Systematics as the Language of Agricultural Science

2.1. Taxonomy and Systematics: Part and Whole

Let us begin with the broadest concept. Systematics (from Greek systema — an organized whole) is the science of biological diversity and all aspects of its study. In the classic definition of George Gaylord Simpson, cited by both Stuessy (Stuessy, 2009) and Judd and coauthors (Judd et al., 2018), systematics is “the scientific study of the kinds and diversity of organisms and of any and all relationships among them” (Simpson, 1961: 7). This definition is so broad that it includes not only classification but also the study of evolutionary processes, population variability, hybridization, biogeography, and much else.

Modern systematics, as Pandey and Kasana write (Pandey & Kasana, 2021), includes several closely related divisions: taxonomy, nomenclature, and phylogenetics. Thus, systematics is an umbrella term denoting the entire set of disciplines studying the diversity of life.

Taxonomy is a narrower concept. The term was introduced in 1813 by Augustin Pyramus de Candolle, who formed it from the Greek words taxis (order, arrangement) and nomos (law, rule) (Pandey & Kasana, 2021). In the most general sense, taxonomy is the theory and practice of classifying organisms. As Stuessy writes (Stuessy, 2009), taxonomy deals with “methods and principles of classification.” It includes description, identification, nomenclature, and classification itself — four components often remembered by the abbreviation DINC (Description, Identification, Nomenclature, Classification) (Pandey & Kasana, 2021).

It is important to understand the relationship: systematics is broader than taxonomy. A systematist, in addition to classification tasks, studies evolutionary processes, phylogeny, and speciation. A taxonomist, by contrast, focuses on developing principles for constructing classifications and rules for naming taxa. In English-language literature, this distinction is sometimes emphasized by calling systematics a “broader discipline” and taxonomy its “theoretical core” (Pavlinov, 2021).

2.2. Classification: Process and Result

Classification is one of the central concepts. Stuessy (Stuessy, 2009) defines it as “the placement of an object in a logically organized scheme of relationships.” Judd and coauthors (Judd et al., 2018) clarify: it is “the process and result of ordering organisms into groups based on their similarities and differences.”

Classification is a two-stage process (Pandey & Kasana, 2021):

1. Grouping — combining objects into groups based on similarities and differences.

2. Ranking — arranging these groups into a hierarchical system of subordinate categories.

The result of classification is a system — a hierarchically organized set of taxa. Classification can be:

• Artificial — based on arbitrarily chosen, convenient characters (e.g., Linnaeus’s sexual system, based on the number of stamens).
• Natural — reflecting the maximum number of characters and, ideally, evolutionary relationships (Stuessy, 2009).

It is important to emphasize: classification is a hypothesis about the structure of diversity, not an eternal truth. As Stuessy writes, “classifications are conventions, not the workings of nature; we decide what groups we want to talk about” (Stuessy, 2009: 62).

2.3. Phylogeny: The History of Evolutionary Relationships

Phylogeny is the evolutionary history of a group of organisms, the sequence of divergence events and associated changes (Judd et al., 2018). Phylogeny describes kinship relationships between organisms: who is more closely related to whom, who descended from whom.

The key difference between classification and phylogeny is that phylogeny is a reconstructable history, while classification is a system we create on the basis of that history (or, in the case of artificial systems, without it). Phylogeny exists objectively, as a fact of the past, although our knowledge of it is always incomplete and hypothetical. Classification, by contrast, is a human construction that may correspond to phylogeny to a greater or lesser degree.

In modern systematics, the phylogenetic approach dominates, according to which classification should reflect phylogeny (Judd et al., 2018). This means that we should recognize only monophyletic groups — groups consisting of an ancestor and all its descendants. Groups that do not satisfy this condition (paraphyletic and polyphyletic) are considered unacceptable in phylogenetic classification.

The relationship of concepts can be represented as follows:

Phylogeny → (reconstruction) → Classification → (nomenclature) → Names of taxa

Phylogeny is reconstructed on the basis of character analysis (morphological, molecular, etc.) using cladistic methods. Classification is built on the basis of phylogeny by recognizing monophyletic groups and assigning ranks to them. Nomenclature provides these groups with universal scientific names.

2.4. Identification: Determining Belonging

Identification is the process of determining to which known taxon a given organism belongs (Stuessy, 2009). Unlike classification, which creates a system, identification uses an already existing system to determine a specific object.

Imagine a herbarium specimen of an unknown plant. You want to know its name. You use a key that step by step leads you to the correct taxon. This is identification. As Stuessy writes, “if someone goes outside, picks a twig with leaves, brings it to the laboratory, and tries to find a name, they are seeking identification of the specimen, not classification” (Stuessy, 2009: 9).

Identification can be carried out in several ways (Pandey & Kasana, 2021):

• Comparison with reference specimens in a herbarium or collection.
• Use of identification keys (dichotomous, polytomous).
• Consultation with a specialist systematist.
• Use of molecular methods (DNA barcoding).

Key difference: classification creates a system; identification places a specific object into it. The former is a theoretical task; the latter is practical.

