|
Modern Evolutionary Systematics:
Introduction August 12, 2009 |
|
MODERN EVOLUTIONARY SYSTEMATICS:
AN INTRODUCTION Contents: 2. A short note on consistency 4. Phylogenetics and
evolutionary systematics compared 5. Example of extinct
paraphyly 8. Phylogenetics and
creationism 9. Quotations 10. Other authors 11. Manifesto and additional comments Evolutionary systematics, or
evolutionary taxonomy, is the science of apprehending nature through a naming
system of nested groups, with the species as basic unit of classification,
using the Linnaean system and, to the extent possible, what is known about
evolutionary relationships.
Evolutionary systematics uses both sister-group relationships and
ancestor-descendant relationships as recommended by Given that it is still standard practice to be eclectic
or syncretic with methods in taxonomy, we might also call evolutionary
systematics orthodox systematics. This is in contradistinction to the now popular
phylogenetic system of Hennig, which focuses exclusively on sister-group
relationships (splitting of lineages).
Phylogenetics now incorporates powerful analytic tools, including
statistical analysis of molecular data, but the elimination of
representations of macroevolution in phylogenetic trees has led to various
problems that have been pointed out in recent literature. Major examples of
this critical literature are gathered together on this Web site. Is
phylogenetics truly revolutionary as it is commonly presented? If it were,
the present author would be at the first barricade waving a red flag. Modern evolutionary systematics uses recent developments
in analyzing evolutionary relationships but extends such into evaluations of
the results of anagenetic change leading to macroevolution, and presents both
classifications and trees of life that reflect both sister-group and
ancestor-descendant relationships. All evolutionary systematists generally agree that
recognition of paraphyletic groups (ancestral groups denied recognition at
separate and taxonomically equal rank to that of their descendants by phylogeneticists)
contain important evolutionary information that should be represented in
classifications. Well-known examples are the sinking or attempted sinking of
Aves into Reptilia, or Cactaceae into Portulacaceae. Detailing macroevolution
in classification through recognition of paraphyletic groups is fundamental
to evolutionary systematics. Macroevolution is a real scientific concept
supported by plenty of data showing autophyletic lineages arising from the
midst of paraphyletic lineages. Phylogenetics is methologically inconsistent. For
example, one taxon represented by two OTUs may appear on a molecular tree
(phylogenetic paraphyly or apparent polyphyly). Given the structuralist justification for evolutionary
classification, the only explanation must be “convergence.” But a cladogram
does not diagnose exactly what different ancestors the two paraphyletic OTUs
came from. The explanation is inconsistent with the method because it uses a
different method. An alternative evolutionary systematics explanation is the
scientific theory of a deep shared ancestor with the same diagnosis inclusive
of both OTUs, which is consistent. A morphological cladogram may be different from a
molecular cladogram, and both may be intuitively convincing, the one
clarifying morphological changes, and the other gene changes. Phylogenetics
cannot explain this inconsistency, but tries to combine both in “total
evidence” analysis, lumping all data together. This combines inconsistent
results into a jumble where strong signals of one process (mostly non-coding
changes in DNA) overwhelm, usually, weak signals of another, different
process (fixation of expressed traits). An alternative evolutionary
systematics theory is that taxa basal in a morphological cladogram but
terminal in a molecular cladogram signal the status of that taxon as
surviving ancestor of possibly many lineages (a kind of coelacanth). This
last theory renders the differences between morphological and molecular
analyses consistent. It is only a
theory, but this is far better as a basis for classification than the
apparent deductive perfection of a phylogenetic cladogram. [Added March 7, 2011.] There are three
patterns that are reconciled by pluralistic evolutionary systematics.
These patterns give three different views of the evolutionary process, and
are not equivalent, thus one is not better at charting evolution than the
others. Assuming
that one pattern is fundamental and other patterns and data may be relegated
to that one fundamental pattern is “structuralism.” Structuralism as a
retrogressive force in modern systematics is discussed at length in this paper. The
three patterns are: (1)
Classical systematics produces classifications of macroevolutionarily
distinguished hierarchical sets of taxa. These are generated through taxa
distinguished by overall similarity of conservative and apparently homologous
traits, and distinction of major evolutionary transformations at the taxon
level associated with habitat change and other criteria. Conservative traits
are those stable at different collecting sites and across different habitats.
