2413605

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Society of Systematic Biologists
Cladistic Taxonomy, Phylogenetic Systematics, and Evolutionary Ranking
Author(s): Martin L. Christoffersen
Source: Systematic Biology, Vol. 44, No. 3 (Sep., 1995), pp. 440-454
Published by: Oxford University Press for the Society of Systematic Biologists
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440
Syst.
SYSTEMATIC
Biol.
BIOLOGY
VOL.
44
44(3):440-454,1995
Cladistic Taxonomy, Phyl
Evolutionary Rankin
Martin L. Christoffersen
Departamento de Sistematica e Ecologia, Universidade Federal da Paraiba,
58059-900, Joao Pessoa, Paraiba, Brasil
The ancient discipline of biologicalrated
tax? by the codes, simply conflict with
onomy has been very slow to incorporate
phylogenetic representations (Griffiths,
major shifts in world views throughout
the
1974a,
1974b, 1976). For example, manda?
millennia. Impervious to the derision
tory of
categories, the names of genera as
scientists from the more glamorousparts
fields
of binomials, typification and syn?
of research, many taxonomists today
sim?tied to Linnaean categories, and re?
onymy
ply take for granted secular traditions
dundant
of taxon names (Christoffersen,
de Queiroz and Gauthier, 1992) all
describing and naming the diversity 1987;
of tiature. They may persist stoically forconflict
a life? with evolutionary approaches. The
time in such a self-appointed descriptive
codes thus help perpetuate essentialistic
role, avoiding theory, philosophy, and
ex?
taxonomic
traditions rather than promote
planation. Some of these taxonomists
may
conceptual
evolutionary innovations.
venture intuitive classifications for their
Conceptual Lineages
named groups but will often delegate to
others the task of deriving evolutionary
Taxonomists, like other segments of th
meanings from their proposals.
scientific community, are presently divi
Evolutionary concepts have still not pen?
ed into several factions that support con
etrated the core of nomenclature. The in?
flicting conceptual systems. Following
ternational codes (International Commis?
Hull's (1984) and Mishler's (1987) analog
sion on Zoological Nomenclature, 1985;
with biological phylogenies, these differe
International Botanical Congress, 1988; In?
research groups, rather than being define
by the presence of some necessary and su
ficient set of shared ideas, are viewed as
eties, 1992) are totally couched in a tradi?
tional Linnaean framework developed
intellectual lineages, with strong historic
coherence, social cohesion, and adversaria
more than 100 years before the widespread
acceptance of evolutionary ideas. Purport?
relations with other lineages. I propose
edly not to interfere with taxonomic free?
tentative phylogeny for these intellectua
dom, the codes provide no rules for the
systems of biological taxonomy (Fig. 1). F
recognition and definition of taxa and cat?
those that would have preferred to se
characters (shared ideas) and Characte
egories. Yet the available rules significantly
constrain taxonomic practice by tying tax(individual spokespersons) on the phyl
on names to categorical ranks. This struc?
genetic tree, I defer to Carpenter (198
ternational Association of Microbial Soci?
ture interferes with the codes7 own avowed
who provided a numerical cladistic stud
goals of providing explicit, universal, and of phylogeneticists and a review of prev
stable names for taxonomy because a taxonous single-character classifications of t
name must be changed every time it isthree main contemporary schools of ta
placed in a different category (de Queiroz onomy.
and Gauthier, 1994). Furthermore, several Different concepts of taxonomy, system
taxonomic conventions, variously incorpo-atics, and classification have been advocat?
ed by various authors (e.g., Simpson, 196
1 E-mail: [email protected] .bitnet.
Blackwelder, 1967; Mayr, 1969; Nelson
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1995
POINTS
OF
VIEW
441
schools of taxonomy (Fig. 1) are as follows.
Aristotelian taxonomy proceeds by logical
subdivision, in which each member of a
pair of taxa is characterized, respectively,
by the presence and absence of a chosen
feature. All present attempts to derive a
taxonomy from an identification key reflect
this process. In Linnaean taxonomy, there
is an explicit attempt to distinguish the im?
portant (stable, essential) properties from
the unimportant (variable, nonessential)
properties. In traditional taxonomy, groups
are reconstructed based on perceived sim?
ilarities and differences among taxa. Qui-
Figure 1. A possible
phylogeny
o
narian taxonomists
(e.g., MacLeay, 1819)
eages in biological
taxonomy
looked for idealistic
groupings in circles of A-M
cestor-descendant lineages; N: mon
five, supposed
reveal the harmonious
multiple lineages
or to
single
lineag
and lawful relations of numbers as evi?
populations. A = Aristotelian taxo
an
(essentialistic,
tax
dence oftypological)
the rational plan of creation. In?
tional taxonomy;
Dt evolutionary
= extinct
quin
corporating
theory, conven?
= conventional taxonomy; F = om
tional taxonomy involves interpretation of
latory, practical, utilitarian) taxo
and differences
as reflecting
taxonomy; H = similarities
phenetic
(numeric
netics);
I
=
orthodox
taxonomy;
degrees of phylogenetic
relationships. Om-
(Mayrian, Simpsonian,
synthetic,
nispective taxonomists
explicity reject any s
tic, eclectic) taxonomy
(phyletics);
connections between
a practical and utili?
onomy; L = phylogenetic taxonomy
distics); M = cladistic taxonomy (pattern,
tarian taxonomy and the processes
thought to be responsible for biological di?
methodological, transformed ); N = phylogenetic sys?
tematics (phylogenetics).
versity (e.g., Blackwelder, 1964). In natural
taxonomy, groups are supposed to be dis?
