Phylogenetics

History

Classification of the natural world into meaningful and useful categories has been a basic human impulse, and is systematically evident at least since time of ancient Greece. Dominant for close to 2,000 years in the West was the notion of a “great chain of being” or scala natura, which emphasized a static notion of reality and depicted a hierarchy or ascending ladder starting from matter and nature (such as rocks) and moving upward to humans, angels, and eventually and highest of all, God. Since Linnaeus, and especially since Darwin, classificatory schemes have not only quickly put aside such notions as the scala natura, but have also slowly moved away from postulating relationships between species based on either presumed essential traits or based on overall similarity. The field of phylogenetics takes a functional and more scientific turn in its attempts to construct an ever-more objective depiction of ancestral and evolutionary relationships between organisms based on derived similarities found via the integration of genetic, molecular, archaeological and historical studies and with the specific purpose of explaining, predicting, and testing similarities and differences between organisms, and specifically between groups of organisms or species.

The Tree of Life

Ancestral relationships among species are commonly represented as phylogenetic trees (also called cladograms or dendrograms). A cladogram is most significantly a physical representation of a hypothesis of inferred relationship between species. The evolutionary relatedness between species is reflected by branching pattern of the tree, and specifically, the represented distance between species on the tree. Any two species will have a common ancestor at the point where their respective branches are traced back to intersect. The more recent a common ancestor to humans, the more likely it is more related to humans. For example, the common ancestor of modern humans and (now extinct) Neanderthals would be traced back to approximately 500,000 years ago. Similarly, the common ancestor of humans/Neanderthals and chimpanzees existed approximately 6.5 million years ago. Thus, since humans and Neanderthals share a common ancestor not shared by chimpanzees, we have reason to believe that humans are more closely related to Neanderthals than to chimpanzees. Similar retracing can be done farther and farther back on the branches of the tree of life to connect the common ancestry humans have with unicellular species some billions of years ago.

Estimating Relatedness

Cladograms can be constructed with the aid of technologies that estimate molecular divergences in key sequences of DNA or protein amino acids.

Similar to the progress seen in estimating the age of organic substances with the use of radioactive decay technologies and carbon dating, the advent of [Page 1379]molecular biological technologies in the later half of the 20th century have increasingly allowed scientists to accurately estimate the degree of evolutionary relatedness at the genetic level. Taking two homologous DNA sequences in different species, one can estimate evolutionary distance by measuring the number of nucleotide substitutions that have occurred over time. Alternatively, using protein products of DNA expression, one can measure the number of amino acid substitutions that have occurred between homologous protein sequences. A number of statistical and computational methods have been developed to account for biases in point mutation substitution rates in target DNA or protein sequences, for example, that transitions (nucleotide substitutions between purines [A/G] or between pyrimidines [C/T]) occur at greater rates than transversions (substitutions between purines and pyrimidines).

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