Hi there,

You want something conserved enough that you can be assured you are working with orthologous sequences, but it also needs to have some freedom to change over time so that you can find patterns in historical differences in order to build your phylogeny. When trying to resolve deep phylogenies, more conserved sequences are likely more useful. But if you are trying to tease apart recent divergences, you may find quickly evolving regions to be very useful as long as you can still be sure of orthology.

UC Berkeley offers a graduate level course entitled Principles of Phylogenetics, and that course maintains a website where all of the readings, labs, and lecture notes are available for free. If you want to delve deeper, you should check it out. I think you will find the resources to be pretty interesting: http://ib.berkeley.edu/courses/ib200b/IB200B_SyllabusHandouts.shtml

Dr. Mukhopadhyay,

I would advice to read the work of Konstantinidis KT, Ramette A, Tiedje JM. Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Appl Environ Microbiol. 2006 Nov;72(11):7286-93

some notes on your question:

1) You did not say about organism of your study - even conserved gene can be absent in related species of bacteria. Non-conserved gene can be absent in some strains of the same species with high probability.

Conservation level often depends on position of the chosen 300 bp on complete gene sequence.

The studied gene must be present in single copy in the whole genome, it is easier to select such fragment for viruses and bacteria, but difficult for amphiploid plants.

3) Nucleotide sequence of conserved cds between two related genera of bacteria may have greater difference than expected, due to different GC/AT composition of the genomes, and protein sequence will be more conservative and useful for taxonomy.

4) Thus, the use of non-conserved cds is risky way

Both nucleotide and aa sequence of conservative cds must be analysied.

Anyway, for one conserved gene sequence you will get phylogeny of just the chosen gene, and you must prove congruence of such phylogeny to others obtained for the same organisms by different methods.

@ Dr Alex Ignatov,

thanks for your prompt reply. I will go through the paper.

I may communicate with you for any further query.

Regards

Hi.

In every clade, usually the rates of evolution are different, and so, the different sequences would serve in different ways, always the level of the taxonomic categories (v.g. species, genera...) and the specific rate of evolution in sister groups are very significant and gives you important information about your investigation.

Hi there,

You want something conserved enough that you can be assured you are working with orthologous sequences, but it also needs to have some freedom to change over time so that you can find patterns in historical differences in order to build your phylogeny. When trying to resolve deep phylogenies, more conserved sequences are likely more useful. But if you are trying to tease apart recent divergences, you may find quickly evolving regions to be very useful as long as you can still be sure of orthology.

UC Berkeley offers a graduate level course entitled Principles of Phylogenetics, and that course maintains a website where all of the readings, labs, and lecture notes are available for free. If you want to delve deeper, you should check it out. I think you will find the resources to be pretty interesting: http://ib.berkeley.edu/courses/ib200b/IB200B_SyllabusHandouts.shtml

If you want reconstruct phylogeny you may note some features:

1. What level of taxonomy you interested in? In general you must use more variable and less conservative sequences. For high-level taxonomy you may to use conservative sequences.

2. What you want to reconstruct. You must to assembe your sampling into aligned matrix. Many things of phylogeny depend on sampling greately. you can't reconstruct phylogeny only on the basis of your own sequences. You must to use another for sampling and comparing.

3. Using of amino acid or DNA sequences have some differences. Amino acid sequences in general are quite less informative than DNA because nonsingularity of amino acid code, so all DNA base changes that not caused change of amino acid are eliminated from sequence analysis. Moreover, not all DNA sequences which used in phylogeny are protein-coding.

@ Dr. Andrii Tareiev, thanks for the reply.

Would you please elaborate the statement "you can't reconstruct phylogeny only on the basis of your own sequences. You must to use another for sampling and comparing". Its not much clear to me.

Moreover, I have read (in a book) that protein sequences are more useful due to mre no. of amino acids than nucleotides, and the second reason was the same which you have used to say that DNA is more useful. But I was not fully convinced. So please explain your logic, i time permits.

Thanks in advance.

Regards

@ Dr Jeremy Chase Crawford,

thanks for your answer and providing the useful link.

Dear Dr. Mukhopadhyay,

when I sad that you can't reconstruct phylogeny only on basis of your own sequences, I mean only these two sequences you noticed here. If we have 2 sequences we can't reconstruct phylogeny in principle. This is only comparison of 2 sequences, not phylogeny. But if you have more your own sequences to analyse? of course ou can try reconstruct phylogeny. If you haven't more any your own sequences, you must to use sequenses from databases to do this and locate the position of your own sample.

What literature you read about amino acid sequences.

As for my viewpoint on DNA and aminoacid sequences, I can provide you some exaples. I hope these ones will be clear for you:

1. Not all sequences, which used widely in phylogeny can translated in amio acid sequences. Most popular - ribosomal cluser genes, which contains also noncoding spacers.

2. As you know, DNA sequences translated into aminoacid sequences (onlyin case when it possible) by some rules (http://www.google.com.ua/imgres?imgurl=http%3A%2F%2Fwww.science-explained.com%2Fwp-content%2Fuploads%2F2013%2F08%2Fcodon_table.jpg&imgrefurl=http%3A%2F%2Fwww.science-explained.com%2Ftheory%2Fdna-rna-and-protein%2F&h=902&w=962&tbnid=591nQ9yzLMxx4M%3A&zoom=1&docid=o635ozIh6PmB1M&ei=aE6PU9CKJKfa4QTFy4HQDA&tbm=isch&ved=0CEsQMygVMBU&iact=rc&uact=3&dur=320&page=2&start=18&ndsp=23). As you can see, most amioacids have more than 1 triplet of coding (i.e. Ser coded by 6 different triplets etc.), so aninoacid seqences are less informative. But in general every change is more significant than in DNA.

3. In phylogeny in general most algorhythms based on base change / aminoacid changes with different options and weights. Purposed that 1 subtitutiuon is evolutionary act. So if you get sequences of DNA and aminoacids I suppose you to compare phylogeny based of ech of them and make the consensus tree/ This will be the best way.

If you need I can advise you some basic literature on phylogeny

Best wishes

@ Dr. Andrii Tareiev, thanks for your prompt reply.

I request you to recommend some very useful and pertinent literature in this regard.

Best.

That is depend primarily on how deep level of genetic divergence (between groups of study) you are about to investigate.

You can please refer to the links below to obtain certain interesting informations:-

1. http://www.ncbi.nlm.nih.gov/books/NBK21122/

2. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98952/

3. http://a-little-book-of-r-for-bioinformatics.readthedocs.org/en/latest/src/chapter5.html

4. http://eebweb.arizona.edu/blast/rna_lecture.pdf

You can also download the pdfs of the files attached herewith.