|
WHEN
CLASSIFICATIONS CONFLICT |
|
When Classifications Conflict Richard H. Zander Summary Three criteria are proposed for identifying the
best of competing classifications based on scientific value. Morphologically
based classifications are expected to continue to be important because
molecularly based classifications are not generally demonstrable as reliable
in detail, and the former may include identifiable biological hypotheses or
theories that integrate with other fields. A problem common to all
of systematics is exactly how and when is a new classification better than a
previous one? This paper rebuts several recent treatments of the Pottiaceae
(Musci) that go back to generic classifications popular prior to my new
proposals (Zander 1993), which taxonomically emphasize gametophyte
characters. A reason sometimes given
for rejection of new classifications and retention of largely traditional
generic concepts is that a natural classification is to be preferred,
generally meaning giving equal weight to characters of the sporophyte and
gametophyte. This is opposed to my rationale which consists of basically two
ideas: First, that new concepts are warranted by the fact that several
separate series of cleistocarpous and stegocarpous peristomes (including the
eperistomate and all levels of peristome length and twist from rudimentary,
to short and straight, to medium length and weakly twisted with a short basal
membrane, to long and well twisted from a high basal membrane), with the
peristome teeth grading from flattened to filamentous, are all or mostly
present in species with quite similar gametophytes previously placed in Phascum, Pottia, Desmatodon, Stegonia, Tortella and Tortula. Because there are more
gametophytic characters than sporophytic characters, a natural classification
thus requires emphasis on gametophytic characters. Second, when gametophytic
characters are used to organize the sporophytic characters (instead of vice
versa or some combination), the variation in morphology of the sporophytes in
the various newly emended genera (especially the large genera Henediella, Microbryum, and Tortula)
may be explained as nearly identical transformation series involving
reduction (parallel elaboration of a peristome is improbable unless genes are
turned off and on controlling expression of several complex characters, for
which there is presently no evidence). Mayr (1982: 275) defined
a natural system as a classification “based on the degree of similarity of
their morphological or anatomical systems…,” noting that its overall success
is ultimately explained by shared ancestry. Similarly, Stuessy (1990) pointed
out that a natural system “is one based upon states of several to many
characters selected a posteriori
for their value in positively correlating with states of other characters to
form a hierarchical structure of groups in ranks containing high information
content and predictive value.” A taxonomist may choose intuitively as major
characters those relatively stable features that best organize or maximize
the similarity of other, possibly more variable characters; e.g. using flower
morphology for higher categories of angiosperms, or may use numerical
taxonomy to identify such organizing characters, and the resultant similarity
among taxonomic units is informative and predictive. This is not the same as
simply giving equal weight to all characters. Stuessy (1990: 60) pointed out
that equal weighting is simply a preliminary part of the method of phenetics
(numerical taxonomy), while natural classification differentially weights
characters after evaluation of perceived utility in maximizing similarity.
The result is the same, but a numerical analysis is needed to maximize
similarity among species of recognized genera. An emphasis on the
utility of gametophytic characters is based on two synergic rationales: (1) a
natural system choosing certain gametophytic characters (primarily leaf
shape, costal anatomy, and areolation features) to maximize similarity of
other characters among the genera, especially the sporophytic characters
which self-organize into neatly parallel transition series, and (2)
interpretation of the sporophyte transition series as evolutionary
adaptations that hypothetically involve selected fine control of diaspore
dispersal in different environments, as with reduced sporophytes and larger
spores or late-rupturing capsules (Carlquist 1966; Van der Pijl 1972; Zander
1993: 14), similar transition series in sexual condition (dioicy to autoicy
to synoicy in Weissia s.lat.) that
may have been selected for control of degree of outbreeding. There is good
evidence that reduction also occurs in the gametophyte, e.g. see my (1993)
treatment of Trichostomum. So which classification
is better for others to use, old one(s) or new ones (e.g. mine)? The only
proper judgement must be on the basis of the proposals themselves. Although we may all
subscribe to a dictionary-style definition of science as “gathering,
organization and analysis of information about the natural world and
inference of general principles therefrom,” when scientific methods compete,
such as in systematics, a judicious perspective on the question “which
produces the better model of reality?” is a way to approach the dilemma.
