The concept of species and the classification of living things

The public is increasingly bombarded by mass media messages about the need to protect the environment and the species it supports. But are we sure the concept of species is understood, and that modern classification of living things is sufficient to provide a clear understanding of what is being proposed?

I believe it is essential to clarify at least the modern concept of species and provide the foundations of the classification of living things, to provide the non-specialist public with the correct interpretative keys, so that they can validly evaluate the information they receive.

In biology, the concept of species has completely changed since the Darwinian revolution, and since it is impossible to have a clear vision of the history of life and the very definition of an organism, I believe it is essential to grasp this fundamental concept. When Carl von Linné (1707-1778) proposed his classification system in 1735, species were considered fixed and immutable. Organisms that shared the same morphological characteristics were considered to belong to the same species.

Image: Key to the Sexual System (from the 10th edition of Systema Naturae, 1758)

This initial definition of species was subsequently refined to incorporate the definition provided by the authors of the new synthesis. For them, the criterion for distinguishing between species is reproductive isolation. In practice, individuals that share the same genetic heritage belong to the same species and are therefore reproductively isolated. The concept of reproductive isolation does not necessarily imply sterility between different species, but rather the existence of isolating mechanisms that make mating virtually impossible. 

This definition already appears more satisfactory than the previous one, but not entirely. The crucial problem, which taxonomists have debated for over a hundred years, clearly highlighted for viruses by Eigen and subsequently extended by Dawkins to all living things, is that the concept of species is a naturalist's artifice. If we are dealing with two organisms that meet the definitions above, the scholar will ascribe them to the same species, but this does not mean that they actually share their entire genetic heritage. The incessant work of natural selection on intraspecific mutations and the variability present in populations will continually produce differences that, however imperceptible, will further differentiate the different populations we ascribe to the same species. 

While these variations will be continually remixed among members of the same population, the differences between isolated populations will continually increase. Indeed, if we broaden the definition of species over time, we realize that we are defining organisms that share less and less of their genetic heritage. This, which we might call a conceptual revolution, has led, together with the increase in knowledge derived from genetics, to an overturning of classifications, previously based primarily on morphology and anatomy, and in which all living things were still divided into two kingdoms, animal and plant, as had been done by Carl von Linné, the man who constructed the first classification of living things based on scientific data and who invented the binomial system still used today. 

It is true that the first who had proposed to adopt a binomial system was Frederick II of Swabia in his work De arte venandi cum avibus, but in the scientific field it is not enough to propose but it is necessary to develop rationally and justify objectively. 

 
Image: De arte venandi cum avibus

Furthermore, unfortunately, even today it happens that the evolutionary scheme of living things is presented as a progressive ladder at the top of which is Man, while Darwin had already presented it as a coral with different branches joining at the base, to represent what is defined by the acronym LUCA (Last Universal Common Ancestor).

Despite advances in biological knowledge, the description of thousands of new species, and the discovery of bacteria, the division of living things into animals and plants persisted for decades until recently. However, as early as 1894, Ernst Haeckel had proposed distinguishing unicellular organisms, which he called protists, from plants and animals. About a century later, in 1895, Herbert Copeland proposed distinguishing bacteria from other prokaryotes, calling them monera. 
 
     Image: The Tree of Life by Ernst Haeckel, 1866

A refinement of the classifications took place in 1969, by Robert Whittaker who, based on the studies of Lynn Margulis, in turn inspired by the proposals of Ernst Haeckel and Herbert Copeland and corroborated by his studies on endosymbiosis, of which it was the first and greatest theorist, had divided living things into five Kingdoms: the Monera, that is, prokaryotic organisms, that is, without a cellular nucleus, which have a single circular chromosome. At that time, the only representatives of that Kingdom were Bacteria, discovered in the eighteenth century by Antoni van Leeuwenhoek; the Protists, eukaryotic organisms, that is, those which have a true nucleus and which, since their discovery in the eighteenth century by the first microscopists, such as van Leeuwenhoek, were "forcibly" inserted into the Kingdoms then recognized, that is, that of Plants and that of Animals; the Plants, autotrophic organisms, that is, capable of feeding on inorganic matter; the animals, heterotrophic organisms, and the Fungi which, despite being heterotrophic, have absolutely peculiar characteristics and origins. 

