Proposal (474) to South American Classification Committee
A general criterion for translating phylogenetic trees into linear sequences
[The graphics for this proposal are unreadable on most browsers – to see as pdf, click here: SACCprop474.pdf]
In most of the books, papers and check-lists of birds (e.g. Meyer de Schauensee 1970, Stotz et al. 1996; and other taxa e.g. Lewis et al. 2005, Haston et al. 2009, for plants), at least the higher taxa are arranged phylogenetically, with the “oldest” groups (Rheiformes/Tinamiformes) placed first, and the “modern” birds (Passeriformes) at the end. The molecular phylogenetic analysis of Hackett et al. (2008) supports this criterion. For this reason, it would be desirable that in the SACC list not only orders and families, but also genera within families and species within genera, are phylogenetically ordered.
In spite of the SACC’s efforts in producing an updated phylogeny-based list, it is evident that there are differences in the way the phylogenetic information has been translated into linear sequences, mainly for node rotation and polytomies.
This is probably one of the reasons why Douglas Stotz (Proposal #423) has criticized using sequence to show relationships. He considers that we are creating unstable sequences with little value in terms of understanding of relationships. He added, “We would be much better served by doing what most taxonomic groups do and placing taxa within the hierarchy in alphabetical order, making no pretense that sequence can provide useful information on the branching patterns of trees. This would greatly stabilize sequences and not cost much information about relationships”.
However, we encourage creating sequences that reflect phylogeny as much as possible at all taxonomic levels (although we agree with Douglas Stotz that the translation of a phylogenetic tree into a simple linear sequence inevitably involves a loss of information about relationships that is present in the trees on which the sequence is based). Furthermore, the idea that sequences cannot provide phylogenetic information is not restricted to species but is also pertinent to other taxonomic levels, such as genera, families, etc.
In this context, it appears necessary to unify the criteria used by all members of the Committee for translating phylogenetic trees into linear sequences. In an attempt to find a general criterion, we propose the following approach, to be applied over all taxonomic levels, based on five rules. This approach is valid only for those trees (or clades, e.g. Campylorhamphus in the Dendrocolaptinae tree -see Examples-) including all or nearly all the known species:
1) First-splitting taxon:
The taxon that splits first (presenting the lesser number of ancestors, that is, internal nodes*) is placed at the top of the sequence (taxon A). The same rule is applied to the next taxa, following the order of the branching pattern.
*Each node with descendants represents, in a rooted tree, the inferred most recent ancestor of those descendants. Nodes can be rotated without altering the relationships between taxa.
C/D or D/C (see rule 4)
2) Sister clades:
For sister clades, the clade containing the taxon that splits first (taxon A, clade 1) is arranged first. After it, the next clade is listed (clade 2).
When the number of nodes is the same between the first-splitting taxon in both sister clades (taxon A and F in X; A/B and F/G in Y), the less diverse clade is arranged first (clade 1).
When the number of nodes is the same between the first-splitting taxon (taxon F and A) in equally diverse sister clades, the order of the SACC list is followed for selecting the first taxon to be placed (e.g. taxon A, clade 2).
In the case of polytomies, the taxon that splits first (taxon O), or the clade containing the taxon that splits first, is placed at the top of the sequence. Then, if the number of nodes between the first-splitting in sister clades is equal (taxon F, A and K), the less diverse clade is arranged first (clade 3); if these clades are equally diverse (clade 1 and 2), the SACC list is followed to select the first taxon (e. g. taxon A, clade 2).
4) Sister taxa:
At the tips of the tree, when branch lengths are scaled (in phylograms), the taxon that has the shortest branch (that is, having the lowest amount of genetic change) is placed first (taxon B).
In polytomies, the clade with the taxon that has the shortest branch is placed first (taxon B, clade 3). Then, the clade with the shortest branched taxon follows (taxon G, clade 1) and so on (clade 2).
In equal terminal branches (in phylograms) or unscaled branch lengths (in cladograms), the SACC list is followed.
5) Trees comprising different levels of taxa
In trees that analyze different levels of taxa, the rules explained above are applied within each taxonomic level. The figure shows a tree of genera and species.
For ordering genera, the species should be removed from the tree and the tree analyzed under the rules previously suggested.
Then, the species must be ordered within genera under the rules previously suggested.
In green, taxa whose position is defined following the order in the SACC list.
Tangara (Sedano and Burns 2010)
Rhinocryptidae (Ericson et al. 2010)
Dendrocolaptinae (Claramunt et al. 2009)
In this example, it is possible to make the sequence of genera (except for Sittasomus, Glyphorynchus and Deconychura that were not included) and the sequence of species of Campylorhamphus.
Ericson, G.P., Olson S.L., Irestedt, M., Alvarenga H. and FjeldsĆ, J. 2010. Circumscription of a monophyletic family for the tapaculos (Aves: Rhinocryptidae): Psilorhamphus Kin and Melanopareia out. Journal of Ornithology DOI. 10.1007/s10336-009-0460-9.
