Microbial Evolution, Phylogeny and Diversity

1. Origins of Life

1. Evidence of Evolution

Evidence for evolution has been obtained through fossil records, embryology, geography, and molecular biology.

Learning Objective

  • Explain the development of the theory of evolution

Key Points

    • Fossils serve to highlight the differences and similarities between current and extinct species, showing the evolution of form over time.
    • Simila anatomy across different species highlights their common origin and can be seen in homologous and vestigal structures.
    • Embryology provides evidence for evolution since the embryonic forms of divergent groups are extremely similar.
    • The natural distribution of species across different continents supports evolution; species that evolved before the breakup of the supercontinent are distributed worldwide, whereas species that evolved more recently are more localized.
    • Molecular biology indicates that the molecular basis for life evolved very early and has been maintained with little variation across all life on the planet.


  • vestigial structure

    genetically determined structures or attributes that have apparently lost most or all of their ancestral function in a given species

  • biogeography

    the study of the geographical distribution of living things

  • homologous structure

    the traits of organisms that result from sharing a common ancestor; such traits often have similar embryological origins and development

Evidence of Evolution

The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the signature of past and present evolution. Darwin dedicated a large portion of his book, On the Origin of Species, to identifying patterns in nature that were consistent with evolution. Since Darwin, our understanding has become clearer and broader.

Fossils, Anatomy, and Embryology

Fossils provide solid evidence that organisms from the past are not the same as those found today; they show a progression of evolution. Scientists calculate the age of fossils and categorize them to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years. For example, scientists have recovered highly-detailed records showing the evolution of humans and horses . The whale flipper shares a similar morphology to appendages of birds and mammals, indicating that these species share a common ancestor . Over time, evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the same overall layout. Scientists call these synonymous parts homologous structures.

Common Ancestors

The similar construction of these appendages indicates that these organisms share a common ancestor.

Evolution of Humans and Horses

(a) In this display, fossil hominids are arranged from oldest (bottom) to newest (top). As hominids evolved, the shape of the skull changed. (b) An artist's rendition of extinct species of the genus Equus reveals that these ancient species resembled the modern horse (Equus ferus), but varied in size.

Some structures exist in organisms that have no apparent function at all, appearing to be residual parts from a common ancestor. These unused structures (such as wings on flightless birds, leaves on some cacti, and hind leg bones in whales) are vestigial.

Embryology, the study of the development of the anatomy of an organism to its adult form, provides evidence for evolution as embryo formation in widely-divergent groups of organisms tends to be conserved. Structures that are absent in the adults of some groups often appear in their embryonic forms, disappearing by the time the adult or juvenile form is reached. For example, all vertebrate embryos, including humans, exhibit gill slits and tails at some point in their early development. These disappear in the adults of terrestrial groups, but are maintained in adults of aquatic groups, such as fish and some amphibians. Great ape embryos, including humans, have a tail structure during their development that is lost by birth.

Another form of evidence of evolution is the convergence of form in organisms that share similar environments. For example, species of unrelated animals, such as the arctic fox and ptarmigan living in the arctic region, have been selected for seasonal white phenotypes during winter to blend with the snow and ice . These similarities occur not because of common ancestry, but because of similar selection pressures: the benefits of not being seen by predators.

Adaptations: Winter Coats

The white winter coat of the (a) arctic fox and the (b) ptarmigan's plumage are adaptations to their environments.


Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia compared to that of the southern continents that formed from the supercontinent Gondwana.

The great diversification of marsupials in Australia and the absence of other mammals reflect Australia's long isolation. Australia has an abundance of endemic species (those found nowhere else) which is typical of islands whose isolation by expanses of water prevents species from migrating. Over time, these species diverge evolutionarily into new species that look very different from their ancestors that may exist on the mainland. The marsupials of Australia, the finches on the Galápagos, and many species on the Hawaiian Islands are all unique to their one point of origin, yet they display distant relationships to ancestral species on mainlands.

Molecular Biology

Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a common ancestor for all of life is reflected in the universality of DNA as the genetic material, in the near universality of the genetic code, and in the machinery of DNA replication and expression. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences. This is exactly the pattern that would be expected from descent and diversification from a common ancestor.

DNA sequences have also shed light on some of the mechanisms of evolution. For example, it is clear that the evolution of new functions for proteins commonly occurs after gene duplications that allow the free modification of one copy by mutation, selection, or drift (changes in a population's gene pool resulting from chance), while the second copy continues to produce a functional protein.

Elements of Life

Key elements were needed for early life to start on earth.

Learning Objective

  • Define the key elements of life

Key Points

    • While the exact substituents for early life to form are not completely agreed upon, most theories agree that methane, ammonia, water, hydrogen sulfide, carbon dioxide or carbon monoxide, and phosphate were needed in the absence of molecular oxygen and ozone.
    • From a soup of the primordial earth it's debated whether RNA or protein were the first molecules needed to start simple life, as both can catalyze their self-assembly.
    • Once simple molecules formed on primordial earth they could then be placed unde selective pressure to replicate, starting the evolution of the first life-forms on earth.


  • ribozyme

    A fragment of RNA that can act as an enzyme.

  • phospholipid

    any lipid like lecithin or cephalin consisting of a diglyceride combined with a phosphate group and a simple organic molecule likecholine or ethanolamine; they are important constituents of biological membranes

There is no "standard model" of the origin of life. However, most currently accepted models draw at least some elements from the framework laid out by the Oparin-Haldane hypothesis. The Oparin-Haldane hypothesis suggests that the atmosphere of the early Earth may have been chemically reducing in nature, composed primarily of: methane (CH4), ammonia (NH3), water (H2O), hydrogen sulfide (H2S), carbon dioxide (CO2) or carbon monoxide (CO), with phosphate (PO43-), molecular oxygen (O2) and ozone (O3) either rare or absent.

In such a reducing atmosphere, electrical activity can catalyze the creation of certain basic small molecules (monomers) of life, like amino acids. This was demonstrated in the Miller–Urey experiment by Stanley L. Miller and Harold C. Urey in 1953. Phospholipids (of an appropriate length) can form lipid bilayers, a basic component of the cell membrane .

Miler-Urey Experiment

An outline of the apparatus used by Miller and Urey. Using this apparatus, and using conditions thought to approximate the conditions on pre-biotic earth, they were able to catalyze the molecules of life like amino acids.

A fundamental question is about the nature of the first self-replicating molecule. Since replication is accomplished in modern cells through the cooperative action of proteins and nucleic acids, the major schools of thought about how the process originated can be broadly classified as "proteins first" and "nucleic acids first. " The principal thrust of the "nucleic acids first" argument is as follows:

  1. The polymerization of nucleotides into random RNA molecules might have resulted in self-replicating ribozymes (RNA world hypothesis).
  2. Selection pressures for catalytic efficiency and diversity might have resulted in ribozymes which catalyse peptidyl transfer (hence formation of small proteins), since oligopeptides complex with RNA to form better catalysts. The first ribosome might have been created by this process, resulting in more prevalent protein synthesis.
  3. Synthesized proteins might then out-compete ribozymes in catalytic ability, therefore becoming the dominant biopolymer, relegating nucleic acids to their modern use as a carrier of genomic information.

Biologist John Desmond Bernal coined the term biopoiesis for this process,and suggested that there were a number of clearly defined "stages" that could be recognized in explaining the origin of life:

  • Stage 1: The origin of biological monomers
  • Stage 2: The origin of biological polymers
  • Stage 3: The evolution from molecules to cell