    http://www.astraean.com/borderwars/2008/09/breed-apart-ii.html

    The researcher who added the Border Collie spin has a particular political bias in favor of such a split (if it exists).

NEW ON DISCOVER
OPEN
CITIZEN SCIENCE
ADVERTISEMENT

Discover's Newsletter

Sign up to get the latest science news delivered weekly right to your inbox!

Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

ADVERTISEMENT

See More

ADVERTISEMENT

RSS Razib’s Pinboard

Edifying books

Collapse bottom bar
+

Login to your Account

X
E-mail address:
Password:
Remember me
Forgot your password?
No problem. Click here to have it e-mailed to you.

Not Registered Yet?

Register now for FREE. Registration only takes a few minutes to complete. Register now »