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Evolutionary research - from classical biology to molecular phylogeny

“Nothing in biology makes sense except in the light of evolution,” evolutionary biologist Theodosius Dobzhansky once said. The conclusion that common features of different species (homologous features in modern terminology) can be traced back to a common ancestor has not been seriously questioned by scientists since the time of Darwin. However, there are still some people who reject this finding. Only a few mouse clicks away on the Internet, ample evidence can be found of the anger, bold statements and untruths that religious and pseudoreligious zealots still use to deny this reality 150 years after Darwin.

The basic principles of the relationships between different organisms have been clarified in astonishing detail in comparative examinations of living species. The artistic and detailed genealogical trees that were drawn by Ernst Haeckel, a contemporary and fervent admirer of Darwin, can only be admired. They harbour deep insights and findings and a keen sense of evolutionary relationships. Such genealogical trees were initially based on findings from comparative anatomy/morphology and developmental history/embryology.
Ernst Haeckel: Monophyletic tree of organisms. (Figure: University of Jena)
Of course, there were many unclarified issues, which were often subject to acrimonious academic disputes, and from a modern-day perspective, were blatantly false judgements. While Haeckel for example, in a near clairvoyant insight, regarded whales as a sister group to hippos and as relatives of cloven hoofed animals (Artiodactyla), he made the big mistake of also taking manatees (Sirenia) to be relatives of whales. In this case, Haeckel mistook a convergent with a homologous development. In modern times, genetics as well as physiology, biochemistry and behaviour research have become important instruments in evolutionary research.

Fossils are important

Middle Cambrian trilobites (Photo: University of Tübingen)
Of course it was also clear that the study of living organisms is insufficient in order to explain the process of evolution. The descent of birds from reptiles can be deduced from comparative anatomic and embryologic investigations, but not their descent from theropode dinosaurs. Only fossils are able to tell us that dinosaurs actually lived. The same is true for therapsides from which mammals developed, as well as for trilobites and other strange animals that populated the Cambrian oceans 520 million years ago together with a crayfish species that was recently discovered.

Over the last few decades, DNA sequence comparison has become an important tool for analysing the relationship between species and genera. The comparison of DNA sequences is generally restricted to recent organisms (sequence analyses of fossil DNA fragments have attracted huge attention, for example with regard to solving the relationship of modern humans to Neanderthals, but can in the best case only be used for a timespan of some tens of thousands of years). Molecular evolutionary research using DNA analysis has not only provided access to entire groups of organisms of which hardly any fossil information is available, it is even able to provide precise information on the date when evolutionary lineages divided way back in the past. Many years ago, Linus Pauling and Emile Zuckerkandl were the first to postulate the ‘molecular clock’, a technique used to relate the divergence time of two species which roughly scales with the number of amino acid differences in proteins. However, this approach is very time-consuming and cumbersome, so it was abandoned in favour of nucleic acid analytics once reliable sequencing methods became available. Detailed genealogical trees for all groups of organisms have been set up and chronologically grouped using molecular phylogenetic tools.

DNA – a unique historical archive

Ernst Haeckel 1904: Artforms of Nature. Section of the 49th print.
Such far-reaching conclusions about long forgotten events on the basis of DNA sequences of modern organisms seem rather daring. Richard Dawkins has given a concise explanation of the self-assurance of molecular geneticists (R. Dawkins 2004, “The Ancestor’s Tale”, quoted from p. 21 f):”[…] The important point about DNA is that, as long as the chain of reproducing life is not broken, its coded information is copied to a new molecule before the old molecule is destroyed. In this form, DNA information far outlives its molecules. It is renewable – copied – and since the copies are literally perfect for most of its letters on any one occasion, it can potentially last an indefinitely long time. Large quantities of our ancestors’ DNA information survives completely unchanged, some even from hundreds of millions of years ago, preserved in successive generations of living bodies. Understood in this way, the DNA record is an almost unbelievably rich gift to the historian. What historians could have dared hope for a world in which every single individual every species carries, within its body, a long and detailed test: a written document handed down through time?

Moreover, it has minor random changes, which occur seldom enough not to mess up the record yet often enough to furnish distinct labels. It is even better than that. The text is not just arbitrary.[…] It follows from the fact of Darwinian evolution that everything about an animal or plant, including its bodily form, its inherited behaviour and the chemistry of its cells, is a coded message about the worlds in which its ancestors survived. […] The message is ultimately scripted in the DNA that fell through the succession of sieves that is natural selection. When we learn to read it properly, the DNA of a dolphin may one day confirm what we already know from the telltale giveaways in its anatomy and physiology: that its ancestors once lived on dry land. Three hundred million years earlier, the ancestors of all land-dwelling vertebrates, including the land-dwelling ancestors of dolphins, came out of the sea where they had lived since the origin of life. Doubtless our DNA records this fact if we could read it.”

EJ – 19.02.2008
© BIOPRO Baden-Württemberg GmbH


  • Desoxyribonucleic acid (DNA) is a double-stranded, helical macromolecule encoding the genetic information of an organism.
  • A gene is a hereditary unit which has effects on the traits and thus on the phenotype of an organism. Part on the DNA which contains genetic information for the synthesis of a protein or functional RNA (e.g. tRNA).
  • Being lytic is the feature of a bacteriophage leading to the destruction (lysis) of the host cell upon infection.
  • There are two definitions for the term organism: a) Any biological unit which is capable of reproduction and which is autonomous, i.e. that is able to exist without foreign help (microorganisms, fungi, plants, animals including humans). b) Definition from the Gentechnikgesetz (German Genetic Engineering Law): “Any biological unit which is capable of reproducing or transferring genetic material.“ This definition also includes viruses and viroids. In consequence, any genetic engineering work involving these kinds of particles is regulated by the Genetic Engineering Law.
  • Genetic sequences are successions of the bases adenine, thymine, guanine, and cytosine on the DNA (or uracil instead of thymine in the case of RNA).
  • Biochemistry is the study of the chemical processes in living organisms. Therefore it touches the studies of chemistry and biology as well as physiology.
  • Molecular means: at the level of molecules.
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