Editing Cladistics (section)

== Issues ==

=== Ancestors ===
The cladistic method does not identify fossil species as actual ancestors of a clade.<ref>{{Cite journal|last1=Krell|first1=Frank-T|last2=Cranston|first2=Peter S.|date=2004|title=Which side of the tree is more basal?: Editorial|journal=Systematic Entomology|language=en|volume=29|issue=3|pages=279–281|doi=10.1111/j.0307-6970.2004.00262.x|s2cid=82371239|doi-access=free|bibcode=2004SysEn..29..279K }}</ref> Instead, fossil taxa are identified as belonging to separate extinct branches. While a fossil species could be the actual ancestor of a clade, there is no way to know that.  Therefore, a more conservative hypothesis is that the fossil taxon is related to other fossil and extant taxa, as implied by the pattern of shared apomorphic features.<ref>Patterson, Colin. "Significance of fossils in determining evolutionary relationships." Annual Review of Ecology and Systematics 12, no. 1 (1981): 195–223.</ref>

=== Extinction status ===
An otherwise extinct group with any extant descendants, is not considered (literally) extinct,<ref>{{Cite book |last1=Ross |first1=Robert M. |url=https://books.google.com/books?id=gw3vHelHbusC&dq=paraphyly+can+not+be+precisely+extinction&pg=PA133 |title=Causes of Evolution: A Paleontological Perspective |last2=Allmon |first2=Warren D. |date=1990-12-18 |publisher=University of Chicago Press |isbn=978-0-226-72824-7 |pages=133 |language=en}}</ref> and for instance does not have a date of extinction.

=== Hybridization, interbreeding ===
Anything having to do with biology and sex is complicated and messy, and cladistics is no exception.<ref>{{Cite web |title=Introduction to Cladistics |url=https://ucmp.berkeley.edu/clad/clad1.html |access-date=2022-05-08 |website=ucmp.berkeley.edu}}</ref> Many species reproduce sexually, and are capable of interbreeding for millions of years. Worse, during such a period, many branches may have radiated, and it may take hundreds of millions of years for them to have whittled down to just two.<ref>{{Cite journal |last1=Harrison |first1=Richard G. |last2=Larson |first2=Erica L. |date=2014-01-01 |title=Hybridization, Introgression, and the Nature of Species Boundaries |journal=Journal of Heredity |volume=105 |issue=S1 |pages=795–809 |doi=10.1093/jhered/esu033 |pmid=25149255 |issn=0022-1503|doi-access=free }}</ref> Only then one can theoretically assign proper last common ancestors of groupings which do not inadvertently include earlier branches.<ref name="Hörandl-2010">{{Cite journal |last1=Hörandl |first1=Elvira |last2=Stuessy |first2=Tod F. |date=2010 |title=Paraphyletic groups as natural units of biological classification |url=https://www.jstor.org/stable/41059863 |journal=Taxon |volume=59 |issue=6 |pages=1641–1653 |doi=10.1002/tax.596001 |jstor=41059863 |issn=0040-0262}}</ref> The process of true cladistic bifurcation can thus take a much more extended time than one is usually aware of.<ref>{{Cite journal |last1=Mehta |first1=Rohan S. |last2=Rosenberg |first2=Noah A. |date=2019-10-01 |title=The probability of reciprocal monophyly of gene lineages in three and four species |journal=Theoretical Population Biology |language=en |volume=129 |pages=133–147 |doi=10.1016/j.tpb.2018.04.004|pmid=29729946 |pmc=6215533 |bibcode=2019TPBio.129..133M }}</ref> In practice, for recent radiations, cladistically guided findings only give a coarse impression of the complexity. A more detailed account will give details about fractions of introgressions between groupings, and even geographic variations thereof. This has been used as an argument for the use of paraphyletic  groupings,<ref name="Hörandl-2010" /> but typically other reasons are quoted.

=== Horizontal gene transfer ===
Horizontal gene transfer is the mobility of genetic info between different organisms that can have immediate or delayed effects for the reciprocal host.<ref>{{Cite journal |last1=Emamalipour |first1=Melissa |last2=Seidi |first2=Khaled |last3=Zununi Vahed |first3=Sepideh |last4=Jahanban-Esfahlan |first4=Ali |last5=Jaymand |first5=Mehdi |last6=Majdi |first6=Hasan |last7=Amoozgar |first7=Zohreh |last8=Chitkushev |first8=L. T. |last9=Javaheri |first9=Tahereh |last10=Jahanban-Esfahlan |first10=Rana |last11=Zare |first11=Peyman |date=2020 |title=Horizontal Gene Transfer: From Evolutionary Flexibility to Disease Progression |journal=Frontiers in Cell and Developmental Biology |volume=8 |page=229 |doi=10.3389/fcell.2020.00229 |pmid=32509768 |pmc=7248198 |issn=2296-634X|doi-access=free }}</ref> There are several processes in nature which can cause [[horizontal gene transfer]]. This does typically not directly interfere with ancestry of the organism, but can complicate the determination of that ancestry. On another level, one can map the horizontal gene transfer processes, by determining the phylogeny of the individual genes using cladistics.

=== Naming stability ===
If there is unclarity in mutual relationships, there are a lot of possible trees. Assigning names to each possible clade may not be prudent. Furthermore, established names are discarded in cladistics, or alternatively carry connotations which may no longer hold, such as when additional groups are found to have emerged in them.<ref>{{Cite journal |last=Dubois |first=Alain |date=2007-08-01 |title=Naming taxa from cladograms: some confusions, misleading statements, and necessary clarifications |url=https://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2007.00151.x |journal=Cladistics |language=en |volume=23 |issue=4 |pages=390–402 |doi=10.1111/j.1096-0031.2007.00151.x |pmid=34905840 |s2cid=59437223 |issn=0748-3007}}</ref> Naming changes are the direct result of changes in the recognition of mutual relationships, which often is still in flux, especially for extinct species. Hanging on to older naming and/or connotations is counter-productive, as they typically do not reflect actual mutual relationships precisely at all. E.g.  Archaea, Asgard archaea, protists, slime molds, worms, invertebrata, fishes, reptilia, monkeys, ''Ardipithecus'', ''Australopithecus'', ''Homo erectus'' all contain ''Homo sapiens'' cladistically, in their ''sensu lato'' meaning. For originally extinct stem groups, ''[[Sensu|sensu lato]]'' generally means generously keeping previously included groups, which then may come to include even living species. A pruned ''[[Sensu|sensu stricto]]'' meaning is often adopted instead, but the group would need to be restricted to a single branch on the stem. Other branches then get their own name and level. This is commensurate to the fact that more senior stem branches are in fact closer related to the resulting group than the more basal stem branches; that those stem branches only may have lived for a short time does not affect that assessment in cladistics.