1970; Griffiths, 1974a; Wiley, 1981;
covered in nature rather than fabricated in
the mind of the taxonomist. Phenetic tax?
de
Queiroz, 1988). When these denominations
onomists attempt to quantify data and es?
tablish groups by overall similarity. In or?
become interchangeably qualified by such
thodox taxonomy, multiple criteria are
terms as traditional, numerical, phenetic,
used to access taxa (similarity, diversity,
evolutionary, cladistic, and phylogenetic
size of gaps, ecology, behavior, etc.). In
(Fig. 1), their meanings become multifari?
evolutionary taxonomy, species are rede?
ous, extensively overlapping, and suffi?
fined as evolutionary units (Mayr, 1942;
ciently confusing so as to lose much of
Simpson, 1961), and phenetic, patristic,
their heuristic and interpretative value (cf.
Charig, 1982; Hill and Crane, 1982; and
de
cladistic data are combined into a sin?
gle taxonomic system (e.g., Mayr, 1981;
Queiroz and Donoghue, 1990b; Nixon and
Stuessy, 1987, 1990). In Hennigian taxono?
Wheeler, 1990). Terms and concepts are
my, the principle of common descent is
necessarily context bound and should be
granted a central role at all levels in the
allowed to change through time. I provide
taxonomic hierarchy. In the last two de?
here successively more inclusive defini?
cades, a philosophical split has developed
tions for the basic concepts of taxonomy,
systematics, and classification. I hope mywithin phylogenetic systematics (e.g.,
Mishler, 1987; de Queiroz and Donoghue,
assignment of several commonly used
1990a) (Fig. 1). Pattern cladists are empir?
qualifying terms to distinct conceptual
icists that avoid all assumptions and pre?
systems (Fig. 1) will reduce ambiguity,
even if total agreement is not possible. conceptions about process in constructing
Brief characterizations of the several
a taxonomy (Brady, 1985; Nelson, 1985;
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442
SYSTEMATIC
BIOLOGY
VOL.
44
(Hennig,
1966:6). Characters are instanta?
Rieppel, 1988b).
Phylogenetic
taxo
neoustheorists
morphologies (de Queiroz,
1985:
are evolutionary
that
de
296) that are compared
among "specimens a
most useful taxonomic
concepts
at similar stages
in their life history" (Wi?
ods from general
evolutionary
ley, 1981:119).
Character generalities are es?
(de Queiroz, 1985).
Notwithstand
tablished
the ontogenetic method
(Nel?
basic difference
in by
general
outloo
son, 1978;
Nelson promote
and Platnick, 1981;
phylogeneticists
still
soc
Patterson,
1982, 1983)
and the outgroup
sion by sharing
the
same
Henn
method (Watrous
and journal.
Wheeler, 1981; Far?
sights, meetings,
and
In
ris, 1982; Maddison et al.,
1984). Nelson
with the evolutionary
species
c
(1985) called
ontogenystill
a direct method
these two factions
may
be co
and outgroup analysis an indirect
method
interbreeding populations.
Below,
for the
reconstruction of the taxonomic hi?
deemphasize the
individuality
of
taxonomy and erarchy.
attempt to incorp
In cladistic contribution?r
taxonomy, only groups based
most fundamental
on synapomorphies (shared
derived char?
operational, cladistic
analysis?a
acters) arephylogenetic
recognized as monophyletic
procedure within
sy
taxa and named. Because ancestral lin?
ics.
Cladistic Taxonomy
eages are not recognizable by positive cla?
distic data and because ancestor-descen?
lineages in principle do not form a
I define taxonomy as the practice dant
of rec?
hierarchical
pattern, only nested sets of
ognizing, naming, and ordering taxa
into
monophyletic
taxa are admitted in the tax?
a system of words consistent with
any
onomy.
kind of relationships among taxa that
the Taxa become operationally diag?
nosed
investigator has discovered in nature.
Un?by uniquely held characters, and
der this definition, taxonomy becomes
species
thebecome simply the smallest of
these
clusters (Nelson, 1989b). By associ?
most basic activity in biology, dealing
ex?
ating
species names with the least inclu?
clusively with the discovery, ordering,
and
sive monophyletic groups, it will always
communication of patterns of biological
be possible to discover smaller groups in
the future with the refinement of data (e.g.,
Cladistic taxonomy uses a cladogram
(sensu Nelson and Platnick, 1981) as molecular
the
data). Thus, species will not be
taxa.
comparable units and will tend to be much
graphical model for constructing a biolog?
more numerous than those conventionally
ical system. A cladogram is a predomi?
recognized. Furthermore, some organisms
nantly bifurcating, asymmetric, nontrunor populations will not belong to any
cate dendrogram, with no defined vertical
group because ontologically
and horizontal axes. A cladogram is monophyletic
thus
they are direct ancestors or belong to lin?
a more general statement than a phyloge?
netic tree, because it does not attempteages
to
in which apomorphies have not yet
developed.
depict actual ancestors (de Queiroz, 1988:
The logic of cladistic taxonomy requires
250; Rieppel, 1990:187). A cladogram cor?
no distinction between species and mono?
responds to a set of possible trees rather
taxa nor between variable and
than to a single tree (Platnick, 1985; cf.phyletic
Wi?
ley, 1981). Cladograms are constructedfixed
by characters ("character" sensu Nixon
and Wheeler's [1990] "attribute"). Individ?
maximizing the congruence of several
ual organisms logically become the small?
types of derived characters, usually mor?
est terminal entities for cladistic analysis
phological or molecular. Character congru?
(Vrana and Wheeler, 1992). Monophyletic
ence is accessed by the methodological
principle of parsimony (Farris, 1982). taxa
Theare not usually ranked to avoid pro?
basic elements of taxonomy are semaphoducing what Colless (1977) called a "cor?
ronts, or organisms "during a certain, nucopia
the? of categories." Fossil taxa are treat?
ed in the same way as extant taxa, thus
oretically infinitely small, period of life"
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1995
points
avoiding
of truncated hierarchies.
of
view
443
the
time
practices. Cladistic
taxonomy may be iden?axis
tified with what has been called the taxic
The notion of actual ancestry is incom?approach to systematics (Stanley, 1975;
patible with a logically stringent pattern
Eldredge, 1979; Rieppel, 1988a). Pattern
analysis. In the initial version of cladistics
cladistics is a logical and internally consis?
