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.
Sequence
A
B
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).
3) Polytomies:
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.
EXAMPLES
In green, taxa whose position is defined following the order in the SACC
list.
Tangara (Sedano and Burns 2010)
Sequence
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.
Literature Cited
Claramunt, S., E. P. Derryberry, R. T. Chesser, A.
Aleixo, and R. T. Brumfield. 2010.
Polyphyly of Campylorhamphus with the description of a new genus for C.
pucherani. Auk 127: 430-439.
Ericson, G.P., Olson S.L., Irestedt, M., Alvarenga
H. and Fjeldså, 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.
General Literature
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.
December
2010
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?”