2.5. Nomenclature: Rules of Naming

Nomenclature is the system of rules and agreements regulating the assignment of scientific names to taxa (Stuessy, 2009). Nomenclature does not decide which groups to recognize — that is the task of classification. It decides how to name these groups.

Basic principles of nomenclature:

1. Binary nomenclature — each species is designated by two words: the genus name and the species epithet (e.g., Triticum aestivum). This is Carl Linnaeus’s invention, introduced in 1753 in Species Plantarum (Timonin, 2009).

2. Principle of priority — the first published name of a taxon is considered correct if it does not contradict the rules (Timonin, 2009).

3. Typification — each name is tied to a type specimen (holotype, lectotype, etc.), which serves as the standard for applying the name (Stuessy, 2009).

4. Latin language — scientific names must be Latin or Latinized (Timonin, 2009).

Nomenclature is regulated by international codes: for plants and fungi — the International Code of Nomenclature for algae, fungi, and plants (ICNafp); for animals — the International Code of Zoological Nomenclature (ICZN); for viruses — the International Code of Virus Classification and Nomenclature (ICVCN) (Pandey & Kasana, 2021).

It is important to understand: nomenclature does not determine the circumscription of taxa. It only provides rules for assigning names. The boundaries of taxa are the subject of classification.

2.6. Taxon and Taxonomic Categories

We have approached perhaps the most important distinction. A taxon is a really existing group of organisms recognized as a result of classification. A taxonomic category (rank) is a level in a hierarchical system to which a taxon is assigned.

Timonin (2009) emphasizes: taxa are not arbitrary groupings. They “are a natural element of biological diversity arising in the course of its evolutionary development” (Timonin, 2009: 5). Taxa exist really, regardless of whether we can recognize them or not. The task of the scientist is to discover a taxon in nature, not to construct it.

Main taxonomic categories (Timonin, 2009; Pandey & Kasana, 2021):

The difference between taxon and category can be explained as follows: a category is a position; a taxon is the person occupying that position. “Species” is a category. Triticum aestivum is a taxon belonging to the category “species.” “Genus” is a category. Triticum is a taxon belonging to the category “genus.”

In addition to the main categories, intermediate categories are used: subspecies (Subspecies), variety (Varietas), form (Forma), as well as superorder (Superordo), subclass (Subclassis), etc. (Timonin, 2009).

2.7. Organism, Species, Taxon, Name: Four Different Entities

Now that we have examined the basic concepts, let us formulate the key principle that will run through our entire course.

Organism ≠ Species ≠ Taxon ≠ Name.

1. Organism — a concrete individual existing in space and time. This is a real biological object.

2. Species — a biological concept, a hypothesis about a group of organisms possessing common properties (interbreeding, common range, similarity of characters). A species is a taxon of a certain rank, but not the organism itself.

3. Taxon — a formal group in classification that may include one or several species (or other taxa of lower rank).

4. Name — a nomenclatural label tied to a taxon through typification. A name is not the taxon itself, but only its designation.

Important practical conclusions follow from this (Stuessy, 2009; Hyam, 2015):

• One name may designate different taxa. If two different researchers put different circumscriptions into the same taxon (e.g., understand a species broadly or narrowly), the same name may refer to different groups of organisms. This is the problem of “taxonomic concepts.”
• The same taxon may have different names. If a taxon was described under different names by different authors, the principle of priority applies — the oldest available name is chosen.
• A name is not a definition. Knowing a name does not replace knowing the characters of a taxon. A name is a key to information, but not the information itself.

Hyam (Hyam, 2015) illustrates this with an example: if an ecologist wants to combine data from two studies, one using the name A and the other using B, they cannot automatically assume that they refer to the same taxon. Only by knowing the taxonomic concepts used by the authors can one make the correct decision. This is the practical consequence of distinguishing name and taxon.

2.8. Relationship of Concepts: Final Scheme

Let us sum up. All the concepts considered are related as follows:

Systematics — the broadest discipline, studying diversity and all relationships among organisms.

Taxonomy — the part of systematics dealing with the theory and practice of classification.

Classification — the process and result of ordering organisms into a hierarchical system of taxa.

Phylogeny — evolutionary history, which is reconstructed and serves as the basis for phylogenetic classification.

Identification — the practical determination of an organism’s belonging to a known taxon using an existing classification.

Nomenclature — the rules for assigning names to taxa.

Taxon — a real group of organisms recognized in classification.

Category — the rank to which a taxon is assigned.

Name — a nomenclatural label of a taxon.

This scheme is the conceptual framework on which we will string all subsequent content. Understanding these distinctions is necessary for professional work. As we will see in the next chapter, the historical development of systematics consisted precisely in the gradual realization of these distinctions and in the development of increasingly precise methods for reconstructing phylogeny and constructing classifications.

3.1. The Pre-Linnaean Period and Linnaeus’s Artificial System

The first attempts to classify plants go back to antiquity. Theophrastus (c. 370–285 BCE) divided plants by life forms: trees, shrubs, subshrubs, and herbs (Stuessy, 2009). In the Renaissance, with the development of printing, “herbals” appeared — descriptions of medicinal plants, often arranged alphabetically. These classifications were artificial: they were based on one or several arbitrarily chosen characters, convenient for identification but not reflecting natural kinship (Judd et al., 2018).

