Interpreting phylogenetic trees

In this video, I explain how to interpret a phylogenetic tree. As an example, I use a tree reconstructed from a concatenated mtDNA sequence matrix of colugos from Janecka et al. (2008). In this paper, we showed that there is evidence of cryptic species diversity in the Sunda colugo, a remarkable mammal that can glide over 100 meters. I post the link to the paper below, as well as a great article on them in WIRED. In case you would like to make your own tree or also try changing the way a tree looks I posted all files I used in my GitHub repository for you to download.
WIRED article on colugos:
www.wired.com/2014/11/absurd-...
Janecka et al. 2008 paper on cryptic diversity in colugos:
www.cell.com/current-biology/...
Files in GitHub repository:
github.com/janeckaj/sequence-...
ColugoMtDNA_information_on_alignment.docx (description of the sequence file)
ColugoMtDNAnoHSAv2.fas (sequence alignment)
ColugoMtDNAnoHSAv2.mtsx (MEGA tree session)
ColugoMtDNAnoHSAv2_ML_BS.nwk (tree in newick format)
ColugoMtDNAnoHSAv2_ML_BS.png (picture of tree)

[@Carovilleneuve]

Thank you so much for taking the time to do these tutorials. Your explanations were so clear and easy to understand, I will be forever grateful!

[@wanderingfish]

Thank you for this. I am learning about phylogeny since I want to incorporate it in my dissertation.

[@rashmibhattacherjee1818]

Extremely helpful video ! Thanks for your wonderful explanation...

[@sana_haron]

thank you so much sir, easy to understand, but i was here to see video on representation of tree which you have not provided yet.

[@sebastianalvarezpulgarin1343]

Thank you so much! I finally understood this diagram :D

[@ibtissemguergouri7659]

Thank you very much sir, it really helps us to understand in a better way phylogenetic trees

[@safiabenamor7643]

good morning my sister I need your help about interpreting my results about genetic diversity it is not my domain but I have a part of genetic in my thesis

[@nirodhasenevirathna4980]

very useful explanation. Thank you

[@jayachapagain28]

Thank you. It’s very helpful video

[@napapornsriden8890]

It is really useful. Thanks a lot

[@awaladil7402]

thank you very much, it's very helpful !

[@anwesasaha8321]

This video is really helpful, thank you very much sir.

[@neomoonprince69]

Hi, professor. Can I use different gene sequences in one tree? and how should I handle gene duplications? particularly 16S rrna?

[@moulaymhammedakermi3410]

Thank you for your help

[@kuilanyogeswaran1955]

Hi, Dr. The scale bar does not appear when I generate the phylogenetic tree. The distance scale box is being ticked but still, there was no scale bar appearing on my diagram. How do I solve this?

[@anshul0934]

Thankyou sir, god bless you

[@tanzeemazeeza.s9589]

Thank you sir

[@oreoluwaoyadiran]

Do you have a video on annotating phylogenetic trees

[@abhipapu2720]

Sir ,why we use outgroup for construct phylogenetic tree?

[@igorrouzine7502]

I cannot convert .txt file to FASTA format in MEGA. It cannot read them. Even though I added >name before each sequence.

[@janeckagenomics2719]

What did you make the .txt file in? This can happen for several reasons. Here are some suggestions that may work. Make sure it is a flat text file format. Make sure there are no extra hidden characters by opening the file in word and selecting show all characters. Finally, make sure you have show file extensions on so that you are sure you the file has only a .fasta extension. Let me know if these do not work. Good luck !

[@moshiramadhan1082]

You did not explain about circular tree

[@linuxgirl_]

The video is great. The video mastering is not well done. The music is much louder than the vocal sound in the video, and the heavy base when the volume suddenly changes is very jarring.