(Nelson, 1971), taxa were defined bytent approach in which evolutionary theo?
shared characters, and the lines in the
ry, rather than a unifying concept, is
cladogram indicated relative recency of
viewed as an after-the-fact generalization
common ancestry between pairs of taxa. Into be deduced from taxonomy Brady
this way, the notion of hypothetical com?(1985:113) is one philosopher that support?
mon ancestors became associated with
ed a strict independence of "that aspect of
cladograms. This procedure, however,
still
systematics
concerned with the identifica?
of the empirical patterns" from "the?
produces a temporalized version oftion
a clado?
gram resembling a phylogenetic tree,
oriesthus
of process." But is it necessary for
blurring the conceptual gap between
cladists
clato use methodological essentialism
dists and phylogenetic taxonomists.
to construct both cladograms and taxono?
In the more radical version of trans?
formed cladism (Platnick, 1979, 1982,
1985), pattern cladism (Patterson, 1982), or
methodological cladism (Hill and Crane,
1982), evolution is not considered a neces?
sary prerequisite for the practice of taxon?
omy. The same model may be called a syn?
apomorphy scheme, where the connecting
mies?
Phylogenetic Systematics
The theory of evolution was developed
partly as a generalization from taxonomy
(Nelson, 1978, 1985; Patterson, 1983; de
Queiroz, 1985). Thus, the use of taxonomic
methods in general and the use of cladistic
lines in the scheme indicate no more than
methods in particular do not seem to re?
quire any assumption about evolution.
shared sets of character generalities. Such
a synapomorphy scheme, or strictly atem?
However, "if systematics is an attempt to
poral and acausal cladogram, represents
a
reconstruct
evolutionary history, then this
hierarchy of static homologies obtained
assumption will dictate which cladistic
methods are useful" (de Queiroz, 1985:
from downward classification by logical
subdivision (Platnick, 1977; Patterson,
281). Phylogenetic systematics is the at?
1983; Rieppel, 1988a). One of the implica? tempt to deduce evolutionary history from
tions of this approach is that all taxa are the axiom of evolution.
treated as classes that are defined by char?
I define systematics as the theory, prin?
acters (Beatty, 1982). Platnick (1977, 1985) ciples, and practice of identifying (discov?
and Patterson (1978) tried to avoid this es- ering) systems, i.e., of ordering the diver?
sentialistic connotation of cladistics by im? sity of organisms (parts) into more general
plying that taxa are only recognized by systems of taxa (wholes) according to the
apomorphic characters. According to this most general causal processes. Under this
conception, characters would be diagnostic definition, systematics differs from taxon?
rather than defining. This approach, how? omy basically in not attempting to divorce
ever, leaves cladistic taxa without defini? the practice of building a general biologi?
tions. If cladistic theory corresponds to the cal system from our theoretical knowledge
notion that there is order in nature, it is of how general biological processes (in
agnostic about what taxa represent for bi? contrast to particular biological mecha?
ology.
nisms) are supposed to affect the resultant
Pattern cladistics represents the most
empirical, operational, and objective stage
attained by Hennigians. It represents the
logical consequence of striving after the
most formal cladistic principles and of
adopting the least theory-laden taxonomic
patterns of diversity. Feedback loops be?
tween pattern and process information are
considered fundamental for a constant re?
shaping of the best system for biology.
This view is similar to the concept of Mayr
(1969) and approaches what Nelson (1970)
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444
systematic
called
biology
vol.
44
"comparative
biology,"
netic tree or a temporalized
cladogram, in
tematics must deal with the transformation
which ancestor-descendant lineages may
of form through space and time, thus also
be given names. Usually, nested sets of
integrating information on pattern and
multiple lineages are also given names and
process from ontogeny, paleontology, and
all taxa may be further ranked into a series
biogeography. Systematics is thus both
of categories. Of course, there seems to be
broader in scope than taxonomy and nec?no logical requirement for naming both
sets and ancestor-descendant se?
essarily more theory laden. It integratesnested
a
transformational approach (Eldredge,
quences in the same system. In a new phy?
1979; Rieppel, 1988a) with the predomi?
logenetic system proposed by Papavero et
nantly taxic perspective of taxonomy. Riep?
al. (1992), for example, only the lines of the
pel (1988a:170) treated pattern and process
phylogenetic tree are given names. It is
analyses as "different ways of seeing," in?
also not necessary to rank taxa within the
compatible with while complementary system.
to
Such possibilities for choice as to
each other. The world may appear static or
which particular phylogeny-based dendro?
dynamic, discontinuous or continuous, hi?
gram to use as a model for the biological
erarchical or linear, as revealed by the taxic
system, how to name taxa, and whether or
versus transformational approach. These
not to rank taxa have led to several ap?
approaches are complementary in thatproaches
a
within phylogenetic systematics.
serial or linear hierarchy may be translated
Cladistic Analysis
into a subordinated hierarchy by the spec?
ification of inclusive taxa, whereas the sub?Basic methods of phylogenetic taxono?
ordinative hierarchy may be changed to my
a
are the same as those described for cla?
serial arrangement of forms by specifying
distic taxonomy, but several additional re?
actual ancestors. Phylogenetic systematics
quirements and qualifications are necessary.
involves integration of these two world
In phylogenetic taxonomy, not all kinds of
views by recognition of two ontological
characters empirically observed in sema-
kinds of taxa: species, which are continu?phoronts as instantaneous morphologies
ous strings of ancestor-descendant popu?
should be used in the cladistic analysis.
lations ranked serially (the transformation?
Phylogenetic methods are based on the
al approach), and monophyletic taxa,
premise that there exists a nested hierar?
which are discontinuous taxa ranked hi?
chical pattern of relationships. It is thus
erarchically (the taxic approach) (Rieppel,
not appropriate to apply cladistic methods
1988a:105).
to entities that are not expected to be re?