The apex of artificial systematics was the sexual system of Carl Linnaeus (1707–1778). In his works Systema Naturae (1735) and Species Plantarum (1753), Linnaeus divided all plants into 24 classes based on the number, arrangement, and fusion of stamens (Stuessy, 2009). For example, the class Monandria included plants with one stamen, Diandria — with two, and so on. Orders within classes were distinguished by the number of pistils or stigmas.

Linnaeus’s system was extremely convenient for identification: even a novice could quickly identify a plant simply by counting stamens and pistils. However, it often united completely unrelated plants in one group. For example, the class Diandria included lilac, maize, and many other species far from one another (Judd et al., 2018). Linnaeus himself understood the artificiality of his system and strove to create a “natural” system, which he considered the highest goal of botany, but did not manage to develop it.

Despite its artificiality, Linnaeus’s contribution to systematics is enormous. He introduced binary nomenclature — a system in which each species is designated by two words: the genus name and the species epithet (Timonin, 2009). This ensured the universality and stability of scientific names. It is from Species Plantarum (1753) that priority of names is counted for most groups of plants (Timonin, 2009). Linnaeus also standardized the use of Latin and introduced clear rules for describing species.

3.2. Evolutionary Systematics: From Darwin to the Mid-20th Century

The publication in 1859 of Charles Darwin’s On the Origin of Species produced a revolution in systematics. Darwin showed that the similarity of organisms is due to common descent, not to a divine plan. He wrote: “The natural system is founded on descent with modification; that the characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent” (Darwin, 1859: 420, cited in Stuessy, 2009).

After Darwin, systematists realized that classification should reflect phylogeny — evolutionary history. However, methods for reconstructing phylogeny remained intuitive. Systematists distinguished “primitive” and “advanced” characters on the basis of their own experience, built phylogenetic trees, but had no strict criteria for distinguishing homology from homoplasy (Judd et al., 2018).

In this period, large phylogenetic systems appeared, such as the system of the German botanist Adolf Engler (1844–1930), who considered plants with unisexual, wind-pollinated flowers (the so-called “amentiferous” — Amentiferae) to be the most primitive, and the system of the American botanist Charles Bessey (1845–1915), who, by contrast, placed Ranunculaceae with their numerous spirally arranged flower parts at the base of the system (Stuessy, 2009). Both systems were phylogenetic in intention, but their phylogenies were not strictly tested.

The systems of the 20th century — those of Arthur Cronquist, Armen Takhtajan, Rolf Dahlgren — were also evolutionary. They took into account many characters (morphology, anatomy, chemistry, cytology) and strove to reflect kinship relationships. However, they still allowed the recognition of paraphyletic groups — groups including a common ancestor but not all its descendants. For example, “dicotyledons” (Dicotyledones) were traditionally considered a natural group, but, as we now know, they are paraphyletic with respect to monocotyledons (Judd et al., 2018).

3.3. Phenetics: An Attempt at Objectivity

In the 1950s–1960s, phenetics (or numerical taxonomy) arose, associated with the names of Robert Sokal and Peter Sneath. Pheneticists proposed a radically new approach: classification should be based on overall similarity, measured quantitatively across the maximum possible number of characters, without a priori weighting (Stuessy, 2009). They believed that evolutionary considerations introduce subjectivism and strove for objectivity and reproducibility.

Pheneticists used computers to calculate similarity coefficients between organisms and construct phenograms — dendrograms reflecting the degree of overall similarity. However, phenetics encountered a problem: different clustering algorithms gave different results, and it was unclear which was “more correct.” Moreover, overall similarity does not necessarily reflect phylogeny: convergent characters can make unrelated organisms similar. In the end, phenetics did not become the basis for large classifications, but its methods (e.g., cluster analysis) entered the arsenal of systematics (Pavlinov, 2021).

3.4. Cladistics: Strict Phylogeny

A true revolution in systematics was accomplished by the German entomologist Willi Hennig (1913–1976). In his book Phylogenetic Systematics (1966), he formulated the principles of cladistics — a method of reconstructing phylogeny based on synapomorphies (shared derived characters) (Judd et al., 2018).

Hennig argued that only monophyletic groups (classes including an ancestor and all its descendants) should be recognized in classification. Paraphyletic and polyphyletic groups should either be expanded or divided. Synapomorphies are used to determine monophyly: if two taxa have a shared derived character inherited from a common ancestor, they form a monophyletic group.

Cladistic analysis includes the following stages (Pavlinov, 2021):

1. Selection of taxa (operational taxonomic units, OTUs).

2. Selection of characters and determination of their states (primitive/derived).

3. Coding of characters into a matrix.

4. Construction of a cladogram using the principle of parsimony (minimizing the number of evolutionary changes).

5. Assessment of node support (bootstrap, jackknife).

Cladistics gave systematists a strict, reproducible method for constructing phylogenies. However, its application to morphological data was limited: the number of characters is small, and homoplasy (parallelisms, convergences, reversals) can distort the picture. As Pavlinov notes (2021), cladistic analysis requires a large number of characters, which is difficult to provide in comparative morphological studies.