(2)
Morphological cladograms presenting nested sets of trait transformations away
from an apparent primitive (plesiomorphic) state usually represented by an
outgroup taxon. Macroevolution is represented only by the exemplars named
through classical systematics, while renaming of such taxa is solely based on
present-day patterns. The transforming traits are, usually, conservative
characters from classical descriptions. (3)
Molecular trees are variously assembled through parsimony analysis (as in
morphology), or maximum likelihood or Markov chain Some comparisons of phylogenetic and evolutionary systematics: Paraphyly is a phylogenetic somewhat disparaging word
for what is generally known as ancestors involved in macroevolution, that is,
a label for a group from which one or more other groups at the same (or
higher) taxonomic rank have apparently evolved. “Para” implies faulty, wrong, amiss,
recrementitious, or merely similar to the true form. Evolutionary
systematists, however, celebrate that which is presently known as
paraphyly. I offer here new
terminology: “Euphyletic”
is a term for all natural taxa for which lineages (series of nodes) of the
same name on a molecular cladogram are available. The molecular lineages are
reasonable or rendered so by invoking such theory as punctuated evolution
involving surviving ancestors and long stasis of expressed traits. An
euphyletic taxon has been vetted by molecular analysis and found
theoretically reasonable to an evolutionary systematist but not necessarily
to a phylogeneticist. It has the same sense of approbation that
“phylogenetically monophyletic” has to phylogeneticists. Euphyletic taxa
include: (1)
“autophyletic” (or apophyletic) groups, being those named natural taxa that
have evolutionarily diverged directly (i.e. not as a sister group) from a
evolutionarily natural ancestral group, which differs by being at the same or
lower taxonomic rank (an euphyletic group). (2)
“paraphyletic” groups, i.e., all phylogenetically nonmonophyletic natural
taxa on molecular cladograms with contiguous internodes for which a deep
ancestor explains the phylogenetic nonmonophyly, which therefore may be
considered evolutionary monophyly; e.g.: (((A,
B) A) A)… (3)
“extended paraphyletic” groups (i.e., phylogenetically polyphyletic) (e.g. ((((A,
B) C) A) A)… whose
ancestor can be inferred and named (e.g. “A”). This assumes there is no
unreasonable distance between divergent molecular lineages (“A” and other
“A”s) within a tree to make improbable a diagnosable named ancestor (mappable
taxon, virtual fossil). Paraphyletic
and polyphyletic groups together may be termed “heterophyletic.” and
(4) taxa that have been properly moved from one large group to another
because the patristic distance involved does not allow the molecular tree to
be discounted as below resolution of the study or as simple extended
paraphyly. This includes natural taxa when improperly placed because
molecular trees place them with another large group, it is reasonable to move
them. The
antonym of euphyletic is, of course, “dysphyletic,” which refers to: (1)
unnatural taxa that are the products of phylogenetic splitting simply to
preserve phylogenetic monophyly (or “schizophyletic”); (2)
unnatural taxa that are the products of phylogenetic lumping simply to
preserve phylogenetic monophyly (or “mixophyletic”). Thus, Aves is an autophyletic product of the
paraphyletic Reptilia, while Cactaceae is autophyletic to the paraphyletic
Portulacaceae, and Cinclidotaceae, Ephemeraceae, and Splachnobryaceae are all autophyletic to the large, extended
paraphyletic group Pottiaceae (see PDF reprints of Zander 2007, 2008). All these taxa are euphyletic. Thusly
orthodox systematics can use a more robust terminology to match the
tendentious terms of parasystematics (phylogenetics, phenetics, or any system
that offers a quick and easy method to simplify an unsimplifyable field of
research). A natural taxon
(I’m sure you will ask) is any group that is probabilistically the best
representation of the expressed traits as an evolutionary trajectory at that
taxonomic rank. When split to fit a molecular tree, for a split to be a
natural taxon it must be significantly more robustly supported by expressed
traits than any other split in any other way of splitting. This is because
