High School Students
Databasing and Mapping
Vouchering and Archiving
Reconstructing the vaejovid tree
will be computationally challenging, because of the time span for divergence and
size of the data set. Analyses will require heuristic searches and the
exploration of varied parameters. Besides state-of-the-art desktop computers, we
will use the AMNH supercomputer cluster, comprising 560 Pentium III processors (http://research.amnh.org/scicomp/,
allowing multiple analyses to address parameter sensitivity and explore the
analytical space implied by the data.
This project applies the philosophy of “total evidence”
Kluge (1989) or “simultaneous analysis”
Nixon & Carpenter (1996) to analysing molecular and morphological data, the
advantages and disadvantages of which have been thoroughly reviewed and shall
not be elaborated here. Arguments by Nixon & Carpenter (1996) concerning
explanatory power, character independence, and the emergence of secondary
signals are considered sufficient justification for this approach. Separate
analyses of the morphological and molecular data will only be conducted in order
to assess character incongruence among the various data partitions (morphology,
different loci), and only trees obtained from simultaneous analysis of all
evidence will be used for testing a posteriori hypotheses.
The inclusion of morphological data, in turn, provides justification for
the use of parsimony in this project, and simultaneous analysis is a logical
extension of the parsimony criterion (Nixon & Carpenter 1996). The use of
multiple analytical techniques, predicated on fundamentally different
philosophies (“syncretism” sensu Schuh 2000; “pluralism” sensu
Giribet et al. 2001a; “methodological concordance” sensu Grant & Kluge
2003), has been criticised elsewhere (Giribet et al. 2001a; Grant & Kluge 2003;
Prendini et al. 2003).
Searches for most parsimonious trees (Farris 1970, 1983; Kluge 1984) will
use POY (Gladstein & Wheeler 1996–2000) (http://research.amnh.org/scicomp/projects/poy.php),
NONA and Pee-Wee (Goloboff 1997a, 1997b) (http://www.cladistics.com/Software.html),
TNT (Goloboff et al. 2002) (http://www.cladistics.com/Software.html),
and PAUP* (Swofford 2002) (http://paup.csit.fsu.edu/),
each with parallel versions. POY will be used for analyses involving
molecular data, because it is the only program implementing direct optimization
(simultaneous alignment and tree-search), regarded as ideal in principle
(Wheeler 1994, 1996, 1998a, 1999, 2001a, 2001b; Slowinski 1998; Giribet &
Wheeler 1999; Giribet et al. 2000,
2001b; Wahlberg & Zimmermann 2000), albeit computationally demanding. The
widely used approach to analysing sequences of unequal length by first aligning
and then subjecting the prealigned sequences to a normal parsimony analysis has
come under increasing criticism (Wheeler 1994, 1996, 1998b, 1999, 2000, 2001a,b;
Slowinski 1998; Edgecombe et al. 1999; Giribet & Wheeler 1999; Giribet & Ribera
2000; Giribet et al. 2000, 2001b, 2002; Wahlberg & Zimmermann 2000; Giribet
2001; Prendini et al. 2003). This approach clearly violates the logic of
parsimony because whether or not an indel is postulated depends on the phylogeny
in question. As has been cogently argued by Wheeler (1996, 1998b, 1999, 2000,
2001a,b), a phylogeny should be evaluated according to how many substitutions
and how many indels it requires postulating so that analyses should
simultaneously consider the indels and substitutions required by alternative
phylogenies, instead of taking them as given. Strategies for rapid parsimony
analysis, e.g. the parsimony ratchet (Nixon 1999b), tree fusing and tree drift (Goloboff
1999), most of which are implemented in the latest version of POY, will
enhance searches throughout tree space.
Partitioned Bremer support (Baker &
DeSalle 1997; Baker et al. 1998) will be used to address the relative
contributions of different loci and morphological character systems to the
simultaneous analysis. Relative support for nodes in trees will be assessed with
branch support indices (Bremer 1988, 1994; Donoghue et al. 1992) and bootstrap
percentages (Felsenstein 1985; Sanderson 1989).
Adaptational and biogeographical hypotheses will be tested by
optimization on the tree obtained by simultaneous analysis, using
WinClada (Nixon 1999a) or
MacClade (Maddison & Maddison 1992). Ambiguous optimizations will be
resolved with ACCTRAN, maximizing homology by favoring reversals over
parallelisms to explain homoplasy (Swofford & Maddison 1987, 1992).
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R. 1997. Multiple sources of character information and the phylogeny of Hawaiian
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Baker, R.H., Yu, X.B.
& DeSalle, R. 1998. Assessing the relative contribution of molecular and
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limits of amino acid sequence data in angiosperm phylogenetic reconstruction.
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Olmstead, R.G., Smith, J.F. & Palmer, J.D. 1992. Phylogenetic relationships of
Dipsacales based on rbcL sequence data. Annals of the Missouri
Botanical Garden 79: 333–345.
Giribet, G. & Wheeler, W.C. 1999. Filogenia de Chilopoda: Combinado secuencias
de los genes ribosómicos 18S y 28S y morfología [Phylogeny of Chilopoda:
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