Numerical experiments with model monophyletic and paraphyletic taxa

Abstract

The problem of how accurately paraphyletic taxa versus monophyletic (i.e., holophyletic) groups (clades) capture underlying species patterns of diversity and extinction is explored with Monte Carlo simulations. Phylogenies are modeled as stochastic trees. Paraphyletic taxa are defined in an arbitrary manner by randomly choosing progenitors and clustering all descendants not belonging to other taxa. These taxa are then examined to determine which are clades, and the remaining paraphyletic groups are dissected to discover monophyletic subgroups. Comparisons of diversity patterns and extinction rates between modeled taxa and lineages indicate that paraphyletic groups can adequately capture lineage information under a variety of conditions of diversification and mass extinction. This suggests that these groups constitute more than mere “taxonomic noise” in this context. But, strictly monophyletic groups perform somewhat better, especially with regard to mass extinctions. However, when low levels of paleontologic sampling are simulated, the veracity of clades deteriorates, especially with respect to diversity, and modeled paraphyletic taxa often capture more information about underlying lineages. Thus, for studies of diversity and taxic evolution in the fossil record, traditional paleontologic genera and families need not be rejected in favor of cladistically-defined taxa.

The Pollination of Mid Mesozoic Seed Plants and the Early History of Long-proboscid Insects1,2,3

“…Evidence for this global turnover is reflected by increased insect origination rates and, to a lesser extent, increased extinction rates demonstrated in family-level diversity studies (Labandeira & Sepkoski, 1993;Jarzembowski & Boss, 1996;Dmitriev & Ponomarenko, 2002;Labandeira, 2005b), as well as saturation of mouthpart disparity (Labandeira, 1997). In this context, Sepkoski and Kendrick (1993) have used model-based analyses to validate the use of taxic diversity data and methodology for understanding major macroevolutionary patterns (e.g., Crepet & Niklas, 2009).…”

“…An alternative explanation is that this plateau represents a lull in the recovery of insect taxa from earlier deposits with high numbers of insect species. Consequently, taxic data analyses can capture fossil insect diversity data (Sepkoski & Kendrick, 1993), indicating that global biotic changes resulted in major decreases in insect diversity. This diversity decrease is wedged between an earlier extinction episode and a subsequent diversification event in seed plants.…”

Survival without recovery after mass extinctions

“…However, paraphyly is unlikely in itself to have artificially produced the results reported here. Regarding the genus-level analyses, numerical simulations have shown that paraphyly is unlikely to mask or generate major patterns of taxonomic origination and extinction, especially given the large number of taxa involved (27)(28)(29)(30)(31)(32). Order-level systematics have been increasingly cast in cladistic terms [e.g., echinoderms (33), trilobites (34), and brachiopods (35)].…”

“…Order-level systematics have been increasingly cast in cladistic terms [e.g., echinoderms (33), trilobites (34), and brachiopods (35)]. Extinct orders that have not been revised from this standpoint probably represent true termination of constituent lineages in most instances, either owing to strict monophyly or because paraclades were split significantly before the last appearance of the ordinal taxon, so that the loss of that taxon is meaningful in terms of biodiversity (27)(28)(29). Extensive ''pseudoextinction'' of orders at or immediately following extinction boundaries is thus unlikely.…”

The effects of taxonomic standardization on sampling-standardized estimates of historical diversity

“…Sepkoski & Kendrick 1993;Robeck et al 2000). These studies focus on synoptic databases of first and last appearances (e.g.…”