Phylogenetic Analysis and its Application in Evolutionary Paleobiology

Stratocladistics: Integrating Temporal Data and Character Data in Phylogenetic Inference

Debate has long simmered over whether data on the order of appearance of taxa in the stratigraphic record should play any role in analyses of phylogenetic relationships among those taxa. Critics argue that temporal data are in principle inapplicable to questions of cladistic relationship, but specific versions of this claim all seem flawed. Stratocladistics offers a methodological context (patterned after that of cladistics itself) within which temporal data participate along with conventional character data in selecting most-parsimonious hypotheses. Stratocladistics outperforms cladistics in tests based on simulated histories, and additional testing will be facilitated by new software automating stratocladistic searches. As with any body of data, we may decide to include or exclude temporal data for specific reasons, but the explanatory power of hypotheses that use both temporal and conventional character data exceeds that of hypotheses based on character data alone.

Phylogenetic Approaches to the Study of Extinction

Species extinction is both a key process throughout the history of life and a pressing concern in the conservation of present-day biodiversity. These two facets have largely been studied by separate communities using different approaches. This article illustrates with examples some of the ways that considering the evolutionary relationships among species—phylogenies—has helped the study of both past and present species extinction. The focus is on three topics: extinction rates and severities, phylogenetic nonrandomness of extinction, and the testing of hypotheses relating extinction-proneness to attributes of organisms or species. Phylogenetic and taxic approaches to extinction have not fully fused, largely because of the difficulties of relating discrete taxa to the underlying continuity of phylogeny. Phylogeny must be considered in comparative tests of hypotheses about extinction, but care must be taken to avoid overcorrecting for phylogenetic nonindependence among taxa.

Extinctions in the fossil record

Direct comparison of ancient extinctions to the present-day situation is difficult, because quantitative palaeontological data come primarily from marine invertebrates, fossilized species are usually drawn from the more abundant and widespread taxa, and time resolution is rarely better than 103— 104 years. A growing array of techniques permits quantitative error estimates on some of these potential biases, and allows calculation of species extinction intensities from genus-level data, which are more robust. Extensive as today’s species losses probably are, they have yet to equal any of the Big Five mass extinctions. Background extinction patterns are potential sources of insight regarding present-day biotic losses; over 90% of past species extinction has occurred at times other than the Big Five mass extinctions. Mean durations of fossil species vary by more than an order of magnitude even within clades, rendering uninformative any global average for background extinction. Taxon-specific variation is evidently related to intrinsic biotic factors such as geographic range and population size. Approaches to extinction analysis and prediction based on morphological variety or biodisparity should be explored as an adjunct or alternative to taxon inventories or phylogenetic metrics. Rebounds from mass extinctions are geologically rapid but ecologically slow; biodiversity communities typically requires 5-10 million years.