Hackett, S.J, Kimball, R.T., Reddy, S., Bowie, R.C.K., Braun, E.L., Braun, M.J., Chojnowski, J.L., Cox, W.A., Han, K., Harshman, J., Huddleston, C.J., Marks, B.D., Miglia, K.J., Moore, W.S., Sheldon, F.H., Steadman, D.W., Witt, C.C., and Yuri, T. 2008. A phylogenomic study of birds reveals their evolutionary history. Science, 320: 1763-1768.
Haston, E., Richardson, J.E., Stevens, P.F., Chase, M.W. and Harris, D.J. 2009. The Linear Angiosperm Phylogeny Group (LAPG) III: a linear sequence of the families in APG III. Botanical Journal of the Linnean Society, 161, 128–131.
Lewis, G.P., Schrire, B., Mackinder B. and Lock M. (eds). 2005. Legumes of the World. Royal Botanic Gardens, Kew.
Meyer de Schauensee, R. 1970. A guide of the birds of South America. Academy of Natural Science of Philadelphia. Pennsylvania.
Sedano, R.E., and Burns, K.J. 2010. Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini). Journal of Biogeography 37: 325–343.
Stotz, D.F., Fitzpatrick, J.W., Parker, T.A.III and Moskovits, D.K. 1996. Neotropical birds: ecology and conservation. University of Chicago Press, Chicago.
Avise, J.C. 2004. Molecular markers, Natural History and Evolution. Chapman and Hall, New York.
Hillis, D. M., Moritz, C. and Mable, B.K. 1996. Molecular Systematics. Sinauer Assoc., Inc. Sunderland, Massachusetts.
Manuel Nores (Centro de Zoología Aplicada); Noemí Cristina Gardenal, Paula Rivera, Raúl González Ittig, (Cátedra de Genética de Poblaciones y Evolución); María Jimena Nores (Instituto Multidisciplinario de Biología Vegetal). CONICET-Universidad Nacional de Córdoba. Argentina.
Comments from Jaramillo: “YES. This looks logical to me, unless I missed something. I look forward to hearing from folks who are negative on this proposal. The big issue for me is if it passes, do we use it from now on…or do we have to go back and make sure every linear sequence is consistent in the entire list? That would be a big job and would require many, many new proposals.”
Comments from Cadena: “I am going to say NO on this not because I feel that Manuel's proposed system is bad per se, but because I feel it is a bit impractical. Who is going to go through all these complicated steps every time a new phylogeny is published? That would be worthwhile if users of our baseline list could retrieve some of the information involved from the final product (i.e., the linear classification), but this is essentially impossible. Also, I do not see how does considering things such as which branch in a sister group is longer or shorter (an indication of the substitution rate in the gene(s) used to build the tree) as a criterion for which lineage goes first in a linear classification makes sense from a systematics perspective. In sum, it may well be that some guidelines for linear sequences should be developed, but I believe this system is way too complicated for what we need.”
Comments from Remsen: “NO. … at least in part. We already follow the first rule, namely the first-spillting taxon in a group is listed first. From that point on, it becomes very complicated and is driven by branch length, itself a volatile metric depending on which loci are studied. I favor the traditional system of sequencing sister taxa etc., simply because it is more stable, i.e., sister taxa are arranged by convention geographically, from NW to SE. As we all know, deriving a phylogeny from a strict linear sequence is already essentially impossible. (This is the basis for Doug’s cynical views on sequences; however, alphabetization does not produce a stable sequence because of taxonomic changes, and I just can’t endure known sister taxa not being placed next to each other in a sequence). Our convention is that we follow Manuel’s et al.’s step 1, and arrange terminal pairs of sister taxa geographically. Where there is ambiguity, we retain the traditional sequence of taxa.
“Manuel et al.’s system is obviously well thought-out, and if it is published and gains widepsread use, then I would definitely reconsider.”
Comments from Stiles: “NO, I agree with Daniel that Manuel's system isn't bad, just impractical and overly complicated, given the amount of not easily available information it would require. However, it would be helpful if Manuel were to go through his procedure with some sequences we have already approved to see the results; if any substantive changes (and improvements) result, I might reconsider, although it might be better to present separate proposals to modify the sequences in question (?).”
Comments from Stotz: “ABSTAIN. This seems unduly complicated and unlikely to be regularly employed to construct a sequence of species. I am basically of the belief that we should give up any attempt to use sequence to indicate relationship. It leads to a great deal of instability, and there is very little information in the sequence on relationships. Essentially the only specific information in a sequence is that non-adjacent taxa are not sister. Given this basic lack of acceptance of the basis of sequencing taxa, I think that I should not vote an attempt to rationalize the process of sequencing taxa.”
Comments from Pérez: “NO. Although I agree we need some operational criteria to unify or standardize SACC decisions on translating phylogenetic information into linear sequences, I think the proposed method (as others) will result in unstable sequences depending on taxon and character sampling. Topology and branch lengths, to name some of the variables on which this method is based, are dependent on taxon sampling, phylogenetic methods, and sequenced genes. Thus, linear sequences, even within a group, might need to be reconsidered anytime new information is available. I like Gary’s idea of working out linear sequences of specific groups to evaluate the proposed method. Furnariidae would be a great candidate: would linear sequences be similar if we use Irestedt et al. (2009) or Derryberry et al. (2011) phylogenetic hypotheses?”