3.5. The Molecular Phylogenetic Revolution

A real breakthrough occurred at the end of the 20th century with the development of molecular biology methods. DNA sequencing made it possible to obtain huge arrays of data on nucleotide sequences. Initially, individual genes were used (e.g., rbcL for plants), then whole genomes (Judd et al., 2018). Molecular data have a number of advantages:

• A huge number of characters. A sequence of 1000 base pairs contains 1000 characters, which is orders of magnitude more than available from morphology.
• Direct reflection of the genotype. Molecular characters are less subject to convergent evolution than morphological ones.
• Possibility of comparing unrelated organisms. Universal genes (e.g., rRNA) are present in all living beings.

The molecular revolution led to a revision of classifications of all groups of organisms. In botany, the key role was played by the Angiosperm Phylogeny Group (APG). Beginning in 1998, APG published a series of classifications (APG I, 1998; APG II, 2003; APG III, 2009; APG IV, 2016) based on molecular phylogenetic analysis (APG IV, 2016).

The APG IV classification (2016) recognizes 64 orders and 416 families of angiosperms. It differs radically from traditional systems:

• “Dicotyledons” are not recognized as a formal group because they are paraphyletic. Instead, eudicots, superrosids, superasterids, etc., are recognized.
• Many families have been revised. For example, Asphodelaceae replaces Xanthorrhoeaceae, Francoaceae includes Melianthaceae and Vivianiaceae (APG IV, 2016).
• New orders: Boraginales, Dilleniales, Icacinales, Metteniusales, Vahliales.
• The position of many families has been changed. For example, Sabiaceae have been transferred to Proteales, Cynomoriaceae to Saxifragales, Apodanthaceae to Cucurbitales (APG IV, 2016).

Similar processes are occurring in virology. The International Committee on Taxonomy of Viruses (ICTV) has been developing a universal classification of viruses since 1966, based on genome type, virion structure, presence of an envelope, and phylogenetic data (King et al., 2012). In the ninth ICTV report (2012), 6 orders, 87 families, 19 subfamilies, 349 genera, and 2284 species of viruses and viroids were recognized. ICTV regularly updates the classification as data accumulate, and these updates are published on the Internet (King et al., 2012).

For an agronomist, classifications of phytopathogens are especially important. For example, the causal agent of potato late blight Phytophthora infestans was previously considered a fungus, but is now assigned to the kingdom Chromista, phylum Oomycota (Sokirko & Gorkovenko, 2019). This has practical significance: as we noted in the first chapter, fungicides effective against true fungi often do not work against oomycetes. Molecular systematics allows the group of the pathogen to be precisely determined and the correct protection strategy to be chosen.

3.6. Why Systems Change and How to Relate to This

We see that classifications of living organisms have been repeatedly revised. Why does this happen? The reasons can be reduced to three groups (Judd et al., 2018; Stuessy, 2009):

1. New data. The appearance of new methods (microscopy, chromatography, DNA sequencing) provides new characters that may contradict old ideas.

2. New methods of analysis. The development of cladistics, maximum likelihood methods, and Bayesian analysis allows phylogenetic hypotheses to be evaluated more strictly.

3. New concepts. Changes in the philosophical foundations of systematics: the transition from artificial systems to natural ones, from paraphyly to strict monophyly, from intuitive constructions to quantitative ones.

How should one relate to this? First of all, it should be remembered that classification is a hypothesis, not absolute truth. As Stuessy writes (Stuessy, 2009), “classifications are conventions; we decide what groups we want to talk about.” A change in classification does not mean that the previous one was “wrong” — it was the best approximation based on available data.

For an agronomist, this has a practical consequence: scientific names may change. For example, Xanthorrhoeaceae is now called Asphodelaceae, and Melianthaceae has been included in Francoaceae (APG IV, 2016). If you use an outdated name, colleagues or information systems may not understand you. Therefore, it is necessary to follow updates in classifications, especially for the groups you work with (pathogens, pests, crop plants).

At the same time, the organisms themselves do not change because we have changed their names. Phytophthora infestans remains the same pathogen, regardless of which kingdom it is assigned to. Names are tools of communication, and their stability is important, but it should not be achieved at the cost of ignoring new scientific data. As Hyam notes (Hyam, 2015), “scientific names are no more than labels; to refer accurately to taxa, one must also indicate the taxonomic treatment (taxon circumscription) that you are using.”

Thus, the historical change of paradigms is not chaos but a regular process of scientific development. Understanding this process helps an agronomist navigate the modern diversity of names and classifications, correctly interpret scientific literature, and communicate effectively with colleagues.

4.1. Diagnostics of Diseases and Pests

The first and most obvious application is diagnostics. When you detect symptoms of damage on a plant, you must answer the question: who is the causal agent? A bacterium, fungus, oomycete, virus, nematode, insect, or abiotic factor? Everything that follows depends on this.

