How to root an NGS SNP-based tree using an outgroup

[Kalpi]

Hi all,

When I was referring to emerson et al. (2010), I noticed that the phylogenetic tree generated with COI gene sequences was rooted using two outgroup species ( Wyeomyia mitchell and Wyeomyia vanduzeei ).  But the RAD tag SNP-based tree was not rooted with outgroup species.

I would like to what is the reason for not rooting SNP-based tree with an outgroup species.

Regards,

Kalpi

[Emerson, Kevin]

Kalpi - the simple answer is that we didn't have RAD data for an outgroup, we only had COI data for the outgroup.  We used RAD data from outgroups in Merz et al. 2013 (Linked below).  

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0072262

Best,

Kevin

--
Stacks website: http://creskolab.uoregon.edu/stacks/
---
You received this message because you are subscribed to the Google Groups "Stacks" group.
To unsubscribe from this group and stop receiving emails from it, send an email to stacks-users...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.

--

------------------

Kevin J Emerson, PhD

Assistant Professor of Biology

Biology Department

St. Mary's College of Maryland

18952 E. Fisher Rd
St. Mary's City, MD 20686-3001

kjem...@smcm.edu

http://faculty.smcm.edu/kjemerson

Office: 240 - 895 - 2123, Shaefer Hall 231

---------------------

[Kalpi]

Hi Kevin,

Thank you very much for the reply and the link. You have done a wonderful work and it really inspired me. I have few more doubts to clarify. Hope I'm not troubling you too much.

1. Did you put your outgroup sequence files and other individual's sequence files in the same samples folder when running usatcks? 

2. As I understand you got 3,741 and 16,858 SNPs for each analysis. But you have trimmed them into 54 and 80 fragment respectively before generating trees. 

   I would like to know why is that. What is the relationship between the sequence length and the accuracy of the tree? I also received around 20,000 SNPs at the end of    the analysis.

3. I could not find hstacks and extract_interpop_chars.pl programs in stacks site. I executed denovo_map.pl and then populatoins program on my data to get a phylip         file.   Is that alright? 

Thank you in advance.

Regards,

Kalpi

[Emerson, Kevin]

Kalpi,

1. Yes.  We ran all individuals through stacks at the same time.

2. We trimmed reads because the data used in PNAS paper were 54 bp reads and the data used in the PLoS ONE paper were 80 bp reads.  When we combined the datasets together we had to use the shorter length so that all were the same.  You should use the longest reads that you can.

3. Yes, I believe hstacks isn't an option any more on its own.  It has all been incorporated into populations and that is how you should do it.  Seems that you are doing it correctly.

Best
Kevin

--

Stacks website: http://creskolab.uoregon.edu/stacks/
---
You received this message because you are subscribed to the Google Groups "Stacks" group.
To unsubscribe from this group and stop receiving emails from it, send an email to stacks-users...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.

[Kalpi]

Kevin,

Thank you very much. Really appreciate your help.

Regards,

Kalpi

On Saturday, January 11, 2014 7:54:50 PM UTC+5:30, Kalpi wrote: