Chris E Buddenhagen

6 Questions 25 Answers 0 Followers

Questions related from Chris E Buddenhagen

Is GBS sequencing for phylogenetics effective on herbarium specimens?

There seems to be a requirement for high quality DNA. But if run with herbarium specimens maybe sequence capture and assembly are poorer relatively but adequate for phylogenetics with a reduced...

07 July 2018 1,539 3 View

Have you had problems with silica and lignin affecting plant DNA extraction success? How did you recognize and deal with it?

I am working in Cyperaceae and suspect that in some cases its well known high silica content (or possibly lignin) may be causing problems with getting high quality DNA during extraction using...

01 January 2014 5,878 10 View

Does anyone have a good article looking at systematics of the genus Furcraea (Asparagaceae)?

I would like a key to distinguish all the taxa, or at least those closely related to F. hexapetala. Phylogeography and phylogenetic studies would be interesting too.

12 December 2013 9,366 1 View

Considering what we know about conflicting gene trees, how can we justify publishing a phylogeny based on one to few gene regions?

The genomes of organisms are thought to contain many “linkage partitions” (sensu Slowinski & Page, 1999), each with its unique history, and it is only with a sampling of many of these that we can...

10 October 2013 9,856 21 View

When extracting plant DNA, if you discover poor yield, how do you change standard DNA easy kit procedures to get good yields?

Context is that I was getting small fragment sizes on my gel. But I'd be curious about anyone's process for troubleshooting poor yield issues of any kind.

09 September 2013 4,641 5 View

How do you align DNA sequences for phylogenetic work? What is the order of events and what software do you use?

I anticipate having to align sequences from hundreds of loci for more than 100 taxa. What is the most efficient way to go about this? I usually use muscle (or clustal), then manual alignment in...

08 August 2013 1,206 23 View