some expressed traits (a combination by chance alone) may support any split
that may have appeared in a molecular cladogram. The traits should include autapomorphic
traits and any traits that particularly fit the organism to a particular
environment. Finding some expressed traits by chance alone that support a
taxon in any particular molecular clade is a problem in statistics called
“multiple comparisons.” A
morphological cladogram is best viewed as a step towards a natural key,
inasmuch as it often conflicts with molecular cladograms, but it does reflect
at least present-day relationships based on expressed traits. Likewise, when a natural taxon is combined with another
natural taxon, the result may be clearly unsatisfactory inasmuch as important
(at that rank) evolutionary features are not represented in classification,
and the resultant salmagundi is “dysphyletic.” Consider a terminal branch of a molecular cladogram
(((((A,B)C)D)E)A) . . . . An exemplar of taxon A is at the far end and another
exemplar of Taxon A is also at the base of the branch. A theory could be made
that Taxon A constitutes the taxon from which B, C, D, and E all
evolved. Consider the same branch but the lowermost A lineage is
extinct. The actual evolution remains the same. Consider the same branch with
only the uppermost A lineage extinct. The evolution still remains the
same. In phylogenetics, the classification would be different
for the different scenarios of extinction of Taxon A. The aim of evolutionary systematics is to
use other information (e.g. biosystematics, geography) such that the
classification of the two scenarios is the same. A basic question is how many branches in between the two
A lineages are tolerable? If too many, then the two As doubtfully infer the
complete continuity of Taxon A. And, if only one very odd taxon is nested in
a large group, it is doubtful that there is an extinct lineage of the odd
taxon at the base of that large group, and therefore the odd taxon evolved
directly from the large group. An example in the mosses is the recent removal
of the small family Ephemeraceae to deep nesting in the large Pottiaceae
family. Ephemeraceae probably directly evolved from the Pottiaceae because of
the many nodes (= deep nesting) between the Ephemeraceae and the base of the
Pottiaceae cladogram, i.e. the chance of an extinct Ephemeraceae lineage
below the Pottiaceae is very small. Can the amount of extinct paraphyly be estimated by the
amount of paraphyly in extant groups? What do you think? I have been
prompted to develop this Web site by several kinds of outrages over the
years, some admittedly theoretic and moot, some terribly obvious and
problematic, particularly: (1)
the elimination in phylogenetic classifications of any aspect of
macroevolution, resulting in synonymy and splitting of what are apparently
well-founded species and higher taxa of organisms through the phylogenetic
classification principle of holophyly (which reflects nothing in nature); (2)
the assumption of no surviving ancestors, or that one taxon cannot be in two
different molecular lineages, though there is plenty of evidence that this
may result from punctuated equilibrium followed by long stasis of taxa
governed by stabilizing selection - there may be in fact up to n − 1
terminal taxa that are ancestral to at least one other terminal taxon. Using
the word “taxon” rather than “species” or “population” is due to my
expectation that genera and higher taxa do evolve as units through joint species’
reference to the paragenetic regulatory functions of a shared particular
selective regime (an “envirosome”); (3)
parsimony using morphological traits assumes independent and unique
distributions, yet selection and epigenetic effects commonly link traits such
that they may be fixed during speciation as a unit; (4)
avoidance of weighting of traits reflects the “automatic classification”
philosophy originating with pheneticists and continued by phylogeneticists as
“theory-free” taxonomy, such that a parsimony analysis of morphology is in
reality based on raw similarity, lacking phyletic weighting - similar
problems occur with molecular traits. If phylogenetics is truly a theory-free
discovery process then there is no hypothesis to test, since the pattern
