Editing Cladogram (section)

===Molecular versus morphological data===

The characteristics used to create a cladogram can be roughly categorized as either morphological (synapsid skull, warm blooded, [[notochord]], unicellular, etc.) or molecular (DNA, RNA, or other genetic information).<ref name="DeSalle">{{cite book |last=DeSalle |first=Rob |year=2002 |title=Techniques in Molecular Systematics and Evolution |publisher=Birkhauser |isbn=978-3-7643-6257-7}}{{page needed|date=March 2015}}</ref> Prior to the advent of DNA sequencing, cladistic analysis primarily used morphological data.  Behavioral data (for animals) may also be used.<ref name="Wenzel">{{cite journal |last=Wenzel |first=John W. |year=1992  |title=Behavioral homology and phylogeny  |journal=Annu. Rev. Ecol. Syst. |volume=23 |pages=361–381 |doi=10.1146/annurev.es.23.110192.002045}}</ref>

As [[DNA sequencing]] has become cheaper and easier, [[molecular systematics]] has become a more and more popular way to infer phylogenetic hypotheses.<ref>{{cite book |last=Hillis|first=David|title=Molecular Systematics |year=1996 |publisher=Sinaur|isbn=978-0-87893-282-5 |author-link=David Hillis}}{{page needed|date=March 2015}}</ref> Using a parsimony criterion is only one of several methods to infer a phylogeny from molecular data. Approaches such as [[maximum likelihood]], which incorporate explicit models of sequence evolution, are non-Hennigian ways to evaluate sequence data. Another powerful method of reconstructing phylogenies is the use of genomic [[retrotransposon marker]]s, which are thought to be less prone to the problem of [[reversion (genetics)|reversion]] that plagues sequence data. They are also generally assumed to have a low incidence of homoplasies because it was once thought that their integration into the [[genome]] was entirely random; this seems at least sometimes not to be the case, however.

[[Image:Cladistics-Apomorphy.png|thumb|250px|[[Apomorphy]] in cladistics.  This diagram indicates "A" and "C" as ancestral states, and "B", "D" and "E" as states that are present in terminal taxa.  Note that in practice, ancestral conditions are not known ''a priori'' (as shown in this heuristic example), but must be inferred from the pattern of shared states observed in the terminals.  Given that each terminal in this example has a unique state, in reality we would not be able to infer anything conclusive about the ancestral states (other than the fact that the existence of unobserved states "A" and "C" would be unparsimonious inferences!)]]