Phylogenetic constraints on paleobiology
Cladograms are not ends in themselves:
Missing Data and the Extant Phylogenetic Bracket: A nice thing about the parsimony method of phylogeny reconstruction is that it is robust to missing data. Indeed, the results of the analysis allow us to hypothesize about what that data might have been using a method called the extant phylogenetic bracket (EPB) - i.e. the bracket formed on either side of the taxon with the missing information by extant taxa in which the character state is known. Using it, we can make three types of inference, listed in order of decreasing confidence. Consider the distribution of a soft-tissue character - the four-chambered heart - among three fossil reptiles:
- Type I Inference: Tyrannosaurus is bracketed by birds and crocodilians, both of which have the derived character. With no contrary positive
evidence, the simplest assumption is that Tyrannosaurus had it also.
- Type II Inference: The basal archosauriform Euparkeria is bracketed by crocodilians and squamates. Crocs have the derived character, squamates don't. Thus, we are much less secure than above in inferring it in Euparkeria , but presence of some sort of hard tissue correlate of that trait might increase our confidence.
- Type III Inference: The basal diapsid Petrolacosaurus is bracketed by squamates and turtles, neither of which have the derived character. Our confidence in
its presence in the extinct form is very low. We would need strong positive fossil evidence to argue for its presence.
Phylogenies and Biostratigraphy: Traditional biostratigraphers - Geologists who use the fossil record to date sedimentary rock units tend to be literal-minded souls who think that either fossils of an organism or group are known to be present at a particular time, or they aren't. Hypotheses of phylogeny tell us when we ought to be cautious about such literal interpretations.
Statistical applications: Biologists are fond of performing statistical studies, looking for meaningful correlations between different parts of animals' anatomies. For instance, one might look at the ratio of the length and depth of birds' beaks vs. the length of their tarsals to see if larger birds have proportionately deeper beaks. Such studies require that all observations be made from the same underlying population.
- Ghost Lineages: When we know that two taxa are sister taxa (descendants of the same recent common ancestor), we in essence know that they originated at the same point in geologic time - the time of their last common ancestor and the speciation event that gave rise to them. Say we know one of these taxa from 100 million year old rocks, and the other from 90 million year old rocks. Even without seeing a fossil, we know that the second group must have representatives dating back at least to 100 million years, simply from its sister-taxon relationship with the other. A lineage like this, whose existence can be inferred from the cladogram, but which is not known from actual fossils is called a ghost lineage. The examination of ghost lineages should allow biostratigraphers to refine their models of the stratigraphic ages of organisms.
- Stratigraphic congruence:. How do we identify ghost lineages and measure their prevalence in a cladogram. All other things being equal, we expect the terminal taxa that branch off of a cladogram first to appear first in the fossil record. When this is true, the cladogram is said to be stratigraphically congruent. Often, cladograms are not stratigraphically congruent. This happens when there are long ghost lineages.
- Measuring Stratigraphic congruence:. A simple measure of stratigraphic congruence is the Stratigraphic Consistency Index (SCI) of John Huelsenbeck. To calculate it, count the number of stratigraphically consistent nodes in a cladogram. A node is stratigraphically consistent if both of the lineages emerging from it occur later than the node's sister taxon. Divide the number of consistent nodes with the total number of nodes in the cladogram to get the SCI.
- Example: Choristoderes.
In 1984, when Jacques Gauthier performed the first major cladistic analysis of diapsid reptiles, he got a surprise. Choristodera, whose members were known from the Late Cretaceous and Paleocene, appeared to have branched off of the reptilian tree by the late Permian. Thus, they sat at the end of a ghost lineage that persisted for over 150 million years. This seemed highly improbable. Was the cladogram wrong or our understanding of the fossil record? As paleontologists began reexamining museum collections, it became apparent that some neglected partially preserved creatures were, in fact, choristoderes. Today, the choristodere record starts in the late Triassic. Some research suggests an alternate phylogenetic placement for choristoderes that further shortens their ghost lineage.
However, when samples are being taken not from a single pool but from groups of populations nested in a heirarchical phylogeny, this assumption is violated. (BSCI393 students take note!!) The above example I showed of how misleading this can be. Fortunately, Joe Felsenstein of the University of Washington developed a statistical technique for adjusting data to account for the phylogeny of the taxa sampled, called independent contrasts. By applying it, meaningful correlation studies can be performed. Without it, they would be meaningless and misleading.