discovered is a fact. Phylogenetics is theoretically speaking bankrupt and
has always been so. Is phylogenetics
“to big to fail”?; (5)
molecular analysis either assumes that traits are independent or if dependent
then of taxonomic importance anyway, yet convergence of molecular traits with
morphological ones because of similar convergent selection supports a wrong
tree, and convergence of molecular traits with each other because of similar
selection may well support a wrong molecular tree over a poorly supported but
correct morphological tree. Pervasive selection on non-coding DNA traits has
been reported in the literature, while entire coding genes, regulator genes, and promoter regions are
commonly included in molecular analyses; and
(6) the common elimination of the environment from consideration in
phylogenetic analysis. E.g., following
the mechanisms for macroevolution of genera and higher taxa summarized by
Gould (2002) in his opus, the environment acts as a regulator and guide
(external chromosome equivalent) of shared change among species of the higher
taxa through stabilizing and disruptive selection acting on individual
species or on traits shared by all species. This shared feature is not
represented in the analytic processes of phylogenetic analysis, but is part
of the expected judgment involved in classification by evolutionary
systematists familiar with the habitats of organisms of their specialization. A few points summarize my own take on modern
evolutionary systematics: (1)
Alpha taxonomy plus biosystematic and ecological study yield well-conceived
taxa as apparent results of past evolution, these correspond to what the
“exemplars” of phylogenetics represent; (2)
phylogenetic sister-group analysis is powerful and effective, but is crippled
by insistence on classification by holophyly (a simplifying classification
principle corresponding to no thing in nature); (3)
molecular trees demonstrate lineage continuity and isolation but not
necessarily speciation; (4)
macroevolution is being unfortunately eliminated from classification by
phylogenetic insistence on (a) classification by holophyly and (b) not naming
ancestral nodes (because this would create paraphyly); (5)
elimination of macroevolution results in phylogenetic trees without names for
ancestral nodes leading to clades but no caulis, i.e. a phylogenetic Tree of
Life may be totally replaced by a Nested Parentheses of Life; (6)
taxa may be found in two (or more) different molecular lineages, commonly as
surviving ancestors, because of stasis associated with punctuated evolution
may also follow isolation of two populations that remain identical at some
taxonomic level, followed by budding evolution, and splitting of lineages is
not necessarily accompanied by speciation; and
(7) stabilizing evolution on morphology and interaction of expressed traits
with the environment may be decoupled from gradual accumulation of changes in
the genome, such as apparently non-coding traits that are used to track
continuity and splitting of lineages.
There is considerable evidence from molecular analyses that this is
true, e.g. “cryptic” species, genera and families. Limits to resolution of molecular phylogenetic analyses by potential
of extinct paraphyly: "Phylogenetically
informative" may prove somewhat of an oxymoron. This is because empty
precision leads to aleatory classification. This is how: In parsimony of
morphology, traits are not necessarily tacked onto a taxon as speciation
gradually continues, but an initial linked set may be necessary for selection
into a new environment. Thus, if A and B share three traits that are
selectively linked, and A and C share two traits that are not (maybe neutral
or sequentially added as the environment changes over time), then A and C
probabilistically share the latest ancestor, not A and B. Although when
dealing with masses of shared traits, main clusters of a parsimony cladogram
may be okay or acceptably approximate, parsimonious decisions about
relationships of small groups of OUT's may need additional information, but
are for now cladogrammed by chance. In
molecular analyses, any sister group pair may have had an extinct lineage
identical in phenotype to one of the sister groups occurring below the split.
