The Joy of Phylogeny: How To Make Your Own Phylogram

Warning! This is a how-to video on how to construct phylogenetic trees using public domain online tools. The content is strictly scientific, and may be daunting to creationists or Discovery Institute Fellows. If you aren't interested in phylogenetics, this may be a bit dry.

Some of the websites featured in the video:

European Molecular Biology Laboratory (EMBL) ClustalW2
http://www.ebi.ac.uk/Tools/clustalw2/index.html

National Center for Biotechnology Information (NCBI)
http://www.ncbi.nlm.nih.gov/

NCBI Homologene
http://www.ncbi.nlm.nih.gov/Homologene

Good luck making your own phylograms! Here's a list of genes that are highly conserved to get you started:
Actin, beta
Actin, alpha
18S rDNA
GAPDH
UBC1
catalase
APRT
HPRT
RPOB
NF-kappaB
EGF and EGFR
all the tyrosine kinases
transducin

Category:

Science & Technology

Tags:

• phylogenetics
• phylogeny
• genetics
• tree
• bioinformatics
• NCBI
• catalase
• homology
• protein
• DNA
• phylogram
• cladogram
• cladistics

[chaosunstabledynamic]

Just to let you know, if you look at this phylogeny, you'll see that rats are the outgroup to the whole tree- you can't say they pair up with the mice like you did, because the tree is actually saying that the mouse GAPDH gene(s) share a more recent common ancestor with ALL of the other GAPDH genes of the other species (e.g. humans, etc.) than ANY do with rats. This isn't saying that mice aren't close relatives of rats, just that the phylogeny of this gene from these data don't support that.

[C0nc0rdance]

@chaosunstabledynamic

unrooted phylogenies don't really have outgroups. It's arbitrary which is the reference sequence. This is the least rigorous kind of phylogram, but I wanted to show people how easy it is to generate them without a background in bioinformatics. Just for fun.

For the record, beta-actin is a 100% match between mus and rattus, for 375 amino acids. It doesn't sound like you challenge that relationship, just how it was graphed. Correct me if I' m wrong.

[DonExodus2]

Why the hate on the lolcats :(

[C0nc0rdance]

Because, like you, I use them so often to add a little levity to my vids. This one REALLY needed it, but I had a hard time finding the right one to express the concept of "phylogeny".

[grayziehobbes]

@chaosunstabledynamic We are a rodent. That does not suck.

[MonotonePeanut]

Thanks! Playing with phylograms is going to be so fun ^^

[jebus6kryst]

HAHAHA!

It is always a hoot to read something from you about a subject you know nothing about. Maybe next post you will inform us about "radio-active" dating methods.

[jebus6kryst]

Thank you for this!

[chaosunstabledynamic]

Just not sure you can say what was said around 9:06/9:07, although I think such a comment would be supported by most phylogenies. Sounds like we're mostly in agreement here.