The evolution of evolutionary thought

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What is the point?

  1. To be able to describe the history of evolutionary thinking
  2. To be able to describe how relics of this historical background clings to and impedes clear evolutionary thinking today
  3. To describe the current molecular phylogenetic tree of life
  4. To describe the advantages of the molecular phylogenetic tree compared to previous trees

The Chain of Being

Well before people discovered that species changed over time, both living and non-living things were organized (in Western culture, including Aristotle) into the “chain of being”:

The Chain of Being Cheezy drawing by Jim Brown

The Chain of Being
Cheezy drawing by Jim Brown

All species & substances were placed onto individual slices of a vertical scale, ascending from inferior to superior. Great thought and energy was put into deciding exactly how to order the major categories of materials, living things, species, races, social classes, and even individuals onto this linear arrangement. (It will come as no surprize to the cynical that the ethnic group placed at the top of the human part of the chain generally matched that of whoever was organizing the chain.) This was an impossible task, with lots of problematic and contradictory issues - in retrospect, it is obvious that the reason for this was that there is no linear relationship between species.

As an aside, this linear arrangement of substances survives, in some form, in the periodic table, in which the elements are arranged in order of increasing atomic number. The chain is broken into segments, and the segments stacked in such a way that elements with similar properties form columns.

The Evolutionary Ladder

The earliest forms of evolutionary thought had each specie (up to but not including humans) moving up the "Evolutionary ladder”, a climbable form of the chain of being. Evolution, in this view, was linear and progressive - species evolved from one rung to the next as an effect of a progressive force.

from “Evolution: what the fossils say and why it matters”.  D.R. Prothero and C.D. Buell (attributed to CD Buell)

from “Evolution: what the fossils say and why it matters”.
D.R. Prothero and C.D. Buell (attributed to CD Buell)

Although the notion of an evolutionary ladder is pre-Darwinian and hopelessly incorrect, we’re discussing it here because this scheme is firmly imbedded in modern biological unconscious thought. You even hear the term 'evolutionary ladder' fairly often by research scientists who actually know better (one at least hopes). The terms 'higher' and 'lower' eukaryotes, and 'missing link', which are in common use, are relics of this view.

Early Phylogenetic Trees

By the time of Charles Darwin, it was clear that this was not a reasonable view of evolution. Darwin describes a much better view, which has proven to be essentially correct, in which species originate by divergence, as shown in this diagram (the only illustration in The Origin of Species):

Speciation by diversification from "The Origin of Species", Charles Darwin
Speciation by diversification
from "The Origin of Species", Charles Darwin

In this diagram, species A and I at the beginning (bottom) split many times and diverge constantly. Most of these divergences don't go anywhere (they become extinct), but some do make it, at least for a while, resulting in this case in species A splitting into 3 separate surviving species and species I into 2 surviving species at time X. Species A and I no longer exist at time X. Note that most of the original species, B-H, K and L, are in stasis, remaining unchanged through the span of time shown here (or at least the part of it during which they survive).

So, species actually evolve by diversification, not by progression (advancement up the ladder). Eukaryotes did not evolve from Bacteria, animals did not evolve from ciliates, plants did not evolve from fungi, humans did not evolve from chimps. Each of these pairs of modern organisms share a common ancestor, from which each diverged. This is a fundamental aspect of evolution that is poorly understood even by many biologists.

One of the best developed of these divergent evolutionary trees was that of Ernst Haeckel, shown here. In this tree, there are 3 major, equivalent divisions of life - plants, animals, & protists.

Early evolutionary tree by Earnst Haeckel (source unknown)
Early evolutionary tree by Earnst Haeckel (source unknown)

This tree is a huge improvement over the “evolutionary ladder”. It's a tree; species are not ranked, and modern species are not considered to be the ancestors of other modern organisms. Plants & animals are not thought of as having evolved from modern prokaryotes (monerans), but are separate groups.

The Whittaker 5-Kingdom tree being taught in various forms in most classrooms today is a version of this tree:

5-Kingdon tree, Whittaker 1967
5-Kingdon tree, Whittaker 1967

In some ways, this 5-Kingdom tree is actually a step backwards toward the 'ladder of life'. 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 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 it morphological complexity only that’s being considered? Why? If it’s time of origin, why aren’t the recent emerges of bacterial families, genera and species 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) shown as relics of the past?

The reality is that the 5-kingdom tree is entirely qualitative and subjective.

Molecular phylogenetic trees

If the traditional 5-Kingdom tree is problematic because it is subjective and qualitative, what’s needed is an objective measure of evolutionary history. With the ability to determine the nucleotide sequences of genes beginning in the 1970’s, it became possible to use variation in these gene sequences as molecular chronometers of evolutionary distance. We’ve cover this is much detail in ;ater lectures, but suffice it to say for now that these sequences provide the information needed to reconstruct evolutionary trees both objectively and quantitatively.

3-Domain tree Redrawn from Norm Pace
3-Domain tree
Redrawn from Norm Pace

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 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 here marked with the star. How this is determined will be described in a later lecture.

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 outcomes of this method early on was the discovery of a new type of organism - the Archaea (a.k.a. archaebacteria). Previously it was thought that all living things were either Bacteria (a.k.a. eubacteria) or Eukarya (a.k.a. eukaryotes). Archaeal species had previously been scattered haphazardly amongst whatever Bacteria they superficially resembled. Indeed, in terms of superficial phenotype, the Archaea are generally similar to Bacteria, but biochemically they are just as similar to Eukarya, and in evolutionary terms they form a distinct group that is, if anything, more closely related to Eukarya than to Bacteria. The Archaea as a group have changed less since their common ancestry than either the Bacteria or Eukarya (they are primitive), and so more closely resemble our common ancestry.

Multicellular eukaryotes, plants (e.g. Arabidopsis), animals (Homo) and fungi (Saccharomyces), are a very small portion of evolutionary diversity in this tree; just the tip of one branch of the Eukarya, not 3/5ths of evolutionary diversity as the 5-Kingdom scheme has it. Notice that Eukarya are as ancient a group as are either Bacteria or Archaea, and that they did not evolve from either of these other groups. Bacteria are not primitive ancestors of “higher organisms”!

The tree also offers proof of the endosymbiont theory for the origin of mitochondria and chloroplasts. These organelles have their own DNA & genes, including ssu-rRNA genes, & 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 the chloroplasts are cyanoabacteria (e.g. Synechococcus).