Systematics: A New Introduction
August 12, 2009
Informal Resource Locator (IRL:) zanevsys3659
Newly published is:
A FRAMEWORK FOR POST-PHYLOGENETIC SYSTEMATICS
by Richard H. Zander, Sept. 1, 2013, Zetetic Publications, St. Louis, CreateSpace Independent Publishing Platform, 214 pages.
Two central problems of phylogenetics are (1) using a model of pseudoextinction of shared ancestors for the more common allopatric (peripatric) scenario leads to imaginary cladogram branches, (2) molecular “lineages” of taxa are actually estimated branching orders of strains, and other strains of the same taxon may crop up in disparate parts of a cladogram or they may be extinct.
Two solutions offered are (1) use a mixed model by constraining morphological cladograms with multifurcations representing transformation of an ancestral taxon to one or more descendants (inferred from non-sister-group informative data) before sister group analysis, (2) molecular strains of the same taxon cropping up in different places in a cladogram imply an ancestral stem taxon of that same name.
Some points of mystification: Over-extension of a good method to an improper analysis is exemplified by using Occam’s Razor to choose which model to analyze (disappearance of ancestral taxon on speciation versus ancestral taxon remains after speciation). In fact, the Razor should be used to choose which explanation for a single model is least demanding on credulity. An example is improperly using pseudoextinction rather than a mixed pseudoextinction and allopatric evolution model. This is done in phylogenetics perhaps because a cladogram is then capable of being fully resolved and is therefore explainable with fewer state changes.
Changes in non-coding molecular traits used for tracking branch order of molecular strains of taxa are not genetic; genetics deals with genes, and evolution is governed by different frequencies of genes.
Although it is implied that every two taxa have a shared ancestor, this is not true when one of them is the ancestral taxon of the other, thus one cladogram branch may be imaginary when the ancestral taxon is in evolutionary stasis.
For the book’s eStore at CreateSpace, click here.
Much of the discussion below is included in the above book.
Review by Medina and Goffinet
Review by Brower
MODERN EVOLUTIONARY SYSTEMATICS: A NEW INTRODUCTION
10. Other authors
The original introduction way somewhat discursive and unfocused; this is a new, more readable version, with some new, hopefully interesting material.
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
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 macroevolutionary transformations of derived lineages arising from the midst of paraphyletic lineages.
Phylogenetics is methodologically 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 over-arching 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.
Molecular trees are variously assembled through parsimony analysis (as in
morphology), or maximum likelihood or Markov chain
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.
Thus, Aves is an autophyletic (= apophyletic, derived) 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”). Unnamed “shared ancestors” are not hypotheses (unless no extant taxon can be named) but are contrivances to ensure full resolution under maximum parsimony;
(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 are supposed to 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), in addition if one branch of a sister group is the ancestral taxon of the other, the node is not a “shared ancestor” but is superfluous and imaginary;
(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.
Systematics is not an exact science.
"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 or otherwise unsampled 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).
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.
"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:
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:
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
anaesthetizes 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.
A Manifesto for the Restoration of Evolutionary Systematics December 12, 2010
(a shortened version of the above in Russian)
Cladistic equivalence of nested parentheses and cladogram April 18, 2011
A Short Glossary of Phylogenetic Terms
July 11, 2012
There are Web sites that deprecate evolutionary systematics, where chuckles are shared among fellow cladists about the perceived failings of the bearded reactionaries of pre-paradigmatic times when evolution was taught by red-bedaubed, feathered shamans telling just-so stories to awe-struck wondering grad students sitting in a circle around a fire in a sooty, dank cave. The Modern Evolutionary Systematics Web site would never stoop to this jejune blogging practice, and urges researchers to feel sorry for cultists of every stripe, and hope for their eventual reprogramming. On the other hand, here is a Glossary that responds to japes and contumely in a kindly and uplifting manner.
Extract from “A Framework for a Post-Phylogenetic Systematics,” by R. H. Zander, in prep.