If so, then this is not a sister group relationships but ancestor-descendant
relationship instead. If the extinct lineage identical in phenotype to one of
the sister groups is even farther down in the tree (phylogenetic polyphyly, or
if within reasonable partristic distance then extended paraphyly) then the
molecular tracking of splits in the gene history is further compromised. The results of macroevolution can give
often statistically certain sets of lineages of present-day specimens
(exemplars). But should we use these patterns for classification. Because
macroevolution involving progenitors in stasis shuffle lineages of taxa, even trying to “fix” the pattern
by renaming taxa that are out of order does not give a classification that
reflects evolution well. Only by going beyond pattern, and using pattern to help infer process, can we create a classification that is not often plain
wrong. The
evolutionary story has been lost to reductionism in ignoring all information
on evolution not in a database of phylogenetically informative traits, and to
irredeemably faulty methods of analyzing evolution and assessing
classification. Phylogenetic analyses might possibly be saved as modified
with information from chromosome counts, ecology, biogeography, phyletic
weighting of traits, and genomics, among other information. Renaming taxa
that occur in two or more different lineages or lumping paraphyletic groups
with their autophyletic macroevolutionary products is just ignoring
significant evolutionary information to preserve assumptions that are
contrary to reality (e.g. "a taxon cannot be in two molecular lineages
at once") and save the hyperexact Method. Systematic
analysis is based on two steps, evaluation of evolutionary relationships and
interpretation in classification. If both morphological and molecular data
are poorly dealt with in software, the first in that many are selected for in
packages of two or more traits, the second in that extinct molecular
paraphyly and extended paraphyly may be common, then highly precise analysis
based on such data is futile. A method that does not necessarily produce
maximum parsimony, like neighbor joining, may be sufficient to ascertain the
gross clusters of extant taxa that reveal evolutionary processes at
acceptable resolution. On-going wrangling over which software yields the
shortest morphological or molecular tree or the most credible Bayesian
molecular tree is doubtless useless for evolutionary detail because the most
detailed results in both the phylogenetic tree and in resulting
classifications are aleatory. Extinct
paraphyly is a problem with resolution of sequence of molecular lineage
splitting. The resolution of a molecular tree depends on distinguishing
extended paraphyly, i.e. a reasonable inference of a deep shared ancestor
(evolutionary monophyly) from evolutionary polyphyly (no reasonable inference
of a deep shared ancestor). The question is whether any particular sister
group is or is not the remnant of a paraphyletic ancestor, which would affect
accuracy of mapping of expressed traits or taxa on the molecular tree.
Without additional information like relative age of the groups involved, the
best guide is the extent of paraphyly or extended paraphyly, by some measure
of patristic distance, of related extant natural taxa. Without other data, a cladogram with 10
percent of the nodes exhibiting paraphyly in extant taxa may indicate that 10
percent of the ancestral nodes at any past time were also paraphyletic, and
all present-day nodes are then only 90% credible due to this one problem
alone. Individual lineages that are well-supported by bootstrapping or
credible intervals are in no way immune to this problem. Other data possibly
of value in evolutionary analysis preliminary to classification include
various autapomorphic (phylogenetically uninformative) traits, paleontology,
chemistry, ecology, biogeography, chromosome numbers, and any other
information that might throw light on ancestor-descendant relationships of
accepted or natural taxa. Also relevant here is recent work on irreversible
traits (Bridgham et al. 2009). See
also “Short Essays on Macroevolution in
Classification” and “Mathematics, Science and
Phylogenetics Compared: An Essay.” Additional
material: In
systematics, the supreme question of our time is whether to abandon science.
Structuralism has its attractions, e.g., precision, statistical certainty,
and solely deductive methods of analysis, but it is not science because it
rejects testable inductive theory that conciliates instead of relegates
facts, and its models involve hidden causes, and unnamable and unobservable
entities. There are practices associated with
phylogenetics that must be rejected for a new systematics to truly conciliate
taxonomic methods that yield disparate results, especially the following: (1) Shared ancestors are not named at the
same rank as their derivative exemplars in phylogenetics because this would
result in paraphyletic groups, and nodes are simply place holders for the
next higher inclusive rank. Thus, if followed to an extreme, an alterative
view is possible that species do not disappear at all but their lines are
bunched as skeins into the “shared ancestor” of a higher rank. There is no
evidence in a phylogenetic classification, or a cladogram, or in the
evolutionary analysis that generated the cladogram, against a species
surviving a speciation event or even of immutability of species. (2) Mapping of traits on cladograms is commonly referred to as instances of
evolutionary change, yet traits do not evolve, species do, an extreme
reductionism. Thus, trait changes mapped on cladograms may be used to infer
only microevolution and not macroevolution (one taxon evolving from another
at the same rank or lower) yielding a microevolutionary rather than
macroevolutionary classification. Modeling descent with modification of taxa
is avoided. Mapping of morphological traits or biogeographic distributions on
cladograms is an attempt to transform evolutionary analysis from hypothesis
and theory to lemma and theorem, i.e., from both deduction and induction to
deduction only. (3) The rejection of naming tree nodes is
said to be due to the fact that then all branches of a tree would need to be
collapsed because a taxon cannot directly evolve from another of the same
rank, according the th phylogenetic principle of holophyly. Classification by
holophyly (strict phylogenetic monophyly) is artificial and leads to
degenerate (as a return to absolutism) non-evolutionary classifications.
