The characters used for inferring phylogenetic relationships must be independent of one another (Kluge, 1989). Suites of morphological characters that evolve in concert violate this dictate. Such correlated evolution is most likely to occur when a set of characters underlie a functionally adaptive phenotype or common developmental pathway (Emerson and Hastings, 1998). Such suites of correlated characters can mislead phylogenetic analyses because they track adaptive history instead of phylogeny (Holland et al., 2010; McCracken et al., 1999) or because they are developmentally linked to other characters (Schlosser and Wagner, 2004; West- Eberhard, 2003). In practice, it is difficult to determine the underlying nature of character correlations. This is because a suite of characters that are highly correlated with one another are expected to produce the same result as a suite of independent characters with good phylogenetic signal: strong support for a given clade (Shaffer et al., 1991).
A relevant paragraph that I wish I’d had a couple weeks ago when teaching about the data one can use for phylogeny estimation.
From Eytan et al 2011