London, 1859.) doi:10.1128/9781555818517.ch2.f2.3
One of the best developed of the early divergent evolutionary trees was that of Ernst Haeckel. In this tree, there are three major, equivalent divisions of life—plants, animals, and protists (Fig. 2.4). This tree is a huge improvement over the evolutionary ladder. It is a tree, species are not ranked, and modern species are not considered to be the ancestors of other modern organisms. Plants and animals are not thought of as having evolved from modern prokaryotes (monerans) but are separate groups.
The Whittaker five-kingdom tree being taught in various forms in most classrooms today is a refinement of this tree (Fig. 2.5). In some ways, however, this five-kingdom tree is actually a step backward toward the evolutionary ladder. In most versions of this scheme (such as the original tree by Whittaker, above), eukaryotes are shown to be descended from within the bacteria (not true), and in many representations eukaryotic algae are shown as descendants of cyanobacteria (not true), fungi are shown as descendants of filamentous gram-positive bacteria (not true), and protists are shown as descendants of wall-less gram-positive bacteria (also not true). Also notice the implied vertical axis: either superiority (sometimes expressed as “complexity”) or time (usually labeled “time of origin”). But if this axis is complexity, what exactly is being measured? Eukaryotes are sometimes morphologically complex, but what about parasites that have simplified; why are these organisms not drawn as downward-pointing arrows? What about metabolic complexity, which would place animals close to the bottom? Is morphological complexity the only factor being considered? Why? If the vertical axis is time of origin, why are the recent emergences of bacterial families, genera, and species not considered? The genus Escherichia emerged about 100 million years ago, about the same time as the primates; why is Escherichia (along with all other bacteria), a modern organism, shown as a relic of the past?
Figure 2.4 The tree of life. (Reprinted from Ernst Haeckel, Generelle Morphologie der Organismen. G. Reimer, Berlin, Germany, 1866.) doi:10.1128/9781555818517.ch2.f2.4
Figure 2.5 The five-kingdom tree taught in most schools in the United States. (Redrawn from Whittaker RH, Science 163:150–160, 1969. Used with permission from AAAS.) doi:10.1128/9781555818517.ch2.f2.5
The reality is that the five-kingdom tree is entirely qualitative and subjective.
Molecular phylogenetic trees
If the traditional five-kingdom tree is problematic because it is subjective and qualitative, we need an objective measure of evolutionary history. With the ability to determine the nucleotide sequences of genes beginning in the 1970s, it became possible to use variation in these gene sequences as molecular chronometers of evolutionary distance. We cover this in much detail in chapters 3 through 6, but suffice it to say for now that these sequences provide the information needed to reconstruct evolutionary trees both objectively and quantitatively (Fig. 2.6).
This example of a molecular phylogenetic tree is an unrooted dendrogram. The length of the branches quantitatively represents the evolutionary distance separating gene sequences within these organisms. This particular tree is based on the analysis of small-subunit ribosomal RNA (rRNA) gene sequences. In this tree, the tips of branches are modern organisms. Each node within the tree represents a common ancestor. The last common ancestor (the root) is marked with a star. The way this was determined is described in chapter 7.
Notice that there is no explicit or implied ranking of above (superior) or below (inferior) in the tree. Evolutionary distance (divergence) is measured along the lengths of the branches connecting species. There are no axes in this graph.
One of the most exciting early outcomes of this method was the discovery of a new type of organism: the Archaea (archaebacteria). Previously it was thought that all living things were members of either the Bacteria (eubacteria) or the Eukarya (eukaryotes). Archaeal species had previously been scattered haphazardly among whatever bacteria they superficially resembled. Indeed, in terms of superficial phenotype, the Archaea are generally similar to the Bacteria, but biochemically they are just as similar to the Eukarya, and in evolutionary terms they form a distinct group that is probably more closely related to the Eukarya than to the Bacteria. The Archaea as a group have changed less since their common ancestry than either the Bacteria or Eukarya (they are primitive), and so they more closely resemble our common ancestry.
Figure 2.6 Phylogenetic tree of representative organisms based on small-subunit rRNA sequences. (Redrawn from a figure provided by Norman R. Pace.) doi:10.1128/9781555818517.ch2.f2.6
Multicellular eukaryotes, the plants (e.g., Arabidopsis), animals (e.g., Homo), and fungi (e.g., Saccharomyces), are a very small portion of evolutionary diversity in this tree: just the tip of one or two branches of the Eukarya, not three-fifths of evolutionary diversity as the five-kingdom scheme has it. Notice that Eukarya is as ancient a group as is either Bacteria or Archaea and that it did not evolve from either of these other groups. Bacteria are not primitive ancestors of “higher organisms.”
The tree also offers confirmation of the endosymbiont theory for the origin of mitochondria and chloroplasts. These organelles have their own DNA and genes, including small-subunit rRNA genes, and so they can be analyzed separately from the nucleus (Eukarya) by molecular phylogenetic analysis. Mitochondria turn out to be members of the proteobacteria (exemplified by Escherichia in this tree), and chloroplasts are members of the cyanobacteria (Synechococcus in this tree).
Taxonomy and phylogeny
A taxonomy is a classification scheme for species (or any other collection of objects, for that matter). There are three related components of a biological taxonomy:
1 1. Grouping: The organization of organisms into groups based on similarity
2 2. Naming: The labeling of organisms and groups of organisms with names
3 3. Identifying: The identification of organisms when they are found
Taxonomies are artificial constructions, methods created and used by humans to organize species. Any self-consistent taxonomy is valid, whether it reflects the natural relationships of the organisms or not.
For example, wildflower field guides organize species by features that are readily observed in the field. The first division might be by flower color, a trivial feature of the plants in evolutionary terms but perfectly reasonable for taxonomy. There is no implication that plants with flowers of the same color are related phylogenetically or that plants with flowers of different colors are not related. The field guide is designed for grouping, naming, and identifying species, and so are useful taxonomies.
A phylogeny is the evolutionary pathway relating species. Think of a phylogeny as a large-scale genealogy of species. Phylogenies represent the actual natural relationships between organisms. They are most commonly displayed graphically in the form of phylogenetic trees.
