HOW TO DECIDE WHICH TO INCLUDE? THE EFFECTS OF TAXONOMIC SAMPLING ON PHYLOGENETIC HYPOTHESES

Decisions must inevitably be made about the inclusion or exclusion of taxa of particular rank in any macroevolutionary phylogenetic study. It is often not possible to sample all taxa truly exhaustively for practical reasons, and extinction alone has rendered most clades of extant taxa paraphyletic. In this study, we explore some implications of decisions made regarding taxonomic sampling in studies of phylogeny and macroevolution. We focus on investigating phylogenetic relationships among named families of Devonian terebratulide brachiopods only, and include all 71 named genera in our analyses. Experiments involving subsets of taxa that are most completely known morphologically from fossil specimens, that occur earliest in the stratigraphic record, or that include only the name-bearing genera from each family were conducted. Including only the 38 most completely known genera produces a result essentially similar to one including all genera, even those genera for which less than half the characters can be coded. Missing or not applicable data do not appear to have a major effect in structuring topologies or reducing their resolution. Including only the stratigraphically earliest genera produces a result at odds with the other analyses; multiple possible explanations are considered and evaluated. Including only name-bearers, representing only 13% of all named genera, produces a result generally similar to the analysis including all taxa. None of the results of our several phylogenetic experiments involving subsets of genera correspond strongly with the recently revised classification in the Treatise on Invertebrate Paleontology, but general similarities can be discerned. The lack of strong correspondence between the classification and several different experimental phylogenetic hypotheses highlights two potential dangers: inferring phylogenetic relationships or erecting classifications with great confidence using morphological characters only, among extinct taxa only; and ascribing far-reaching evolutionary significance to simple counts of named taxa, particularly families, as warned by Alwyn Williams fifty years ago.