The preferred modern graphic models
lated hierarchically. Characters are associ?
for basing biological systems within ated
phy?with different patterns of evolutionary
logenetic systematics are ramifying, asym?
relationships at different hierarchical lev?
metric dendrograms (phylogenetic trees
or example, mutations at the molecu?
els. For
cladograms), which may be viewed
as
lar level
may produce ontogenetic changes
somewhat stylized and simplified deriva?
in organisms, variable characters in popu?
tions of traditional phylogenetic trees.
lations, fixed characters in species, and
There are two ways of applying names
to
transformation
series in monophyletic
such dendrograms (Griffiths, 1974a, 1974b):
groups. Only fixed characters and trans?
(1) the naming of time-extended lineages
formation series produce branching pat?
of ancestor-descendant populationsterns
(e.g., of genealogical relationships. This
taxa A-M in Fig. 1) and (2) the naming
ofcorresponds closely to Hennig's
view
nested sets of these lineages (e.g., taxon
N
(1966:31,
fig. 6) contrasts among ontoge?
in Fig. 1). In cladistic taxonomy, annetic
ahis- (within organisms), tokogenetic
torical cladogram serves as a model
for populations), and phylogenetic (be?
(within
representing relationships, and only tween
nest? species) descent systems, in which
ed sets are given names. In phylogenetic
only the phylogenetic system produces hi?
erarchies. Nixon and Wheeler (1990) liketaxonomy, the model becomes a phyloge-
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1995
points
of
view
445
in phylogenetic
systematics.
When static
wise
noted
that
only
ch
morphologies are treated as lineage
characters,
fixed
in
terminal
both ontogenetic and evolutionary polari?
ing patterns.
ties seem to exist at the same hierarchical
The implication for cladistic analysis is
level. But when characters are viewed dy?
that there are sensible limits to the appli?
cation of cladistic methods. If these bound?
namically as sequences of individual on?
aries are trespassed, cladistic methods willtogenies to be compared among organ?
still produce a hierarchical pattern of char?isms, ontogenetic polarities are seen to
belong to one hierarchical level (i.e., they
acters, however poorly resolved, even
when these are known not to form hier?
exist within characters) whereas evolution?
ary polarities are seen to belong to a dis?
archical relationships in nature. Bryant
(1992:259) noted that "as an inductivetinct hierarchical level (i.e., they exist be?
tween characters). Failure to make these
summary of the data set, a cladogram has
hierarchical distinctions may lead to errors
no separate empirical content; it provides
in cladistic analyses. Ontogenetic polari?
only a consensus of the hierarchical infor?
mation in the data matrix."
ties of instantaneous characters, because of
alterations in developmental timing (hetThus, allelic polymorphisms, ontogenet?
erochrony; see Gould, 1977), do not nec?
ic transformations, and populational vari?
essarily coincide with phylogenetic polar?
able characters must be correctly interpret?
of ontogenies. The sequence of
ed in a phylogenetic context. Amorim et ities
al.
particular ontogenetic transformations
(1993) showed that it is not possible to
within an organism (character adjacency
transpose the phylogenetic concept of syn?
in Wheeler's [1990] nomenclature) may be
apomorphy to the lower hierarchical levels
without further resolution. Two evolution?
irrelevant to cladistic analysis. The critical
elements from ontogeny to be used in cla?
ary events are actually involved: (1) the
distic analysis are the relative generalities
molecular process of apomorphic modifi?
cation of a preexisting gene at a given lo?of different life cycles of organisms. Pattern
cus and (2) the populational process of ple-cladists, by avoiding evolutionary assump?
tions, may produce taxonomies that are
siomorphic allele elimination at the same
locus. They named the shared presence of not only evolutionarily neutral but are "at
odds with evolutionary thinking" (Beatty,
apomorphic alleles syntrepty and the
shared absence of plesiomorphic or apo?1982:33). An important consequence for
phylogenetic systematics is that the onto?
morphic alleles synapousy. Because these
genetic method of determining character
events occur at different times and may be
separated by one or more cladogenetic polarity, like the paleontological method,
becomes a special case of the outgroup
events, allelic polymorphisms will be in?
herited by different species. This concep?method (de Queiroz, 1985:293). In other
words, the two methods are not indepen?
tual resolution should have important con?
dent (Fink, 1982; Kluge, 1985), the distinc?
sequences for the parsimony concept as
tion between direct and indirect polariza?
applied to allele matrices. It also provides
tion methods is nonexistent (Wheeler,
a plausible basis for the intuitive concept
1990), and ontogeny stands to phylogeny
of "underlying synapomorphy" (Saether,
1979). Many characters now interpreted asas a part-whole relationship (Brooks and
homoplasies between taxa may be foundWiley, 1985).
to correspond to independent events of One of the main problems of contem?
synapousy of the plesiomorphic allele. porary cladistic analysis refers to explor?
Likewise, independent events of synapou?ing methods for combining different kinds
of data for the same taxa (e.g., Doyle, 1992).
sy of the apomorphic allele may account
Agreement among trees estimated by dif?
for many cases of multiple reversals in
ferent methods lends greater credibility to
cladograms.
De Queiroz (1985) clarified how onto?
genetic transformations must be handled
the estimates of phylogeny (Kim,p 1993:
335). However, molecular phylogenies may
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446
SYSTEMATIC
BIOLOGY
VOL.
44
gram will other
then be hypothesized
to form
disagree with each
and
with
homologies.
