Phylogeny and evolution
Mandatory reading/listening
- http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01
- https://en.wikipedia.org/wiki/Phylogenetics
- https://www.ted.com/talks/svante_paeaebo_dna_clues_to_our_inner_neanderthal?language=en
- Phylogeny-plos
- Review Article (PDF)
Slides
Videos
- Phylogeny Introduction
- Phylogenetic Trees
- Orthology and Parology
- Mutations in evolution
- Building a phylogenetic tree
- Evolutionary examples
- Human origin
- Neanderthals
- Neanderthals – Svante Pääbo
Discussion Video
Videos by others
- Phylogeny and phyolgenetic trees
- Tree of life
- Archea – phylogeny
- Neighbour joining
- Phylogenetic reconstruction Part 1
- Phylogenetic reconstruction Part 2 (parsimony)
- Phylogenetic reconstruction Part 3
Old Videos
2016
If possible, please go through the ppt (I will ask this every time since I think that it is really helpful 🙂 ).
Please go through the methods of building a phylogenetic tree again.
Also the link for the Phylogeny-plos article is broken and there is no full access to the Review Article.
With respect to the second video where you mention that it is important to include all the relevant data, since one may interpret the tree in the wrong way otherwise (relationships between species or genes), how can you know that this is the case? I think it is difficult to know what sequences to include in a tree to make sure (or as sure as possible) that you can extract the right information.
About xenologues, how similar in sequence are they really? Can they be extremely similar without being related? And if so, how can you detect the difference?
Orthologs: please explain the ideas of COGs, how similar they have to (a threshold) in order to be called orthologs. ( As mentioned later,not all similarities are homologous)
Why b and C is 3 again in Distance Matrices? and the difference between Ultrametric matrices and distance matrices. And explain UPMGA, and neighbour joining
How to choose the best one according to Parsimony method?