Image: Artist's impression of Wittaker's classification

The classification of living things, however, was still based mainly on morphological and anatomical characteristics.

In 1950 a German entomologist, Willi Hennig, published his book Grundzüge einer Theory der phylogenetischen Systematik, in which he proposes a new classification methodology. This book receives very little attention. The bombshell was to explode a few years later, in 1966, when it was published in English by the University of Illinois Press, under the title Phylogenetics Systematics. This is the birth of cladism. Hennig intends to redefine the way systematists work. 

He revisits the phylogenetic trees proposed by Haeckel over a hundred years earlier, not relying on fanciful constructions, but defining procedures and criteria that taxonomists must adhere to in phylogenetic reconstruction. Although his arguments exhibit a certain logical-mathematical rigor, their practical implementation proves flawed. Equally flawed is his idea that each founder species must give rise to two daughter species, from which two additional species arise with each speciation event. 

An important contribution to systematics made by Hennig is the concept that phylogenetic reconstruction must rely exclusively on the recognition of synapomorphies (the shared possession of plesiomorphic, or original, characteristics), and not symplesiomorphies (the possession of apomorphic, or derived, characteristics). According to cladists, the reconstruction of kinship levels boils down to the simple translation of kinship relationships into hierarchical terms, which can be represented graphically in a phylogenetic tree. 

Therefore, each classification level, from phylum to species, must necessarily have a sister taxon, defined as a sister group by Hennig himself and adelphotaxon by Peter Ax. Obviously, each level of taxa must be monophyletic; in fact, each must include only forms derived from the founder. This leads to the rejection of both paraphyletic taxa (taxa that, while including species with common ancestors, do not include all of them) and polyphyletic taxa (i.e., including species originating from different ancestors). 

This systematic methodology, besides treating speciation as a mathematical artifice, ignores a fundamental aspect of the problem: evolution cannot be reduced to cladogenesis (speciation), because adaptation, the overcoming of ecological problems experienced by previous generations, and the occupation of newly available ecological niches (adaptive radiation) are also crucial. Cladism is currently widespread among systematists but will inevitably be refined or replaced with the progressive development and refinement of genetic methodologies.

In 1977, Carl Woese and George Edward Fox published a study based on a comparative analysis of the 16s ribosomal sequences of the RNA subunit of species. In this context, Woese discovered a new Kingdom, the Archaea, prokaryotic organisms completely different from Bacteria and with unique characteristics. In 1990, Woese completed his analysis and proposed the currently adopted classification, which divides living things into three Kingdoms, or rather, Domains: Bacteria, Archaea, and Eucarya.

The latter include all eukaryotic organisms of which Plantae, Animalia and Fungi constitute only branches. 

 

            Image: Phylogenetic tree of living things based on the sequences of the 16s ribosomal subunit of RNA (Carl Woese, 1990)

In 2003, Thomas Cavalier-Smith established a further Domain, that of Chromista, based on some peculiar characteristics: the presence of the periplastidial reticulum located between the two "valves" of the chloroplast and the two external membranes, the presence of chlorophyll α and c. Furthermore, the chloroplast is characterized by being formed, in addition to the two typical membranes, by two external membranes connected to the nucleus. 

This would be due to secondary endosymbiosis caused by the ingestion of a unicellular red alga into another eukaryotic organism. It should be noted that the Domain Chromista is not accepted by most systematists, as it includes polyphyletic organisms, belonging not only to the Protists but also to the lower Fungi: this leads one to believe that these are more likely cases of convergent evolution.