Homologies should be viewed
generated from
morphology
(Garl
al., 1993:289). With
the among
number
of m
as relationships
historical individ?
uals, a perspective that at
combines
taxic
ular analyses increasing
a the
greate
and the transformational views of
homol?
than that of morphological
analyses
derson et al., 1993)
and with
over
ogy (McKitrick,
1994:2). Genetically
and 100
able
methods
developmentally
individualized entities
of
phylogenetic
estim
(Huelsenbeck and
Hillis,
1993:247),
th
form
intraorganismal
homologies. Because
intraorganismal
historical phenomena may
clearly a problem
in identifying
thos
form reticulatedparticular
patterns, only interorgan-me
ditions under which
ismal homologies
will reveal
and models perform
well
or hierarchical
poorly.
relationships.
mality criteria such
as parsimony ar
ful, but they must be recognized fo
they are: tools that Phylogenetic
help Taxonomy
direct perc
Phylogenetic taxonomy
uses a phyloge?
towards reality (Knight
et al.,
1993:3
ny (sensu Hennig,
1966)
or a the
temporalized
Queiroz (1993) noted
that
at
high
cladogram (sensu Rieppel, 1988a)
as a
onomic levels discordances
betwee
graphical
model for
constructing
a biolog?
and species trees
due
to
ancestral
ical vanishingly
system. A phylogeny is a predomi?
morphisms are
sma
consequently
analysis
is
a
nantly bifurcating, asymmetric,
and trun?
combined
approach
to
cate dendrogram,
with time as its vertical
usually
preferable
at su
axis (Griffiths,
1974a, 1974b).
It is only
by
neric levels. At the
species
and
popu
addition of the disparity
time dimension and of
levels, however, the
much
occu
the notation
of ancestry that the
static ho? on
tween phylogenetic
patterns
based
mologies of cladistic
analysis can
be inter?
phology and those
based
on
mol
preted as evolutionary
novelties character?
data (e.g., DeSalle
and Grimaldi,
monophyleticand
taxa (Rieppel,
1988a:
Sage et al., 1993;izing
Patton
Smith,
138). All
taxa are defined in termsthat
of ge?
De Queiroz (1993)
suggested
c
nealogical relationships
ratherare
than ofmo
sus methods of data
analysis
shared attributes
(de Queiroz
and Gau? Ho
propriate at these
lower
levels.
thier, 1990; de Queiroz,ontogenies
1992). "Distin?
gene trees, organismal
guishing
descriptions should
be con?
taxon phylogenies
belong
tonotthree
d
fused with
definitions" (Beatty,
1982:27).
hierarchical levels,
which
show
part
Definitions are
ontological
statements
relationships among
each
other.
Fu
about the existence of
entities that resultanaly
more, disagreements
among
these different levels seem to be the rule
from genealogical relationships among
their parts. Descriptions and diagnoses are
rather than the exception. Does it make
epistemological statements about how we
sense to provide consensus trees for these
recognize the parts of those entities (de
conflicting data sets? I tend to agree with
Queiroz and Gauthier, 1990:307).
Bull et al. (1993) that when different his?
tories are detected by different data anal?In phylogenetic taxonomy, ancestor-de?
scendant relationships are recognized in
yses, it may be best to keep the data sets
addition to the sister-group relationships
separate. The next logical step would be to
of cladistics because ancestors belong on?
identify the causes of heterogeneity and re?
tologically to our evolutionary models. The
interpret the results accordingly.
time-extended lineages of ancestor-de?
If cladistic analysis is to avoid tautology,
scendant populations are conveniently
homology cannot be resolved only by em?
named as species. Under this procedure,
pirical observation. Homology is distinct
however, the notion of monophyly is in?
from synapomorphy (de Queiroz, 1985:
with the notion of ancestry be?
280). Similarities must first be analyzed compatible
by
monophyletic species cannot be an?
parsimony criteria and summarized oncause
a
cestors (Rieppel, 1988a:157). Those authors
cladogram. Synapomorphies on this dado-
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1995
points
of
view
447
that
have breeding)
chosen
that may serve to to
distinguish
em
at
the
lowest
clusters of sexual
levels
organisms from clonesin
of
omy
(e.g.,
asexual organisms.
Rosen,
Cladistic taxonomy19
has
1982;
Donoghue,
1985
surface structure (descriptive
adequacy)
don,
1987)
are
oblige
but lacks
deep structure
(explanatory ad?
some
organisms
equacy) (Brooks and Wiley,
(viz.,
1985). A sys?
tors
and
those
tematic technique justified
that
only in termsha
of
surface structure has not
demonstrated its
apomorphies)
from
t
relevance to studies ofEpistem
characters of the liv?
cies
concepts.
cial distinction must then be made be?
ing world that it classifies. Rather than in?
tween real cladospecies and provisional
sisting on a dichotomy between surface
metaspecies (Donoghue, 1985; Archibald,
and deep structure, pattern and process,
1994), some of which may represent
organisms
actual and groups, cladistics and phy?
logenetic taxonomy, these part-whole re?
It may be tempting to try to avoid
lationships
the
may be more profitably viewed
as complementary.
Under such an ap?
species problem entirely by using only
or?
ancestors.
ganisms as terminal entities for cladistic
proach to systematics, pattern provides
analysis (Vrana and Wheeler, 1992).process
Underwith a direction, and process pro?
this approach, taxa are viewed as relation?
vides an explanation for pattern (Rieppel,
ships among organisms rather than1988a:451).
among
The only alternative to the problem of
groups. Nelson (1989a, 1989b) concluded
Siat a basic taxonomic unit does not
exist
logical
incompatibility between monophy?
ly and ancestry is to recognize two distinct
and that there is no empirical difference
entities in phylogenetic sys?
between species and other taxa. Theontological
prob?
tematics:
lem with this view is that it ignores
the monophyletic taxa and species.
Underin?
this approach, there is still a tension
empirical observation that "character
congruence affects lower levels of between
the ge? those who propose to use inter?
nealogical hierarchy to a greater breeding
degree (e.g., Hennig, 1966; Gould, 1986;
than higher levels" (Rieppel, 1989:57).