The classic method of diagnostics is Koch’s postulates, formulated as early as 1880 (Sigee, 1993). They require:

1. Detect the organism in the affected tissue.

2. Isolate it in pure culture.

3. Inoculate a healthy plant and obtain the same symptoms.

4. Reisolate the same organism.

These postulates remain the basis for proving pathogenicity, but their application requires accurate identification of the organism. If you have isolated a fungus but have not determined its species, you can neither compare it with reference strains nor select a selective medium for reisolation.

Modern diagnostics uses a wide arsenal of methods, each of which relies on systematics (Sigee, 1993):

• Microscopy. Determination of morphological characters (shape of spores, presence of flagella, type of mycelium) allows the pathogen to be assigned to major taxa. For example, the presence of two flagella of different types (smooth and tinsel) indicates the phylum Oomycota, not true fungi (Sokirko & Gorkovenko, 2019).
• Serology. Enzyme-linked immunosorbent assay (ELISA) and immunofluorescence allow the detection of specific antigens of the pathogen. This requires antibodies raised against a particular taxon. The accuracy of diagnostics depends on how well we know the taxonomic diversity of the group and can distinguish the target species from closely related ones (Sigee, 1993).
• Molecular methods. PCR with species-specific primers, DNA probes, and sequencing of genome regions (e.g., ITS rRNA) allow the pathogen to be identified to species, subspecies, or even strain. These methods require databases of sequences organized according to taxonomic principles (Sigee, 1993; Pandey & Kasana, 2021).

For pests and entomophages, identification keys and molecular markers also exist. For example, distinguishing larvae of harmful and beneficial insects often requires knowledge not only of morphology but also of biology and phylogenetic relationships. An error in identification leads to the destruction of the pest’s natural enemy instead of the pest (Judd et al., 2018).

4.2. Choice of Plant Protection Methods

Correct identification determines the choice of preparation. As we have already mentioned, oomycetes (e.g., Phytophthora infestans, Pythium spp.) differ fundamentally from true fungi in the biochemistry of the cell wall (cellulose instead of chitin), the structure of mitochondrial cristae, and the pathways of lysine synthesis (Sokirko & Gorkovenko, 2019; Webster & Weber, 2007). Many fungicides active against fungi do not act on oomycetes. For example, metalaxyl is specific to oomycetes, whereas strobilurins are effective against a wide range of fungi but not against oomycetes (Sokirko & Gorkovenko, 2019). If you incorrectly identify the pathogen, you may apply a useless preparation, lose the harvest, and harm the environment.

Similarly, for insect control it is important to distinguish orders and families. Insecticides from the pyrethroid group are effective against many Lepidoptera but poorly effective against mites (which belong to another class — Arachnida). Acaricides, by contrast, are specific to mites. Without systematic knowledge, it is impossible to choose the correct class of active substance.

Biological control also requires accurate identification. The use of entomophages (e.g., Trichogramma against codling moth) or antagonists (e.g., Trichoderma against soil pathogens) is based on knowledge of their taxonomy, biology, and ecological relationships. One cannot release a beneficial insect without knowing to which species it belongs and against which pest it is effective (Judd et al., 2018).

4.3. Breeding and Search for Genetic Resources

Systematics plays a key role in breeding. As Stuessy notes (Stuessy, 2009), “knowledge of the system of plants directs the search for plants of potential commercial importance.” This statement is also true for the search for genetic resources.

A classic example is the search for resistance to potato late blight. The causal agent Phytophthora infestans originates from Mexico, where wild Solanum species with resistance genes grow. Breeders cross cultivated potato with these wild relatives to transfer resistance. But to find the needed species, it is necessary to know its systematic position and phylogenetic relationships with cultivated potato (Judd et al., 2018).

Another example is tomatoes. In the 1960s, botanist Hugh Iltis collected in Peru the wild species Solanum chmielewskii, which, when crossed with cultivated tomato, improved fruit flavor (Judd et al., 2018). This became possible because Iltis knew the systematics of the genus Solanum and understood that wild relatives could carry valuable traits.

Modern breeding uses phylogenetic trees to select the most promising donors. The closer a species is to the crop plant in phylogeny, the higher the probability of successful hybridization and transfer of useful genes. Therefore, systematists and phylogeneticists work closely with breeders (Stuessy, 2009).

4.4. Plant Quarantine

Plant quarantine is an area where systematics has direct legal and economic significance. To prevent the introduction of dangerous pests, diseases, and weeds, it is necessary to know precisely which organisms are subject to control. Lists of quarantine objects are compiled on the basis of taxonomic classification.

For example, the bacterium Xanthomonas campestris pv. citri causes citrus canker and is a strict quarantine object in many countries (Sigee, 1993). But to identify this pathovar, one must not only determine the species but also know its pathovar affiliation. This requires the use of specific methods: phage typing, serology, DNA probes (Sigee, 1993). Without a systematic basis, such methods do not work.

Quarantine services use identification keys and databases built on a taxonomic principle. If the name of a taxon changes (e.g., as a result of APG or ICTV revision), quarantine lists must be updated. This is a clear example of how changes in scientific classification directly affect practice (King et al., 2012; APG IV, 2016).

