Traditionally, scientists have used fossils to quantify rates and patterns of evolution through long periods of time (sometimes called “macroevolution”). These approaches have been tremendously informative. We now have a detailed picture of the evolutionary dynamics of many groups, from hominids to crocodilians. In some cases, very detailed fossil records of some types of organisms – for example, marine invertebrates – have allowed quantitative tests of particular evolutionary models.
Fossils are particularly good at showing how species diversity and morphological characters change through time. For example, if one has a sequence of fossils with known times of occurrence, one can reconstruct patterns of species diversity through time. A classic example of this is Sepkoski’s (1984) reconstruction of the diversity of marine invertebrates over the past 600 million years. One can also quantify the traits of those fossils and measure how they change across various time intervals (e.g. Foote 1997). In some groups, we can make plots of changes in lineage and trait diversity simultaneously (Figure 1.2). Fossils are the only evidence we have for evolutionary lineages that have gone extinct, and they provide valuable direct evidence about evolutionary dynamics in the past.
However, fossil-based approaches face some challenges. The first is that the fossil record is incomplete. This is a well-known phenomenon, identified by Darwin himself (although many new fossils continue to be found). The fossil record is incomplete in some very particular ways that can sometimes hamper our ability to study evolutionary processes using fossils alone. One example is that fossils are rare or absent from some classical examples of adaptive radiation on islands. For example, the entire fossil record of Caribbean anoles, a well-known adaptive radiation of lizards, consists of less than ten specimens preserved in amber (Losos 2009). We similarly lack fossils for other adaptive radiations like African cichlids and Darwin’s finches. The absence of fossils in these groups limits our ability to directly study the early stages of adaptive radiation. Another limitation of the fossil record relates to species and speciation. It is very difficult to identify and classify species in the fossil record – even more difficult than it is to do so for living species. It is hard to tell species apart, and particularly difficult to pin down the exact time when new species split off from their close relatives. In fact, most studies of fossil diversity focus on higher taxonomic groups like genera, families, or orders (see, e.g., Sepkoski 1984). These studies have been immensely valuable but it can be difficult to connect these results to what we know about living species. In fact, it is species (and not genera, families, or orders) that form the basic units of almost all evolutionary studies. So, fossils have great value but also suffer from some particular limitations.
Phylogenetic trees represent a rich source of complementary information about the dynamics of species formation through time. Phylogenetic approaches provide a useful complement to fossils because their limitations are very different from the limitations of the fossil record. For example, one can often include all of the living species in a group when creating a phylogenetic tree. Additionally, one can use information from detailed systematic and taxonomic studies to identify species, rather than face the ambiguity inherent when using fossils. Phylogenetic trees provide a distinct source of information about evolutionary change that is complementary to approaches based on fossils. However, phylogenetic trees do not provide all of the answers. In particular, there are certain problems that comparative data alone simply cannot address. The most prominent of these, which I will return to later, are reconstructing traits of particular ancestors (ancestral state reconstruction; Losos 2011) and distinguishing between certain types of models where the tempo of evolution changes through time (Slater et al. 2012). Some authors have argued that extinction, as well, cannot be detected in the shape of a phylogenetic tree (Rabosky 2010). I will argue against this point of view in Chapter 11, but extinction still remains a tricky problem when one is limited to samples from a single time interval (the present day). Phylogenetic trees provide a rich source of information about the past, but we should be mindful of their limitations (Alroy 1999).
Perhaps the best approach would combine fossil and phylogenetic data directly. Paleontologists studying fossils and neontologists studying phylogenetic trees share a common set of mathematical models. This means that, at some point, the two fields can merge, and both types of information can be combined to study evolutionary patterns in a cohesive and integrative way. However, surprisingly little work has so far been done in this area (but see Slater et al. 2012, Heath et al. (2014)).