Ridley,
The1989) and those who reject all pro?
cess definitions in favor of strictly morpho?
parsimony method provides a cladogram
logical pattern definitions (e.g., Wheeler
in which there is maximum congruence
and Nixon, 1990; Davis and Nixon, 1992).
among character generalities. However,
this method does not specify the amount
My position is that no distinct biological
of character incongruence that would
entity
re?would exist between the organism
and the
monophyletic taxon if it were not
fute the initial hypotheses of hierarchy
and
for pro?
the biological process of interbreeding.
monophyly. Cladistic methods cannot
vide a rigid test for the expectation
Interbreeding
of hi?
is the most general process
known
to maintain a reticulated pattern
erarchical order in nature. Something
more
than observations of organisms is required
among organisms through time. Conse?
for an understanding of character quently,
gener? interbreeding is of primary inter?
alities at more inclusive levels. A covering
est to phylogenetic systematics (de Quei?
roz and
theory, involving assumptions about
bio?Donoghue, 1988) and should
continue
logical processes such as tokogenesis
and to be the basis of species con?
cepts. My theoretical (ontological) species con?
interbreeding, appears to be necessary.
Otherwise, the recurrent charactercept
incondefines a species as a single lineage of
ancestor-descendant
sexual populations,
gruences between different empirical
data
sets cannot be accounted for. Doubts have
genetically integrated by historically contingent
consequently been raised as to the adequa?
events of interbreeding. This concept is clos?
est to what has been called the evolution?
cy of the cladistic approach to phylogeny
reconstruction at low taxonomic levels ary
(Ar? species concept (see Wiley, 1981:25).
there are empirical limitations to
nold, 1981). Many phylogeneticists haveBecause
re?
jected the very process assumption (interthe possibility of recognizing evolutionary
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448
systematic
species
lowing
vol.
44
practice,
ulated descent systems
I and
also
are not appro?
pro
priately named
within a hierarchical taxo?
operational
(epistemologi
species,
Nixon
Nixon
in
biology
nomic system.
derived
from
Cracraf
and Wheeler
(1990),
a
Evolutionary species are
defined here to
produce
minimal unitary systems
thatid
(1992):
a thespecies
is
irreducible cluster
retrospectively
of
have sexual
functioned as inde?
org
there is
pendent
a parental
evolutionary units and for
patter
which
and descent and
meaningful
that
cladistic analysis
is is
diagno
possible.
At coarser levels
of historical resolution,
from other such
clusters
by a
which
nation
of
the characters.
controversies between cladists and
fixed
My theoretical
phylogenetic
species
taxonomists over
conce
how to dea
formational,
with
i.e.,
the species
dynamic,
problem are circumvent?
are viewed as
ed. It stages
is reassuring that in
no major
the
method?
process andological
ranked
sequen
disagreements remain
at the high?
nodes of a phylogenetic
er levels of the taxonomic hierarchy.
tre
mological concept
Asexual clones
is do
taxic,
not form species.
i.e.
No
species are viewed
general and regular
as biological
the process
sma
i
to produce
(tokogeentities thatknown
can
be a reticulated
recogni
come of the netic)
evolutionary
pattern of descent at the supraorgan
p
ismal level.
Birth that
relationships,it
develop
(1993) pointed
out
w
mental
canalization, stabilizing
impossible to
apply
theselection
spe
with precision
and other
tosuggestions
grojips
may cause
of
organ?
o
isms to remain similar.
But these are pro?
ing in the present.
Althoug
cesses of constraint or
inertia rather than
taxa at the higher
phylogene
cohesion
(de Queiroz and Donoghue, 1988:
be considered
retrospective
321). The
occasional
one-way mechanisms
levels and as
we
approach
of lateral
gene transfer among unrelated i
they become
prospective,
upon expectations
microorganisms (including
of plasmid
what
trans?
w
fer in bacteria) irreducible
or between a virus and a
the future. Those
ing in the present
are do
incom
metazoan host apparently
not qualify
and only prospective
as general biological processes.
decisi
Clones of
cate whether
similarpresently
organisms traditionally treated iso
as
tions will remain
species are better independe
renamed as monophylet?
ic taxa when based on apomorphies.
ture. This indeterminacy
sh
Thefor
evolutionary
concept given r
major concern
a species
general
tem that must
here also
represent
has the advantage that it fits
the
the
graphical model of
a phylogenetic
tree.
ological diversity
as
a whol
The birth of a species corresponds
to its
nition and naming
of the
origin from a branching event, whereas its
permanent phylogenetic
lin
death results
eithera
fromrepresent
terminal extinc?
tainly adequate
as
history of life.
tion or from
Systematic
its splitting into two or more g
like cartographic
daughter species
maps,
(Rieppel, 1988a:99).
cann
In
words, species
become restricted to
ed to deliver other
more
precision
the internodes than
of the phylogenetic
tree. Inbe
tionary chronicle
has
judged adequate
practice, speciation
forwill
the
coincide with
phyl
the
resentation (see
O'Hara,
1993
process of origination
of a separate lineage
characterized
by a new fixed character.
study of gene
relationships
Those species that
are not characterized
by
lations, however,
finer
graph
tations and different methods of data anal?
apomorphies (plesiomorphic synapousies)
ysis are needed. Demes are the ephemeral
may be reduced to the internodes of the
phylogenetic tree, thus providing ancestral
evolutionary units at any given time plane,
including the present, but they form retiespecies for the phylogenetic tree. Descent
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1995
points
of
view
449
relationships
populations forming
among
time-extended lin?
p
eages recognized
as evolutionary species,
hierarchical
when
ne
founded
nested sets
of lineages
including an ances?
by
the
division
tral species and all of its descendants
are
isting
populations
and
named as monophyletic
taxa. De Queiroz
disperse
among
these
these
conditions,
(1992) and de Queiroz andcharac
Gauthier (1990,
1992)
identified three possible ways ofm
de?