4.5. Conservation of Biodiversity of Agrocoenoses

Finally, systematics is important for conserving biodiversity in agrocoenoses. An agrocoenosis is not a monoculture in a vacuum but an ecosystem including crop plants, weeds, soil biota, insects, birds, etc. The stability of an agrocoenosis depends on the diversity of species and their interactions.

To manage this diversity, it is necessary to assess it. Systematists provide tools for inventory: identification keys, databases, molecular markers. For example, to assess the diversity of soil fungi, metagenomic analysis is used, which requires comparing sequences with reference databases organized according to taxonomic principles (Pandey & Kasana, 2021).

Conservation of natural enemies of pests, pollinators, and decomposers all requires knowledge of their taxonomy. For example, to attract wild pollinators to a field, one needs to know which plants they prefer, and for this — to identify both plants and insects. Without systematics, such programs are impossible.

4.6. Conclusion

We have considered five key areas where systematics has direct practical significance for an agronomist: diagnostics, choice of protection methods, breeding, quarantine, and conservation of biodiversity. In all these areas, accurate identification of organisms is the first and necessary step. An error in determining a taxon leads to incorrect decisions, yield losses, and financial costs.

Systematics provides the agronomist with a language for describing problems and tools for solving them. It is not a dogma: classifications change, names are updated, but the organisms themselves and their properties remain unchanged. The agronomist’s task is to follow these changes, use modern data, and understand that behind any name stands a real biological object requiring precise identification.

In the next, final chapter, we will summarize the key principle: “taxon ≠ organism ≠ species ≠ name” and show how this distinction helps avoid errors in practical work.

5.1. Organism: A Concrete Individual

An organism is a concrete individual existing in space and time. It is a real biological object that can be seen, touched, measured, sequenced. Here is a specific wheat plant in your field. Here is a specific Colorado potato beetle larva on a leaf. Here is a specific colony of Phytophthora infestans on a potato tuber. An organism is a single object, not a group.

Organisms possess properties that we can observe and measure: morphology, physiology, genome, behavior. But an organism is neither a species, nor a taxon, nor a name. It is simply an individual. When we say “this organism belongs to the species Triticum aestivum,” we perform an act of identification — we assign a concrete individual to a hypothetical group. But the individual itself is not the species. A species is an abstraction, while an individual is concrete.

5.2. Species: A Biological Concept and Hypothesis

Species is one of the most complex and debated concepts in biology. As Pavlinov writes (2023), the “species problem” has a long history and still has no single generally accepted solution. In the most general sense, a species can be defined as a set of populations of individuals capable of interbreeding to produce fertile offspring, inhabiting a certain range, and possessing common morphophysiological characters (Nayda, 2021).

However, this definition is only one of many species concepts. There exist:

• Biological species concept (BSC): a species is a group of interbreeding populations reproductively isolated from other such groups (Mayr, 1969).
• Morphological concept: a species is a group of organisms differing in morphological characters.
• Phylogenetic concept: a species is the smallest monophyletic group of organisms diagnosable by a unique combination of characters.
• Ecological concept: a species is a group of organisms occupying a certain ecological niche.

It is important to understand: a species is a hypothesis, not a fact. When a systematist describes a new species, they put forward a hypothesis that a given group of organisms deserves the status of a separate species. This hypothesis may be revised when new data appear. For example, two cryptic species, almost morphologically indistinguishable, may be recognized as one species after genetic analysis, or conversely, one polymorphic species may be divided into several (Pavlinov, 2023).

In the agrosphere, this is of enormous importance. For example, cryptic species among insect pests may differ in resistance to insecticides. If you identify a pest as one species, but in fact it is another, your preparation may not work. As Zakhvatkin notes (2001), among Diptera and Lepidoptera many cryptic species are known that differ in ecology and physiology but are almost morphologically indistinguishable.

5.3. Taxon: A Formal Group in Classification

A taxon is a group of organisms recognized in classification and given a certain rank. A taxon is a formal unit, not a biological entity. As Timonin emphasizes (2009), taxa are not arbitrary groupings; they “are a natural element of biological diversity arising in the course of its evolutionary development.” But at the same time, a taxon is our model of this element, our hypothesis about its boundaries and circumscription.

A taxon may include one organism (e.g., a monotypic genus with a single species), several organisms, one species, several species, several genera, etc. A taxon is a hierarchical unit: the species Triticum aestivum belongs to the genus Triticum, which belongs to the family Poaceae, which belongs to the order Poales, and so on (APG IV, 2016).

The key property of a taxon: it is neither an organism nor a species in the sense of a concrete individual. A taxon is a group, not an individual. When we say “genus Triticum,” we mean a group of species united by common descent. When we say “species Triticum aestivum,” we mean a group of populations corresponding to a certain species concept. But neither the genus nor the species is a concrete organism.

It is also important to distinguish taxon and taxonomic category. A category is a rank (species, genus, family), while a taxon is a concrete group occupying that rank. As we have already said, “a category is a position; a taxon is the person occupying that position” (Stuessy, 2009).