“Reality” or that which is “out there” can attain a metaphysical substance in
all fields but a self-correcting science, which assumes that all theories are
only approximations. Most scientists at least implicitly subscribe to
“critical realism,” in which the immediate world is very real (predictions or
manipulations are easy and reliable), but realities that are non-immediate,
being distant in time and space, are in a way “less real” and are usually
dealt with probabilistically (either as empiric extensions of long-run
frequency observations or as psychological expectation based on logic), or at
least in an instrumentalist fashion (are the theories useful?). Science
attempts to make non-immediate reality almost as easily dealt with as the
immediate by creating models based on facts (i.e., well documented
observations). Systematics is a “quasi-experimental” field (Cook &
Campbell 1979) where patterns in nature are discerned in much the same way
that scientific laws or regularities in nature (Carnap 1966) are established
in experimental sciences. The basis null hypothesis for systematics is that
there are no species, for biogeography is that there are no discrete ranges,
for evolution is that there is no evidence that it did occur. Thus, one
expects, in both experimental science and systematics, testable theories to
disprove or support. Given that systematics
is a science, when is one theory better than another? There is a vast
literature on evaluating scientific theories, and directly pertinent, though
often philosophically conflicting treatments include Carnap (1966), Glymour
(1980), Hemple (1963), A system that emphasizes
the taxonomical importance of gametophytic characters (1993) matches these
criteria in the following respects: (1) More characters are used, and more
species examined. (2) It simplifies dealing with sporophytic characters in
that a rather standard transformation series may be assumed unless there are
particular anomalous characters (e.g. the combination of a short seta but elongate,
stegocarpous capsule in Willia).
That is, there are fewer ad hoc explanations. (3) It fits in well with other
theories in that Weissia is now
commonly acknowledged to include past segregates Astomum and Hymenostomum,
these genera apparently being artifactually discontinuous perceptions of a
single transformation series in sporophytic characters (Stoneburner 1985).
(4) The transformation series in sporophytes reflects theories of
environmental patterning, atelochory and r- and K-selection, and is a good
hypothesis that may be tested. With such embedded theories, my system also
matches the “more bold” criterion of Popper (1962). Thus, although some
classifications may differ largely according to “taste” or whether the author
is a lumper or a splitter, in this case there are clear methodological and
biological reasons why taxonomic emphasis on the gametophyte is to be
preferred. The next advance in classification of the Pottiaceae will
doubtless be made at the species level using modern methods of phylogenetic
analysis, but there remain major problems with that technique. An expectation that DNA
data will provide ultimate solutions to intractable systematic problems is
shared by many recent authors. This, however, cannot be expected to be the
case, at least in the next very many years. There are major problems with
reliability on the results of molecular (and morphological) phylogenetic
analyses. This is because the best answer is not necessarily much better
supported than the second best, or the third best, which may be quite
different (Zander 1998). This applies to maximum parsimony in that
bootstrapping cannot evaluate confidence levels for branches not in the
shortest tree, and the gene pool is coarsely heterogeneous due to lineage
sorting (different “speciation” times for genes and species). Also, Bremer
support is a poor measure of branch support in data sets of very many
characters because a branch of length n and Bremer support of x may have an
alternative branch length of n–x, which could be large. Likelihood ratios,
the standard measure of support in maximum likelihood studies cannot be used
in phylogenetic analysis because the likelihoods are already optimizations.
Full Bayesian studies such as Markov chain I have introduced, for
measuring reliability of internal cladogram branches, a new non-parametric
test of reliability (Zander, 2001) called the Conditional Probability of
Reconstruction (CPR), which uses chi-squared analysis after nearest neighbor
interchange under constraint. It tests whether the best choice of the three
possible alternative arrangements for any four nearest neighbor branches is
distinguishable from a random distribution at some chosen level of confidence
(for small data sets, Bayes’ Theorem with uniform priors are used instead of
chi-squared). Analysis of two published data sets (Didymodon morphology and primate mtDNA) indicated that many of
the optimal internal branches of both morphological and molecular trees can
be indistinguishable from a random distribution at a reasonable confidence
level vis-a-vis the lengths of the two immediate alternative branches.
