Editing Evolutionary taxonomy (section)

== New methods in modern evolutionary systematics ==
{{Third-party|section|date=July 2018}}
Efforts in combining modern methods of cladistics, phylogenetics, and DNA analysis with classical views of taxonomy have recently appeared. Certain authors have found that phylogenetic analysis is acceptable scientifically as long as paraphyly at least for certain groups is allowable. Such a stance is promoted in papers by Tod F. Stuessy<ref>{{cite journal | last1 = Stuessy | first1 = Tod F. | year = 2010 | title = Paraphyly and the origin and classification of angiosperms. | journal = Taxon | volume = 59 | issue = 3 |  pages = 689–693 | doi = 10.1002/tax.593001 }}</ref> and others. A particularly strict form of evolutionary systematics has been presented by Richard H. Zander in a number of papers, but summarized in his "Framework for Post-Phylogenetic Systematics".<ref>{{cite book |title=Framework for Post-Phylogenetic Systematics |last=Zander |first=Richard  |year=2013 |publisher=Zetetic Publications, Amazon CreateSpace |location=St. Louis }}</ref>

Briefly, Zander's pluralistic systematics is based on the incompleteness of each of the theories: A method that cannot falsify a hypothesis is as unscientific as a hypothesis that cannot be falsified. Cladistics generates only trees of shared ancestry, not serial ancestry. Taxa evolving seriatim cannot be dealt with by analyzing shared ancestry with cladistic methods. Hypotheses such as adaptive radiation from a single ancestral taxon cannot be falsified with cladistics. Cladistics offers a way to cluster by trait transformations but no evolutionary tree can be entirely dichotomous. Phylogenetics posits shared ancestral taxa as causal agents for dichotomies yet there is no evidence for the existence of such taxa. Molecular systematics uses DNA sequence data for tracking evolutionary changes, thus paraphyly and sometimes phylogenetic [[polyphyly]] signal ancestor-descendant transformations at the taxon level, but otherwise molecular phylogenetics makes no provision for extinct paraphyly. Additional transformational analysis is needed to infer serial descent.

[[File:Cladogram of Didymodon with taxon transformations.png|thumb|right|Cladogram of the moss genus ''Didymodon'' showing taxon transformations. Colors denote dissilient groups.]]The Besseyan cactus or commagram is the best evolutionary tree for showing both shared and serial ancestry. First, a cladogram or natural key is generated. Generalized ancestral taxa are identified and specialized descendant taxa are noted as coming off the lineage with a line of one color representing the progenitor through time. A Besseyan cactus or commagram is then devised that represents both shared and serial ancestry. Progenitor taxa may have one or more descendant taxa. Support measures in terms of Bayes factors may be given, following Zander's method of transformational analysis using decibans.

Cladistic analysis groups taxa by shared traits but incorporates a dichotomous branching model borrowed from phenetics. It is essentially a simplified dichotomous natural key, although reversals are tolerated. The problem, of course, is that evolution is not necessarily dichotomous. An ancestral taxon generating two or more descendants requires a longer, less parsimonious tree. A cladogram node summarizes all traits distal to it, not of any one taxon, and continuity in a cladogram is from node to node, not taxon to taxon. This is not a model of evolution, but is a variant of hierarchical cluster analysis (trait changes and non-ultrametric branches. This is why a tree based solely on shared traits is not called an evolutionary tree but merely a cladistic tree. This tree reflects to a large extent evolutionary relationships through trait transformations but ignores relationships made by species-level transformation of extant taxa.

[[File:DidymCactus.png|thumb|right|A Besseyan cactus evolutionary tree of the moss genus ''Didymodon'' with generalized taxa in color and specialized descendants in white. Support measures are given in terms of Bayes factors, using deciban analysis of taxon transformation. Only two progenitors are considered unknown shared ancestors.]]Phylogenetics attempts to inject a serial element by postulating ad hoc, undemonstrable shared ancestors at each node of a cladistic tree. There are in number, for a fully dichotomous cladogram, one less invisible shared ancestor than the number of terminal taxa. We get, then, in effect a dichotomous natural key with an invisible shared ancestor generating each couplet. This cannot imply a process-based explanation without justification of the dichotomy, and supposition of the shared ancestors as causes. The cladistic form of analysis of evolutionary relationships cannot falsify any genuine evolutionary scenario incorporating serial transformation, according to Zander.<ref>{{cite journal|last1=Zander|first1=Richard|title=Response to a particularly nasty review in the journal Cladistics.|journal=Phytoneuron|date=2014|volume=2014|issue=110|pages=1–4}}</ref>

Zander has detailed methods for generating support measures for molecular serial descent<ref>{{cite journal|last1=Zander|first1=Richard|title=Support measures for caulistic macroevolutionary transformations in evolutionary trees.|journal=Annals of the Missouri Botanical Garden|date=2014|volume=100|issue=1–2|pages=100–107|doi=10.3417/2012090|s2cid=86754093|url=https://www.biodiversitylibrary.org/part/390458 }}</ref> and for morphological serial descent using Bayes factors and sequential Bayes analysis through Turing deciban or Shannon informational bit addition.<ref>{{cite journal|last1=Zander|first1=Richard|title=Classical determination of monophyly exemplified with Didymodon s. lat. (Bryophyta). Part 1 of 3, synopsis and simplified concepts.|journal=Phytoneuron|date=2014|volume=2014|issue=78|pages=1–7|url=http://phytoneuron.net/2014Phytoneuron/78PhytoN-MonophylyPart1.pdf|access-date=4 January 2015}}</ref><ref>{{cite journal|last1=Zander|first1=Richard|title=Classical determination of monophyly, exemplified with Didymodon s. lat. (Bryophyta). Part 2 of 3, concepts.|journal=Phytoneuron|date=2014|volume=2014|issue=79|pages=1–23|url=http://phytoneuron.net/2014Phytoneuron/79PhytoN-MonophylyPart2.pdf|access-date=4 January 2015}}</ref><ref>{{cite journal|last1=Zander|first1=Richard|title=Classical determination of monophyly exemplified with Didymodon s. lat. (Bryophyta). Part 3 of 3, analysis.|journal=Phytoneuron|date=2014|volume=2014|issue=80|pages=1–19|url=http://phytoneuron.net/2014Phytoneuron/80PhytoN-MonophylyPart3.pdf|access-date=4 January 2015}}</ref><ref>Zander R. H. 2018. Macroevolutionary Systematics of Streptotrichaceae of the Bryophyta and Application to Ecosystem Thermodynamic Stability. Edition 2. Zetetic Publications,  CreateSpace Independent Publishing, Amazon, St. Louis.</ref>