5.4. Name: A Nomenclatural Label

A name is a word or combination of words used to designate a taxon. A name is a label tied to a taxon through the procedure of typification. As Hyam writes (Hyam, 2015), “scientific, type-based names are not adequate identifiers of taxa.” A name is not the taxon itself, but only its designation.

A name is subject to the rules of nomenclature, not classification. Nomenclature regulates:

• Form of the name: for species — binary (genus + species epithet), for families — with the suffix -aceae, for orders — -ales (Timonin, 2009).
• Priority: the oldest available name is considered correct (Timonin, 2009).
• Typification: each name is tied to a type specimen (Stuessy, 2009).

A name may change for nomenclatural reasons even if the taxon has not changed. For example, if it turns out that the name Xanthorrhoeaceae was published later than Asphodelaceae, then Asphodelaceae becomes the correct name (APG IV, 2016). The taxon (family) remains the same, but its name changes.

A name may also designate different taxa in different authors. If one researcher understands species X broadly and another narrowly, the same name will refer to different groups of organisms. This is the problem of taxonomic concepts, which Hyam (2015) illustrates with the example of ecological meta-analyses: if two studies use the same name but different taxonomic treatments, their data cannot be automatically combined.

5.5. Relationship of Concepts: Scheme and Examples

Let us summarize the relationship of the four entities:

Organism — a concrete individual (real object).

Species — a hypothesis about a group of organisms (biological concept).

Taxon — a formal group in classification (unit of the system).

Name — a nomenclatural label (designation of a taxon).

Schematically, this can be represented as:

Organism → (identification) → Species (hypothesis) → (classification) → Taxon (group) → (nomenclature) → Name (label)

Feedback: Name → (typification) → Taxon → (species concept) → Organism (identification).

Let us consider an example from the agrosphere. The causal agent of potato late blight:

• Organism: a concrete individual of Phytophthora infestans that has infected a concrete potato tuber.
• Species: a hypothesis that all individuals of P. infestans form a single species corresponding to a certain concept (morphological, biological, phylogenetic).
• Taxon: the species Phytophthora infestans in the classification of oomycetes, belonging to the genus Phytophthora, family Pythiaceae, order Peronosporales, class Oomycetes, phylum Oomycota, kingdom Chromista (Sokirko & Gorkovenko, 2019).
• Name: Phytophthora infestans (Mont.) de Bary — a binary name tied to a type specimen.

If systematists revise the classification of oomycetes and transfer P. infestans to another genus, the name will change (e.g., Phytophthora infestans will become Hyaloperonospora infestans), but the organism will remain the same, the species will remain the same hypothesis, and the taxon will remain the same group. This distinction is critically important for the practitioner: the name may change, but the biology of the pathogen does not.

5.6. Practical Consequences for an Agronomist

From the principle “taxon ≠ organism ≠ species ≠ name” follow important practical consequences:

1. Do not trust a name blindly. A name is a label, not a definition. Knowing a name does not replace knowing the characters of a taxon. If you see the name Fusarium graminearum, this does not mean that you know what this fungus looks like, what diseases it causes, or how to control it. A name is only a key to information that still needs to be found and verified.

2. Clarify the taxonomic concept. If you read a scientific article or plant protection recommendations, pay attention to which taxonomic treatment was used. The same name may designate different taxa in different authors. For example, Botrytis cinerea in the broad sense may include several cryptic species differing in pathogenicity and resistance to fungicides (Webster & Weber, 2007).

3. Follow name changes. Nomenclatural revisions are a normal part of science. If you use an outdated name, colleagues or information systems may not understand you. For example, after APG IV (2016), the family Xanthorrhoeaceae became Asphodelaceae. If you work with ornamental plants, this change may be important for you.

4. Use GUIDs and taxonomic concepts. Hyam (2015) proposes using globally unique identifiers (GUIDs) for taxa to avoid confusion associated with name changes. Ideally, every publication, every specimen, every strain should be tied not only to a name but also to a specific taxonomic concept (treatment).

5. Distinguish species and taxon in breeding. When a breeder looks for a source of resistance, they work not with a name but with concrete organisms and their genes. The species name may be the same, but different populations may differ in resistance. Therefore, it is important not only to know the name but also to understand which particular population or line you are working with.

6. Remember that a species is a hypothesis. If you discover unusual variability in a pest population, this may be a sign that you are dealing with a complex of cryptic species. Do not rush to conclusions based on morphology — use molecular methods to test the hypothesis.

5.7. Conclusion

The principle “taxon ≠ organism ≠ species ≠ name” is not a philosophical abstraction but a working tool. It helps:

• Correctly interpret scientific literature.
• Avoid errors in identification and diagnostics.
• Understand why names change and how to relate to this.
• Communicate effectively with colleagues using precise taxonomic concepts.

In the next, final chapter, we will summarize the course and show that systematics is not a dogma but a developing field of knowledge, the foundation of an agronomist’s professional activity.

6.1. Systematics as Language and as Tool

Throughout the course, we emphasized: systematics is a language of professional communication. But language is not merely a set of words. It is a system that allows reality to be described, knowledge to be transmitted, and actions to be coordinated. Without a common language, neither science nor practice is possible.