fixed
in
a
population
ted
to
the fining
descendant
higher taxon names phylogenetical?p
be
transmitted
ly: (1) a stem-based definition
as associates
pol
the name with a dade of all organisms
a more recent common ancestor
population will be transmitted to all sharing
of its
characters that are fixed in an ancestral
descendants, either in the original state
withorone designated descendant than with
another; (2) a node-based definition asso?
ciates the name with a dade stemming
phylogenetic species therefore constitute
in a modified state. The fixed characters of
from the immediate common ancestor of
evidence that a hierarchical descent system
two designated descendants; and (3) an
exists and provide the means for analyzing
apomorphy-based definition associates the
phylogenetic relationships among these
species (Davis and Nixon, 1992:421). When
name with a dade stemming from the an?
no data on interbreeding are available, in?
cestor in which a designated character
arose. I agree with de Queiroz and Gau?
terbreeding evolutionary systems should
thier (1992:474) that both stem-based and
not be assumed to be larger than the
node-based clades should be named in
smallest units detected by fixed characters
in a cladistic analysis. If a system with ac?
phylogenetic taxonomy. Bryant (1994) di
cussed nomenclatural problems in esta
tive gene exchange is larger than the small?
lishing the valid names for crown clade
est unit detected on a cladogram, the smal?
In practice, stem clades and crown clad
ler unit will not remain diagnosable for
will be identified by apomorphies esta
very long and will retrospectively no lon?
lishing the largest and the smallest clade
ger be ranked as a species.
with recent representatives. As with spe?
My evolutionary species concept satisfies
cies, all monophyletic taxa in phylogenet
the ontological requirements of reflecting
real, discrete, irreducible, and comparable
systematics are pattern based in practi
evolutionary units, withiii which there isbut
a genealogically based in theory.
parental pattern of ancestry and descent
(Cracraft, 1987). Entities cannot be discrete
Evolutionary Ranking
I have envisioned a procedural progre
and still transform over time. Although
sion from taxonomy to systematics. Ran
species are best recognized from the anal?
ysis of pattern, the emphasis of processing
in represents the last epistemological ste
the theoretical species concept has the ad?
within systematics. This view is contrary
to conventional practice, which requir
vantage of integrating pattern analysis
with process theories in systematics. Al?
categorical rank to be established before
taxon can receive its name. Once taxa have
though monophyletic species definitions
such as those of Donoghue (1985) require
been recognized and named, they may be
a previous cladistic analysis, the evolution?
classified into age classes or systematized
into biogeographical categories, depending
ary species concept proposed herein is not
on the
dependent on such a prior analysis. The
available evidence.
Classification
is the establishment of
morphological describer, ecologist, bioge-
classes of biological taxa according to
ographer, population biologist, geneticist,
some useful criterion. Because taxa may be
or molecular biologist can all continue the
job of recognizing evolutionary units with?
referred to many different classes, then
out actually producing phylogenetic tax?
clearly no one principle of classification
can claim to be uniquely valid.
onomies.
In addition to the ancestor-descendant
Linnaean categories were originally
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450
SYSTEMATIC
based
on
BIOLOGY
VOL.
44
Table 1. Phylogenetic
taxonomy of Olbiogastridae
Aristotelian
essentialistic
l
(Diptera: Bibionomorpha),
with biogeographical
With the subsequent
addition
of labels
more
added to each taxon name. Biogeographical labels are
egories to the system,
these
ranks
based on an area cladogram for the history of inter? hav
come quite arbitrary,
representing
continental relationships.
Composite labels indicate no
the distributions of successively
subordinatedhas
ances?
than an empty formalism
that
los
theoretical idealistic foundation. After the
penetrating analysis of Griffiths
tral species (either extinct or not sampled), the last
term indicating the recent representatives (AfOr =
(1974a,
Afro-Oriental; AuN = Northern Australia; CAn = cir-
1974b, 1976) on the difficulties of reconcil?
cumantarctic; G = Gondwana; GTe = Temperate
Gondwana; GTr = Tropical Gondwana; NoAuN =
ing the Linnaean categories with the phy?
Neotropical-Northern Australian; NoAuS =
logenetic system, many phylogeneticists
have abandoned further attempts to clas?Neotropical-Southern Australian; NoN = Northern
Neotropical; NoS = Southern Neotropical; P =
sify taxa into ranks.
Pangaea). The square brackets in the taxonomy follow
Historical classification corresponds to
a convention of Christoffersen (1989) for indicating re?
dundant, phylogenetically uninformative taxa (adapt?
Hennig's (1966) original proposal of cor?
ed from Amorim, 1992:288).
relating absolute ages of origin of taxa
with age classes delimited by convention
Olbiogastridae P-G
from the geologic time scale. Subsequent
new subfamily GTe-CAn-NoAuS-NoS
difficulties in implementing such a scheme
in practice led Hennig (1969, 1981) and
some followers (e.g., L0vtrup, 1977; Willmann, 1989) to adopt an alternative nu-
mericlature. But none of the alternatives to
Olbiogastrinae GTr
new tribe [new genus 1] Af Or
Olbiogastrini NoAuN
new genus 2 AuN
Olbiogaster NoN
the subjective Linnaean categories has won
widespread use.
