Fwd: [Hip] FYI: use of tolweb in research

[Rutger Vos]

Hi all,

FYI, Arlin did a back-of-an-envelope survey of usage of ToLWeb in research. The email about it is reproduced below (with his blessing).

Rutger

---------- Forwarded message ----------
From: Arlin Stoltzfus
Date: Thursday, November 15, 2012
Subject: [Hip] FYI: use of tolweb in research
To: HIP Hackathon Participants <h...@nescent.org>

Here is some information for folks interested in reuse of phylogenetic information in ToLWeb.  We have had some discussion in the past about how ToLWeb gets used, and whether it gets used at all in research (as opposed to education).  

I spent an hour this afternoon doing an informal survey that was very helpful for me to clarify this issue. Here are the results.  

The ToLWeb paper is cited 21 times in Web of Science, and 130 times in Google Scholar.   I went through the first 2 or 3 dozen papers in google scholar.  A handful were ignored on grounds of being unlikely to have substantive uses (e.g., newsy pieces, blue-sky papers, reviews on the construction of large trees).  About half of them were inaccessible due to paywalls.  I ended up looking through 8 papers in detail.  

The 8 papers are listed below, in increasing order of the amount of phylogenetic information re-used.  Probably all but the last are based on visual inspection of the tree (rather than computation from it).  The first one probably does not use any information from ToLWeb.  The second one only cites ToLWeb for the fact that fungi are "a major clade in the tree of life".  The last paper uses a considerable amount of ToWeb phylogenetic information, but it is used to illustrate a new computational method rather than to test a hypothesis or analyze data.  

The lesson here is that people are using ToLWeb, but they are using it in relatively modest ways for constructing trees by eye, often combining multiple sources.  Sometimes they are citing it for textbook knowledge about relationships, i.e., ToLWeb provides a reference point for mundane knowledge of the tree of life.  The alternative is to get these results from separate textbooks, reviews and papers-- I don't know how often people do that instead of going to ToLWeb.  

Arlin

Here are the 8 papers (as noted, ordered by increasing apparent use of phylogenetic info from tolweb): 

1. R Stelkens, O Seehausen - Evolution, 2008 "Genetic distance between species predicts novel trait expression in their hybrids".  this appears to be a mistake.  The text cites APGII and tolweb as the source of the phylogeny used in independent contrasts, but it appears to come entirely from APG.  The phylogeny is given in Fig S1, and the caption of the supplementary data link says "Angiosperm phylogeny used for calculating independent contrasts, modified from APG II (The Angiosperm Phylogeny Group 2003)."  This exact same text is repeated inside the supplementary data file. 

2. Shenoy, Jeewan and Hyde, a review on fungal taxonomy.  first sentence "Fungi represent a major clade in the tree of life (Maddison and Schulz, 2006) "

3. Smolenaars, et al 2006.  this is a substantive reference to a relationship and it implies that having a current view ("present view") is important: "The present phylogenetic analysis suggests a closer relationship between the Vtgs from nematodes and insects compared with Vtgs from vertebrates, in agreement with the present view on animal phylogeny (74)."  74 = tolweb

4. Farris & Roberts, 2005 PNAS.  hand-constructed tree of just 7 taxa is constructed following relationships in 2 sources, one of which is tolweb.  so this is a substantive re-use although it isn't a computational re-use.

5. Bininda-Emonds, et al "Forelimb-hindlimb developmental timing changes across tetrapod phylogeny" actually use a cladogram (Fig 1) that combines the mammal tree of Bininda-Emonds and tolweb.  The tree has 2 anurans, 2 birds, 2 reptiles, and 8 mammals, with a trichotomy of the two reptiles (turtle, lizard) with birds.  I'm guessing its manually constructed given the simplicity of it.

6. Martinson, et al "Detritivory: stoichiometry of a neglected trophic level"  "To describe species relationships, we built a composite phylogeny to family level, using the following published phylogenies: Wheeler et al. (2001, Hexapoda); Caterino et al. (2002), Shull et al. (2001) and Hunt et al. (2007, Coleoptera); Yeates et al. (2006, Diptera); Maddison and Schulz (2007, other taxa). Below family level, we used a multifurcating phylogeny based on taxonomic classification at the subfamily and genus levels. To reflect lack of branch lengths, two models were tested against the data: setting all lengths to 1, or scaling them according to taxonomic depth (Grafen 1989) using the compute.brlen() function in the ape package."

7. Whitney and Garland, 2010 "Did Genetic Drift Drive Increases in Genome Complexity?"  there are 28 species in this tree-- from the set of species invoked by Conery & Lynch in their arguments about population size and genome size.  "A composite tree for the species was constructed in Mesquite v. 2.71 [25] based on phylogenetic trees reported in [26]–[28].  As a visual heuristic, genome sizes were traced onto the phylogeny using the Parsimony Ancestral States method [29] with an assumption that all branch lengths equal 1.0." 27=tolweb

8.  Blanchette, et al 2002.  a methods paper-- method to identify regulatory elements by "phylogenetic footprinting", using a tree and an alignment of orthologues.  They use tolweb, but the main result of the paper is the method itself, not the results of using it via the tolweb tree.

-------
Arlin Stoltzfus (ar...@umd.edu)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD, 20850
tel: 240 314 6208; web: www.molevol.org

--
Dr. Rutger A. Vos
Bioinformaticist
NCB Naturalis
Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
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http://rutgervos.blogspot.com