A deeper view of the historical background of the phylogenetic revolution is provided by Vernon (1993). In the late 1950s, there were two contending factions: (1) classical taxonomists, who felt that taxonomy could exist on its own and produce, using standard methods, classifications that evolutionists could use in their own work, and (2) evolutionary systematists, who, by “putting evolutionary issues as the primary focus of taxonomy, ... sought to connect it to one of the most important biological questions of the time.” The problem was that although some groups of birds and mammals had good fossil records and known breeding behavior, and some beetles, mollusks and butterflies were amenable to the evolutionary analysis of the day, most invertebrate zoologists, most botanists, and all microbiologists were not counted among practitioners of the cutting edge of evolutionary systematics.
So who won the mid-Century contest described by Vernon (1993)? Given the present-day hegemony of phylogenetics, it would seem that the evolutionary systematists won. But consider this—a cladogram is much like a dichotomous key, with similar nested state changes. A cladogram can be viewed as a classification as long as the classification principle of holophyly is used to reject putting names of higher rank under names of lower rank, or the same rank nested in another rank. A classification as imbued in a dichotomous key is presupposed and imposed on evolutionary evaluations in systematics. A tree of life is not an evolutionary tree, it is a classification based on a dichotomous key. This leads to the horrendous fact that all evolutionary analyses done in phylogenetic systematics must fit a classificatory dichotomous key as a basic structure. In fact, modern systematics is the triumph of classical taxonomy over evolutionary systematics.
Vernon, K. 1993. Desperately seeking status: evolutionary systematics and the taxonomists’ search for respectability 1940–60. Brit. J. Hist. Sci. 26: 207–227.
September 12, 2012, St. Louis.
To Taxacom listserver, September 9, 2013:
I appreciate the response, pro, con, and incensed. Okay, here is the shortest way I can describe what passes for optimality in phylogenetics.
Take two taxa or clades (at the end of a larger cladogram with other taxa or clades), one characterized by advanced traits xy and the other by advanced traits xz. Phylogenetics assumes that parsimoniously the shared ancestor, now extinct through pseudoextinction (anagenetic change into another taxon), had the plesiomorphic trait x, then one daughter taxon differentiated with y and the other with z. That is three (3) steps.
Okay. BUT suppose the ancestral taxon did not go extinct but survived and generated a daughter taxon by peripatric evolution. With the same data set, the ancestral taxon had traits xy, and the daughter taxon had trait z and -y (reversal). That is four (4) steps.
In phylogenetics, optimality is always BOTH shortest tree and simplest model (i.e., universal pseudoextinction). The argument is that you do get the shortest tree with both assumptions. Of course the parsimony or other optimality part is okay but the simplest model is nonsense, since this sort of argument would throw out that complicated theory of relativity in favor of the simpler Newtonian mechanics. Occam’s Razor does not work that way since the Razor deals multiple explanations for one model.
My suggestion is that the best model for any optimality (morphology or molecular) analysis is generating a mixture of pseudoextinction and peripatric evolution for a group, THEN find maximum parsimony, likelihood or credible interval for that evolutionarily composite model.
The old complaint is that detailing such a composite model requires experience, judgment and reasoned evaluation based on theories of taxon transformation in nature. (Read: subjective just-so story.) It is in fact easy to examine a group of classically grouped species and discern generalized species and highly specialized potential daughter species. THEN constrain the cladogram.
Although using universal pseudoextinction makes for ease of generation of cladograms, the results are in often large part imaginary, that is, all divergence branches involving a single surviving ancestral taxon are not real.
“Be very, very careful what you put in that head because you will never, ever get it out.”
― Thomas Cardinal Wolsey
Added January 14, 2014:
Hennigian phylogenetics requires that two of every three taxa be more closely related. This fails when one species survives in expressed trait stasis while it generates two or more descendent species. This is common in every situation where one species has greater population density than its descendant and selection is slowed by swamping, or if an ancestor has strong stabilizing selection.
Thus, a node on a cladogram is commonly not a placeholder, or locum tenens, for an unknown shared ancestor. In most cases it is a locus pocus, a magical organizing principle that keeps cladograms well resolved. It can be expected that there are lots of loci poci in published cladograms. Only if it can be demonstrated that a node cannot be confidently named can a locum tenens be distinguished from a locus pocus.