2.2 Viruses: A Special (Unresolved) Case
Viruses are not usually considered to be living entities and therefore do not have a kingdom of their own. This, however, is a hotly debated topic. For example, although Moreira and Lopez‐Garcia (2009) argue strongly against viruses being living entities, Koonin and Starokadomskyy (2016) consider the very question of whether viruses are alive to be unscientific because the definition of what one means by life is arbitrary. Didier Raoult and his co‐workers argue that the giant viruses called nucleocytoplasmic large DNA viruses (NCLDVs) should be considered as an additional distinct domain of living organisms (Boyer et al. 2010). NCLDVs are so large that they can be mistaken for bacteria, and their genomes are typically twice the size of other viruses. The suggestion that a specific group of viruses might be living organisms has generated a great deal of controversy for which no resolution is in sight. Nevertheless, phylogenetic analysis suggests that NCLDVs evolved before modern eukaryotes, that is, before the organisms that are their current hosts. Furthermore, they may have been the source of two DNA‐dependent RNA polymerases and a DNA topoisomerase that are found in modern eukaryotes (Guglielmini et al. 2019).
2.3 Taxonomic Hierarchy
Kingdoms are subdivided into units or taxa (singular taxon) such as class, family, genus (Table 2.1). There are no rules about how many species constitute a genus, how many orders constitute a class, or whether families are divided into subfamilies. However, it is essential that a ‘taxon’ forms a natural grouping. Consequently, research, especially molecular phylogeny, causes taxonomists to re‐arrange the hierarchy of individual species and groups of organisms on a regular basis. A class, family or any other category within one group of organisms is therefore not evolutionarily comparable with those in another group.
Table 2.1 The taxonomic hierarchy with specific reference to the sheep nasal bot fly Oestrus ovis.
| Taxonomic division | Taxon name | Common name |
| Kingdom Subkingdom Branch Infrakingdom Phylum Subphylum Class Infraclass Division Subdivision Superorder Order Suborder Superfamily Family Subfamily Genus Subgenus Species Subspecies | Animalia Bilateria Protostomia Ecdysozoa Arthropoda Hexapoda Insecta Pterygota Neoptera Endopterygota Panorpita Diptera Cyclorrhapha Oestroidea Oestridae Oestrinae Oestrus ovis, Linnaeus, 1758 | Animals Moulting invertebrates Insects and related species Insects Winged insects True flies Higher flies |
Not all taxonomists agree on the appropriate division for a grouping (taxon). For example, some workers consider there to be two suborders of Diptera: the Nematocera and the Brachycera and that the term Cyclorrhapha should be considered a division of the Brachycera rather than a suborder. Note that only the genus name and lower taxonomic descriptors are placed in italics.
The International Commission on Zoological Nomenclature (ICZN) provides rules on legal aspects of nomenclature (e.g., precedence). However, it is not unusual for workers to continue using old names that have been superseded or to fail to agree on an accepted single name. For example, the blowflies known as Lucilia cuprina and Lucilia sericata within the United Kingdom and Europe are often called Phaenicia cuprina and Phaenicia sericata by workers in the United States.
2.3.1 The Binomen System
All organisms (apart from viruses) have a two‐part name, or binomen – hence, the term binomial nomenclature. The two parts consist of the generic (or genus) name and the trivial name (also called the specific epithet or specific name).
The trivial name may be followed by the naming authority, i.e., the name of the person who first described the organism, along with the date the description was published – this is placed in brackets.
| Italics | ‘normal’ script |
Ascaris lumbricoides (Linnaeus, 1758)
| Genus | specific epithet | naming authority |
Genus + specific epithet = the binomen, also called the ‘species name’.
Surprisingly, there is no universally accepted definition of what is meant by the term ‘species. Indeed, there are currently over 20 different definitions. Furthermore, over the course of thousands of years, there is never a single point at which one species becomes two: it is like attempting to identify the day one ceases being a child and becomes an adult. To further complicate matters, some species have distinct forms that are called sub‐species, and these are distinguished through the use of trinomens. For example, the human body louse Pediculus humanus humanus and the head louse Pediculus humanus capitis are usually distinguished as separate sub‐species. However, for many years there has been a debate about whether the reported differences in their morphology and behaviour are consistent enough to justify them being considered closely related sub‐species or separate species in their own right. Current molecular evidence suggests that they are morphotypes of a single species (Light et al. 2008). Similarly, there are two physiological variants of the mosquito Culex pipiens: Culex pipiens pipiens, which bites only birds, and Culex pipiens molestus, which only bites humans. The two variants of Culex pipiens cannot be differentiated morphologically. They can be crossed in the laboratory, but, in the United Kingdom, the populations remain genetically isolated in the wild. Distinguishing between the variants is important because this mosquito can act as a vector for the potentially fatal West Nile Virus, and therefore its biting behaviour has a major impact on whether the disease spreads from birds to humans.
The difficulty of differentiating between species and sub‐species can give rise to ‘taxonomic inflation’ in those groups that are particularly well studied. For example, ant taxonomists tend not to recognize sub‐species, so everything is separated at the species level. By contrast, butterfly taxonomists are enthusiastic users of trinomens. Not surprisingly, this often results in ecological surveys revealing a greater species diversity of ants than butterflies.
Some scientists state that the increasing use of the phylogenetic concept of species rather than the older biological species concept is driving taxonomic inflation. The traditional biological species concept operates on the premise that two organisms should be considered different species if either they are incapable of mating or, if they do mate, then their progeny are infertile. Allowances have to be made for the likelihood of gene flow between populations. For example, the fact that tigers and lions can hybridise does not mean that they are the same species, as this would never happen in the wild. By contrast, the phylogenetic species concept is based on the observation that separate populations of organisms often have distinct inheritable differences (for example, a colour pattern or the size of a body part). What constitutes an inheritable difference sufficient to qualify a population as a ‘species would depend upon the views of the taxonomist. The increasing use of DNA analysis by taxonomists has undoubtedly contributed to the popularity of the phylogenetic species concept, because it often identifies differences in gene sequences between populations. Some workers have suggested that the adoption of a phylogenetic species concept can result in up to 48% more species than the biological approach