Holophyly has no ontological basis as a process in nature, that is, it is not
refutable and so is not a scientific hypothesis. It is ostensibly used for
simplifying taxonomy, but in doing so requires one to lump and split taxa
that in any way appear to represent macroevolution in classification.
Holophyly clearly eliminates representation of ancestor-descendant evolution
in classification. Thus, nodes cannot be assigned scientific names (other
than a general and trivial attribution as ancestors belonging to the general
group of all taxa distal on the tree).
Not naming ancestors gives them an ineffable, metempirical, and
recondite substance. It leads to faith-based taxonomy. Curiously, these three points (apparent
immutability of species, microevolution acceptable but not macroevolution,
and ineffable or mystical generation of species) are quite those of
“scientific creationism” or phylogenetic baraminology, which uses
phylogenetic software to group diachronic skeins of lineages, each of a
single immutable species. This does not instill confidence in phylogenetics. Though one may doubt that
phylogeneticists as a group are crypto-creationists, they are definitely
“fellow-travelers.” It is not the literal interpretation of the Bible of
creationists that is problematic, that is their right. And it is not the
Judaeo-Christian ethics of believers that is wrong, in fact there may be
everything right about such. But it is the imposition on secular science by
both creationists and phylogeneticists of pseudoscientific logic and
unreasonable assumptions contrary to fact that is a blow against long and
hard fought for reason and intellectual progress. Phylogenetics has, somehow,
distilled the essence of everything that is wrong about fundamentalist
Christian creationism, and has imposed that on science. *** An Entirely Relevant Quotation: "I think," she said carefully,
"that perhaps too many people want things to be simple when they are not
and cannot be. Encouraging that desire is seductive and rewarding, but also
dangerous." He looked away a little, as if inspecting
something far in the distance over her left shoulder. "I think power has
always been like that," he said, his voice low. — Iain M. Banks, Against a Dark
Background, Orbit: Hachette Book Group, 1993, p. 378. *** More relevant quotations: According
to Dewey (1957), Darwinian logic and empiricism is opposed to and replaces the
ancient but long-regnant Greek philosophy of a transcendent first cause with
progressive organization to a final perfect form, where pre-Darwinian science
was “compelled to aim at realities lying behind and beyond the processes of
nature . . . .” Nowadays, Dewey averred, “in the twilight of intellectual
transition” there are new, intellectually atavistic, absolutist technical
philosophies that abstract “some aspect of the existing course of events in
order to reduplicate it as a petrified eternal principle to explain the very
changes of which it is the formalization.” -- Dewey, J. (1957) The influence
of Darwinism on philosophy. In: Likewise,
Jaynes (1990: 441), in explaining the attractions of modern “scientific
mythologies,” pointed out that “this totality [of scientific method] is
obtained not by actually explaining everything, but by an encasement of its
activity, a severe and absolute restriction of attention, such that
everything that is not explained is not in view.” -- Jaynes, J. (1990) The
origin of consciousness in the breakdown of the bicameral mind. Houghton-Mifflin,
Mariner Books, Edition 2000, In discussing how “But if
thought corrupts language, language can also corrupt thought,” Orwell (1950)
warned against complacent acceptance of jargon and clichés: “This invasion of
one’s mind by ready-made phrases (lay
the foundations, achieve a radical transformation) can only be prevented
if one is constantly on guard against them, and every such phrase
anaesthetises a portion of one’s brain.”
G. Orwell. 1950. Politics and the English Language. In: G. H. Muller.
1982. The McGraw-Hill Reader. *** Other evolutionary systematists
have different priorities and illuminations, and may challenge the above. The
reader is invited to examine the here-collected PDF reprints of other authors
describing and advocating modern evolutionary systematics. Additional discussions relevant to evolutionary systematics A Manifesto for the Restoration
of Evolutionary Systematics December 12, 2010 Cladistic equivalence of
nested parentheses and cladogram April 18, 2011 |
|
|