I have never had to pay to deposit data in Dryad (last use was for Mol Ecol in 2012). I have never used TreeBase. I think your choice will depend on which repository will best facilitate access to the data. Dryad is more general-purpose, as I understand. I have deposited data there mainly because it was more appropriate for population genetic analysis than phylogenetic analysis. Also I have added in environmental data and other non-genetic data to accompany the genetic info; I assume one can do the same in TreeBase

Hey Justin! Small world - I know both you and Evan :-D. I prefer using Dryad over TreeBase for two main reasons - 1) TreeBase was being a nightmare for me the last time I used it. Apparently you have to label all tree tips exactly how they appear in the corresponding sequences, which would have been a pain to do manually. 2) The TreeBase help people took a long time to respond to my questions compared to help people at Dryad. So, based on my experiences with both TreeBase and Dryad, I would say that Dryad was much easier to use.

In addition to sequence raw and metadata you might also think of depositing your physical DNA and tissue samples in a publicly available DNA and tissue bank (if you haven't done already). The Global Genome Biodiversity Network (GGBN) aims to provide access to such samples and related data. The partners and sample providers define access restrictions for third parties. Have a look at www.ggbn.org or the data portal at http://data.ggbn.org. Links to sequence portals such as GenBank are established already, as well as information on the underyling voucher specimen.

Thanks to everyone for responses on this. And, Hey Brittany! Sorry for the delayed response, but it was great hearing from you on this! So, the general consensus seems to be that Dryad is preferable to TreeBASE, particularly for population genetics or phylogeographic datasets.

Regarding my experiences, I admit that using TreeBASE was a bit of a pain for just the reasons that Brittany mentioned. Indeed, (1) I found properly formatting the tree tips to be easy but time-consuming and a bit annoying since you can envision a system in which you could keep all the tip labels in their original format and still be able to link all the corresponding species and locality info. (2) The TreeBASE staff never even replied to multiple emails requesting assistance, until after I had completed my submission and finalized it on my own; and of course their email was just like "Sorry." (3) TreeBASE was also sort of tricky to get some of the taxonomic designations (e.g. linking tip names to NCBI Taxonomy etc.) correct to clear the submission. And because of these issues I had to re-do my submission several times to get it right.

In defense of TreeBASE, they provide a great free service to which metadata can be linked, and I was able to figure out their system and complete my submission. So, I would go the TreeBASE again, despite the downfalls, although more likely for phylogenetic data.

But I am listening to the group wisdom here, and so I will likely first attempt to use Dryad for my next data submission, especially since you guys said it was free for Mol Ecol (thus it might be free for other evolutionary biology journals).

One thing that people haven't mentioned is that the Dryad submissions get a doi and a publication reference, whereas it seems the TreeBASE ones do not. This is beneficial because others can cite your dataset if they use it, regardless of whether they cite your study or not (although we might argue that they should cite both).

To Gabriele, thanks so much for this info!! I had never heard of the Global Genome Biodiversity Network before, and this seems like a really great option for preserving physical samples. Honestly, it kind of blew me away. Take care.