These difficulties notwithstanding, the formation (characters). Griffiths (1974a,
demand for evolutionary ranking is still 1974b, 1976) showed compellingly that be?
warranted because ranking adds retrieva? cause of the noncomparability among dif?
ble information content to the biological ferent characters, we are still very far from
system. I like the broader connotation of being able to measure overall differences
the term evolutionary, as intended by the among taxa.
evolutionary taxonomists, for transmitting
Amorim (1992) proposed a method of
the idea of added information. However, I systematization in which a label corre?
am here advocating Hennigian principles sponding to the biogeographical compo?
to attain evolutionary ranking. In this re? nent of each taxonomic level is added to
spect, theorists of the evolutionary school the name of a taxon (Table 1). One of the
such as Mayr (1969, 1974, 1981) and Mayr great advantages of this proposal is that it
and Ashlock (1991) have misunderstood does not interfere with the names of taxa
the distinction between classification and
in the preexisting classification nor must
systematization. The systems structure of
the Linnaean categories be abandoned im?
real phylogenies is cladistic (branching), ir?
mediately. The new label may nevertheless
respective of what principle for classifying
form the basis for biogeographical catego?
taxa is adopted (Griffiths, 1974a). Further?
ries. The same biogeographical label indi?
more, Mayr and Ashlock's (1991) concept
cates taxa that have the same age of origin
of evolutionary ranking is not evolutionary
and that have ancestral species living in
at all because it is based on overall simi?
the same geographical area. Thus, infor?
larity of included taxa rather than on mation
any
on the history of biogeographical
explicit evolutionary criterion. Cladistic
areas may be gradually associated with in?
and phenetic data cannot be successively
formation on the phylogenetic history of
combined into a single taxonomic system
taxa into a single biological system. One
(cf. Mayr, 1981; Stuessy, 1987) because
limitation of this proposal refers to taxa
these data are obtained from different and
originating before the fragmentation of
conflicting analyses of the same basic in- Pangaea. Although progress is being made
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1995
points
of
view
451
the
reconstruction
o
tionary ranking. Transformed cladistic
cesses
in
when
the
divested Paleozoic
from evolutionary theory
detailed
biogeographic
becomes a strictly methodological activit
still
not
possible
It will not produce the best
for
taxonomyb
be
these
cases,
cause groups
Amorim
known to form reticulate
(
visional
labels
patterns in nature based
will be nevertheles
age
classes
forced (for
into a hierarchy.exam
When evolution
made
the basis of taxonomy, a split b
etc.,
for
successively
tween pattern
cladists and phylogenet
Triassic
and
similarly
er
time
periods).
taxonomists is no longerThes
justified. Und
es
determined
evolutionary assumptions,
by
the most usef
p
could
be
gradually
methods developed by cladists can
su
be s
and used fortaxon
the construction of a
origin
of lected
the
an
in
graphical
ical evidence ever becomes available. Even
phylogenetic
category
taxonomy. At the higher
if
lev? t
els of systematic generalization, all phylo?
though provisional age classes will always
genetic hypotheses become retrospective
narratives. In these cases, there is basic
remain partially arbitrary and subjective
(Craske and Jefferies, 1989), they are still
agreement
of
between pattern cladists and
some heuristic value.
phylogenetic taxonomists on how to rec?
Ranking according to Amorim's (1992)
ognize and name monophyletic taxa. Con?
proposal is based on biogeography and
ceptual and methodological disagreements
at the lower taxonomic levels result be?
stratigraphy. Such extrinsic data are best
kept separate from the intrinsic datacause
of
gene trees, organismal ontogenies,
phylogenetic taxonomy. The evolutionand
of taxon phylogenies may produce in?
histories for each of these hier?
the earth, however, is causally relatedcongruent
to
the evolution of its biota (Rosen, 1978).
archical levels. My evolutionary species
concept is ontologically based on inter?
Congruence between these largely empir?
ical data sets and their representation side
breeding and epistemologically recog?
nized by diagnostic characters. Codes of
by side in a general reference system
nomenclature that do not tie taxon names
should provide the best hypothesis against
which particular evolutionary mechanisms
to categorical ranks are required. Such a
release from Linnaean conventions would
may be tested.
In phylogenetic systematics, only mono?
immediately promote stability of taxon
names. Furthermore, this action would
phyletic taxa with extant representatives
are ranked into age classes or biogeopermit ranking to proceed gradually and
graphical categories. Species, which are
independently of taxonomy. Ranks based
time-extended lineages logically distinct
on the systematization of biogeographical
from monophyletic taxa, and taxa com?
components add extrinsic evolutionary in?
formation on the age of origin and distri?
posed exclusively of fossils, which form
bution of the ancestral species of a dade
truncated phylogenies and have unstable
positions in the system (Griffiths, 1976),
and may provide the most useful general
reference framework for comparative biol?
should not be formally ranked. Fossils may
ogysimply be sequenced or indented in the
system of extant taxa, with such designa?
tions as monophylum (Lauterbach, 1989) for
Acknowledgments
monophyletic taxa and plesion (Patterson
A research
scholarship from Conselho Nacional
and Rosen, 1977) for the remaining taxa.
Desenvolvimento Cientifico e Tecnologico during t
Conclusions
last 15 years has permitted me to accumulate a com
prehensive collection of literature even though I w
in relative isolation 2,500 km away from the near
procedure
provisioned libraries. Researchers on the whole h
I have argued for a three-step
in phylogenetic systematics: cladistic
been anal?
particularly generous in sending me reprin
Editor
Michael Miyamoto has been courteous a
ysis, phylogenetic taxonomy, and
evolu-
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452
systematic
biology
vol.
44
new families
for the Crangonoidea and Alpheoidea
constructive in his
handling
of the
(Crustacea, Decapoda,Rieppel,
Caridea). Cladistics 3:348ham Griffiths, Olivier
Kev
Dalton Amorim, 362.
through their insig
have done much
Christoffersen,
to focus
M. L. 1989. Phylogeny
my
andideas
classifi?
anonymous
script.
cation of Pandaloidea
(Crustacea,
Caridea). Cladis?
referees
and
one
asso
tics 5:259-274. on
suggestions
earlier vers
Colless,
D. H. 1977. A cornucopia
of categories.
Syst. t
Such joint
efforts
did
much
helpful
quality
of
26:349-352.
this Zool.
manuscript.
Yet
Cracraft, J. 1983. Speciesthat
concepts andIspeciation
made me very conscious
can
analysis.
Pages 159-187
in Current ornithology,
Vol?
for all the errors
and
hybrid
results
ume 1 (R. F. Johnston, ed.). Plenum, New York.
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