Although some lineages are well supported probabilistically, probabilities of
individual branch reconstruction when multiplied give rather low summary
probabilities to the whole tree. Thus, cladistic analysis, when recouched in
terms of statistical analysis (probability) rather than an optimality
criterion (parsimony) is no longer as promising. To bring this home, consider
a coin flipped 100 times, coming up tails 57 times and heads 43 times. Under
parsimony, the hypothesis that the coin is unfairly loaded to come up more
often as tails is valid, though poorly supported; statistically, however,
there is no reasonable degree of confidence that the result was not due to
chance, and no hypothesis is reasonably considered (although the null of
random generation of data is not proven). The CPR method can also
be used to evaluate the problem of conflicting gene lineages in molecular
phylogenetic analysis, which is also entirely relevant here. For example,
there has long been controversy over the relationships of humans, chimpanzees
and gorillas. A meta-analysis of the Homo-Pan-Gorilla
data sets was recently done by Satta et al. (2000) who surveyed data from the
literature for 45 loci consisting of 46,855 bp. There was conflict between
data sets, with 23 loci supporting the ((Homo
Pan) Gorilla) gene tree, 8 that
support ((Homo Gorilla) Pan), 8 that support ((Gorilla Pan) Homo), while 6 support a (Homo
Gorilla Pan) trichotomy. This incongruence was attributed by them to
different gene and species phylogenies associated with the different loci. A
CPR analysis (Zander 2001) treating each gene as a character, with
alternative branch lengths of 23, 8 and 8, provided a probability of reconstruction
of the species tree of .997. A similar high probability (.999) is obtained
when only data sets with bootstrap values greater than 80% are used. Thus,
species evolution can indeed be probabilistically reconstructed using
molecular techniques. It also implies, however, that, absent this way of
probabilistically identifying genes that actually track species evolution,
the prior probability that the absolute order of an internal branch of any
molecular tree really reflects species evolution rather than a contrary gene
lineage may be on the order of 23/(23+8+8) or 59%. Additional papers that
reflect on the use, particularly the successful versus the unsuccessful use,
of statistics in evaluating the reliability of individual branch arrangements
in a cladogram were published recently (Zander in press). Given the perspective
that (1) many cladograms, though presented as fully resolved in the
literature, may be poorly supported, and (2) that genes may be expected to
provide significantly conflicting (through differential lineage sorting) but
sometimes well supported trees, one cannot expect present phylogenetic
techniques to result in a reliable evaluation of the evolution of the
Pottiaceae in the immediate future. It is therefore more, not less, important
to produce morphologically based, predictively useful, fruitful, illuminating
and broadly applicable classifications that may have embedded biological
theories relevant to other fields. Carlquist, S. 1966. The biota of long-distance
dispersal. III. Loss of dispersibility in the Hawaiian flora. Brittonia 18:
310-335. Carnap, R. 1966. An Introduction to the
Philosophy of Science. Basic Books, New York. Glymour, C. 1980. Theory and Evidence. Princeton
University Press, Princeton, New Jersey. Hemple, C. G. 1963. Aspects of Scientific
Explanation. Free Press, Collier-Macmillan, New York. Hull, D. L.
1974. Philosophy of Biological
Sciences. Prentice Hall, Englewood
Cliffs, New Jersey. Mayr,
E. 1982. Systematics and the Origin of Species. Introduction by N. Eldredge.
Columbia University Press., New York. Pap, A. 1962. An Introduction to the Philosophy
of Science. Macmillan Co., New York. Popper, K. R. 1962. Conjectures and Refutations:
The Growth of Scientific Knowledge. Harper Torchbooks, Harper & Row, New
York. 1965 Edition. Steel, M. & D. Penny. 2000. Parsimony,
likelihood and the role of models in molecular phylogenetics. Mol. Biol.
Evol. 17: 839-850. Stoneburner, A. 1985 [1986]. Variation and
taxonomy of Weissia in the
southwestern United States. II. Taxonomic treatment. Bryologist 88: 293-314. Stuessy, T. 1990. Plant Taxonomy: The Systematic
Evaluation of Comparative Data. Columbia University Press, New York. Van der Pijl, L. 1972. Principles of Dispersal in
Higher Plants. 2nd. Ed. Springer-Verlag, New York. Zander, R. H. 1989. Seven new genera in
Pottiaceae (Musci) and a lectotype for Syntrichia.
Phytologia 65: 424-436. Zander, R. H. 1993. Genera of the Pottiaceae:
Mosses of Harsh Environments. Bull. Buffalo Soc. Nat. Sci. 32: i-vi, 1-378. Zander, R. H. 1998. Phylogenetic reconstruction,
a critique. Taxon 47: 681-693. Zander, R. H. 2001. A conditional probability of
reconstruction measure for internal cladogram branches. Syst. Biol. Zander, R. H. 2001. Reliable phylogenetic resolution of morphological
data can be better than that of molecular data. Taxon 52: 109-112. 2003. Zander, R. H. (in press) Minimal values for
reliability of bootstrap and jackknife proportions, decay index, and Bayesian
posterior probability. Phyloinformatics |
|
|