I apologise for my lack of knowledge on this subject but it's something I've always struggled with. I was given data which contains cytochrome b gene sequences taken from Vipera berus, a widespread species of snake found throughout Europe. I then aligned the data etc and produced two trees. One neighbour-joining tree and a maximum likelihood tree. The problem is I'm not sure how to read/analyse the tree and what to discuss. A few pointers would be great or if you could point me in the right direction such as where to learn how to properly interpret the trees. Thank you.
The following link contains a document regrading Constructing and interpreting phylogenetic trees, if you haven't already gone through it, you can have a look. It is better to understand and then make an interpretation, this will help in future studies too. Good luck.
https://pdfs.semanticscholar.org/231a/8ebbebdf6ac3cf59cf677aac7121e609520a.pdf
The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendants of that ancestor. As you move from the root to the tips, you are moving forward in time. When a lineage splits (speciation), it is represented as branching on a phylogeny.
you should use other types of phylogenetic analyses, as Maximum Likelihood or Bayesian Inference. In my opinion, NJ is good for a first approximation to the sequences, but not for constructying strong phylogenies. In any case, surely you would get lower bootstrap and bayesian posterior probabilities.
And no: you cannot say that with gene A K is paraphyletic: is polyphyletic (diphyletic, in that case).
Hope this helps.
A more important question is if this is your true philosophy. Are you evolutionary, adaptationist, creationist, 'designist', or something else. A creationist wouldn't even discuss phylogeny, for example, and might write about adaptation or just describe current events. So you need to decide your overall approach first and be consistent, with strong evidence, otherwise it's not scientific :)
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