Editing Cladistics (section)

== Methodology ==
{{Main|Phylogenetics|Cladogram}}
{{See also|Phylogenetic tree}}
{{more citations needed section|date=April 2016}}

The cladistic method interprets each shared character state transformation as a potential piece of evidence for grouping. [[Synapomorphies]] (shared, derived character states) are viewed as evidence of grouping, while [[symplesiomorphies]] (shared ancestral character states) are not.  The outcome of a cladistic analysis is a [[cladogram]] – a [[Tree (graph theory)|tree]]-shaped diagram ([[dendrogram]])<ref>{{Harvnb|Weygoldt|1998}}</ref> that is interpreted to represent the best hypothesis of phylogenetic relationships. Although traditionally such cladograms were generated largely on the basis of morphological characters and originally calculated by hand, [[DNA sequencing|genetic sequencing]] data and [[computational phylogenetics]] are now commonly used in phylogenetic analyses, and the [[Maximum parsimony (phylogenetics)|parsimony]] criterion has been abandoned by many phylogeneticists in favor of more "sophisticated" but less parsimonious evolutionary models of character state transformation. Cladists contend that these models are unjustified because there is no evidence that they recover more "true" or "correct" results from actual empirical data sets <ref>{{Citation |last1=Rindal |first1=Eirik |last2=Brower |first2=Andrew V. Z. |date=2011 |title=Do model-based phylogenetic analyses perform better than parsimony? A test with empirical data |journal=Cladistics |volume=27 |issue=3 |pages=331–334|doi=10.1111/j.1096-0031.2010.00342.x |pmid=34875779 |s2cid=84907350 |doi-access=free }}</ref>

Every cladogram is based on a particular dataset analyzed with a particular method. Datasets are tables consisting of [[Molecular phylogenetics|molecular]], morphological, [[Ethology|ethological]]<ref>{{Harvnb|Jerison|2003|p=254}}</ref> and/or other characters and a list of [[operational taxonomic unit]]s (OTUs), which may be genes, individuals, populations, species, or larger taxa that are presumed to be monophyletic and therefore to form, all together, one large clade; phylogenetic analysis infers the branching pattern within that clade. Different datasets and different methods, not to mention violations of the mentioned assumptions, often result in different cladograms. Only scientific investigation can show which is more likely to be correct.

Until recently, for example, cladograms like the following have generally been accepted as accurate representations of the ancestral relations among turtles, lizards, crocodilians, and birds:<ref>{{Citation |title=Vertebrate Palaeontology |last=Benton |first=Michael J. |author-link=Michael Benton |year=2005 |publisher=Blackwell |isbn=978-0-632-05637-8 |pages=214, 233}}</ref>
{{clade |style=margin:1em auto;
|label1={{color|LimeGreen|▼}}
|1={{clade
   |label1=[[Turtle|Testudines]]
   |1=[[turtle]]s
   |label2=[[Diapsid]]a {{font|size=150%|color=OrangeRed|text=♦}}
   |2={{clade
      |label1=[[Lepidosauria]]
      |1=[[lizard]]s
      |label2=[[Archosaur]]ia
      |2={{clade
         |label1=[[Crocodylomorpha]]
         |1=[[crocodilia]]ns
         |label2=[[Dinosaur]]ia
         |2=[[bird]]s
         }}
      }}
   }}
}}

If this phylogenetic hypothesis is correct, then the last common ancestor of turtles and birds, at the branch near the {{color|LimeGreen|▼}} lived earlier than the last common ancestor of lizards and birds, near the {{font|size=150%|color=OrangeRed|text=♦}}. Most [[Molecular phylogenetics|molecular evidence]], however, produces cladograms more like this:<ref>{{Citation |last1=Lyson |first1=Tyler |last2=Gilbert |first2=Scott F. |date=March–April 2009 |title=Turtles all the way down: loggerheads at the root of the chelonian tree |journal=Evolution & Development |volume=11 |issue=2 |pages=133–135 |doi=10.1111/j.1525-142X.2009.00325.x |pmid=19245543 |url=http://www.mrfdigs.com/publications/2009_lyson-gilbert-loggerheads.pdf |archive-url=https://ghostarchive.org/archive/20221009/http://www.mrfdigs.com/publications/2009_lyson-gilbert-loggerheads.pdf |archive-date=2022-10-09 |url-status=live|citeseerx=10.1.1.695.4249 |s2cid=3121166 }}</ref>
{{clade |style=margin:1em auto;
|label1=[[Diapsid]]a {{font|size=150%|color=OrangeRed|text=♦}}
|1={{clade
   |label1=[[Lepidosauria]]
   |1=[[lizard]]s
   |label2=[[Archosauromorpha]]{{color|LimeGreen|▼}}
   |2={{clade
      |label1=[[Turtle|Testudines]]
      |1=[[turtle]]s
      |label2=[[Archosaur]]ia
      |2={{clade
         |label1=[[Crocodylomorpha]]
         |1=[[crocodilia]]ns
         |label2=[[Dinosaur]]ia
         |2=[[bird]]s
         }}
      }}
   }}
}}

If this is accurate, then the last common ancestor of turtles and birds lived later than the last common ancestor of lizards and birds. Since the cladograms show two mutually exclusive hypotheses to describe the evolutionary history, at most one of them is correct.

[[File:Monophyly, paraphyly, polyphyly.svg|thumb|upright=1.8|Cladogram of the [[primate]]s, showing a [[Monophyly|monophyletic]] taxon (a [[clade]]: the simians or Anthropoidea, in yellow), a [[Paraphyly|paraphyletic]] taxon (the prosimians, in blue, including the red patch), and a [[Polyphyly|polyphyletic]] taxon (the nocturnal primates – the [[loris]]es and the [[tarsier]]s – in red)]]

The cladogram to the right represents the current universally accepted hypothesis that all [[primate]]s, including [[Strepsirrhini|strepsirrhines]] like the [[lemur]]s and [[loris]]es, had a common ancestor all of whose descendants are or were primates, and so form a clade; the name Primates is therefore recognized for this clade. Within the primates, all anthropoids (monkeys, apes, and humans) are hypothesized to have had a common ancestor all of whose descendants are or were anthropoids, so they form the clade called Anthropoidea. The "prosimians", on the other hand, form a paraphyletic taxon. The name Prosimii is not used in [[phylogenetic nomenclature]], which names only clades; the "prosimians" are instead divided between the clades [[Strepsirrhini|Strepsirhini]] and [[Haplorhini]], where the latter contains Tarsiiformes and Anthropoidea.

Lemurs and tarsiers may have looked closely related to humans, in the sense of being close on the evolutionary tree to humans. However, from the perspective of a tarsier, humans and lemurs would have looked close, in the exact same sense. Cladistics forces a neutral perspective, treating all branches (extant or extinct) in the same manner. It also forces one to try to make statements, and honestly take into account findings, about the exact historic relationships between the groups.

{{clear}}