DNA: The New Taxonomic Platform


With increasing implication of DNA sequencing in paleontological and evolutionary studies, the science of classifying fossilized species is poised toward a new taxonomic platform namely the DNA. In case of enigmatic fossils that are hard to classify by traditional morphological standards, DNA taxonomy emerges as the sole criterion to establish evolutionary connections between different species of fossils including human beings.

The science of paleontology and evolutionary biology is witnessing a new turn in the course of its understanding through discoveries on a microscopic level. Fossilized organisms are being related through closer linkages by using detailed studies of one single molecule-the DNA. As DNA sequencing finds greater implication in relating fossilized species, the science of taxonomy approaches closer to facing a new question of fundamental import: will DNA be the next taxonomic platform for defining ‘species’?

The conventional definition of a ‘species’ has been ‘a group of individual organisms that can successfully interbreed to produce fertile offspring’. The basis of identifying species has centered mainly on morphological and anatomical resemblance. Owing to the advances in genetics, this definition of species has been modified more recently to include genetic resemblance as well. Thus we come to think of species as a group of individual organisms that bear close mutual resemblance in morphological, anatomical, and genetic characteristics, and are able to interbreed successfully to produce fertile offspring.

However, when classifying fossilized organisms as belonging to the same species, it is not possible to verify their ability of successfully interbreeding and producing fertile offspring. Paleontologists have based all their classifications on the basis of resemblance in morphological characteristics. The species thus identified among fossils are more precisely termed as ‘typological species’. Fossilized organisms are placed in different typological groups on the basis of certain ‘fixed’ properties. The problem with this concept of ‘species’ is the fact that all organisms bearing morphological differences may not be different species, e.g. a four-winged Drosophila fly descending from a two-winged mother. And yet, paleontologists had to rely on typological characters of the fossil specimens for comparison and categorization up to the species level.

The last two decades saw some remarkable technological advances in genetics, including the ability to extract and sequence DNA from fossils. The ordering of the base pairs in DNA were quickly put to use for establishing evolutionary relations among different groups of organisms that appeared to have had common ancestors. By the late 1990s, study of the mitochondrial DNA had been employed to trace the evolutionary course of Neanderthals. Lately, another leap in genetic research technology has enabled scientists to sequence nuclear DNA that not only reveals more of the biology of Neanderthals but also serves as an evolutionary clock with a record of the time when the ancestors of Neanderthals and humans diverged.

Using the more sophisticated technique of pyrosequencing, a team of researchers led by Richard Green directly sequenced the DNA extracted from a 38, 000-year-old Neanderthal femur found in a cave in Croatia. Pyrosequencing increases the amount of fossil DNA, processed for the purpose of studying, by about 100 times as compared to the more ‘classical’ method of DNA sequencing called metagenomics. Accordingly, the divergence time for the ancestors of humans and Neanderthals, as calculated by pyrosequencing (500, 000 years), is some 130, 000 years farther in the past than that worked out by metagenomics (370, 000 years). The evolutionary changes occurring in these 130, 000 years can be predicted only by means of DNA sequencing. The rarity of well-preserved large fossils, like those of higher vertebrates including humans, demands a meticulous analysis of one single fossil (or its fragment) for drawing taxonomic relations. DNA structure seems to be the ideal parameter for the purpose of such a classification.

Another ‘taxonomic pressure’ in the direction of DNA-based classification of species is the difficulty in tracing the exact evolutionary linkages of certain living forms due to the remarkable similarity among their fossilized parts. Fossils of the cat family are such a case. They are very hard to classify into different species groups because most of them differ just in size. Only the DNA data acquired over the past ten years or so has made it possible to distinguish between various groups of fossilized cats. By analyzing the DNA of the 37 living species, a new evolutionary history of the family Felidae has been researched by Warren E. Johnson and Stephen J. O’Brien and their colleagues.

Basing taxonomic relatedness on the ordering of DNA’s base pairs overcomes one other hurdle that can hamper the exact categorization of fossil organisms-the problem of ‘evolutionary masking’. While competing for life resources in the same area, genetically unrelated groups of organisms may develop very similar physical features which, if preserved, can mislead paleontologists to place them in the same taxonomic category. One of the living examples of such competitor species is the case of Geospiza fortis (Darwin’s finch species) and its competitor species Geospiza magnirostris. Only the large-beaked members of G. fortis population are capable of feeding on seeds of Tribulus cistoides, the principle food of G. magnirostris. Due to depletion in the supply of Tribulus cistoides, there has been a shift in the direction of a small beak size in G. fortis in areas where the two species are in competition. Such natural mimicking of physiological characters by members of different species may baffle the paleontologist in classifying fossilized organisms on the basis of morphology. DNA sequencing, on the other hand, provides a more detailed map of similarities and differences among the genetic characters of organisms.

As the genetic blueprints of both living and fossil species are being explored in greater detail by DNA sequencing, both evolutionary biology and taxonomy appear to rest increasingly on the genetic platform that itself stands on the study of a single, yet vital, molecule. In one corner of this emerging taxonomic platform is a bridge between the evolutionary divergences of different species groups. On the other end is a reshuffling of the scientific understanding of the term ‘species’ and ‘evolutionary kinship’. Perhaps the adage of ‘deceptive appearances’ has finally started shaking our consciousness in the direction of singling out genetic commonalities as the sole criterion for the purpose of redefining taxonomic categories.


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