Systematics gives an agronomist:

• Universal names for the organisms they work with. When you say “Phytophthora infestans,” you are understood by all specialists in the world — from a farmer in Peru to a phytopathologist in Japan (Sokirko & Gorkovenko, 2019).
• Predictive power. Knowing the phylogenetic relationships of taxa, we can predict the properties of their representatives. If one species of Trichoderma suppresses soil pathogens, its close relatives probably also possess this property (Judd et al., 2018).
• A basis for decision-making. The choice of fungicide, insecticide, herbicide, or biological agent depends on which taxon the target organism belongs to. An error in identification leads to an incorrect decision (Sigee, 1993).

But systematics is not only a language. It is also a tool of cognition. It provides methods:

• Morphological — for primary identification in the field and laboratory.
• Molecular — for precise determination of species, subspecies, and strains (Pandey & Kasana, 2021).
• Bioinformatic — for working with databases, GIS, and global identifiers (Hyam, 2015).

As a tool, systematics requires skills: the ability to use identification keys, work with a microscope, analyze DNA sequences, and interpret phylogenetic trees. These skills are formed in the process of education and practice. But the main thing is systematic thinking: the ability to see behind a name an organism, behind an organism a species, behind a species a taxon, behind a taxon an evolutionary history.

6.2. Systematics as a Developing Field of Knowledge

We have repeatedly emphasized: systematics is not a dogma. Classifications change. Names are revised. Phylogenetic hypotheses are refined. This is not a shortcoming but a property of science. As Stuessy wrote (Stuessy, 2009), “taxonomy is a dynamic, beautiful, complex, and exciting science.” Changes in systematics reflect the progress of knowledge, not its instability.

The historical change of paradigms — from Linnaeus to APG and ICTV — shows that systematics develops together with other biological disciplines. The molecular revolution of the late 20th century radically changed our ideas about the kinship of organisms. Cladistics gave strict methods for reconstructing phylogeny. Bioinformatics opened new possibilities for working with big data (Pavlinov, 2021).

What does this mean for an agronomist? First of all, the need for continuous learning. The names you learned at university may change in ten years. Taxa that were considered natural may turn out to be paraphyletic. Pathogens that were assigned to fungi may be transferred to another kingdom (as happened with oomycetes). An agronomist who does not follow these changes risks losing connection with modern science and practice.

But there is another side: fundamental principles do not change. The principle of monophyly, the principle of priority, the principle of typification — these foundations remain stable. Concrete classifications change, but not the rules of the game. Therefore, it is important to master not a set of names but the methodology of systematics: how classifications are built, how hypotheses are tested, how data are interpreted.

6.3. Systematics and the Professional Identity of an Agronomist

At the beginning of the course, we said that systematics is the language of agricultural science. Now we can say more: systematics is the foundation of an agronomist’s professional identity. An agronomist is not simply a person who grows plants. This is a specialist who understands biological diversity, can manage it, and bears responsibility for their decisions.

Systematics forms in an agronomist:

• Precision of thinking. The habit of distinguishing organism, species, taxon, and name is a habit of precision, which is necessary in any professional activity.
• Breadth of outlook. Knowledge of phylogeny and classification allows one to see connections between different groups of organisms, understand ecological interactions, and predict the consequences of one’s actions.
• A critical attitude toward information. Understanding that names may change, that taxonomic concepts may differ, that classifications are hypotheses, forms critical thinking necessary for working with scientific literature and making decisions under uncertainty.
• Responsibility. An error in identifying a pathogen or pest can lead to yield loss, financial losses, and sometimes environmental problems. Systematics teaches responsibility for the accuracy of determination.

As the outstanding evolutionary biologist Ernst Mayr wrote, “the study of diversity... has given us a reverence for each product of evolution, one of the most important components of conservation thinking” (Mayr, 1974: 8–9, cited in Stuessy, 2009). This reverence for the diversity of life is an integral part of the professional ethics of an agronomist. We work with living organisms, each of which is unique and irreplaceable. Systematics helps us see this uniqueness and learn to handle it.

6.4. A Look into the Future: Systematics in the 21st Century

Systematics continues to develop. What trends determine its future?

Molecular methods are becoming routine. Next-generation sequencing (NGS) allows genomic data to be obtained quickly and relatively cheaply. This opens possibilities for:

• DNA barcoding — the use of short standard genome regions for species identification (Pandey & Kasana, 2021).
• Metagenomics — analysis of all genetic material in a sample (soil, water, plant tissues) without isolating individual organisms (Pandey & Kasana, 2021).
• Phylogenomics — construction of phylogenies based on hundreds and thousands of genes (Pandey & Kasana, 2021).

Integrative taxonomy is becoming the norm. Modern systematics uses not one but many sources of data: morphology, anatomy, molecular sequences, ecology, geography. Only the integration of these data allows reliable classifications to be built (Pandey & Kasana, 2021).

Digital technologies are changing practice. Databases, online identification keys, GIS, global identifiers (GUIDs) — all this makes systematic knowledge accessible and convenient for users. As Hyam writes (Hyam, 2015), “tagging data with GUIDs is the most important step for ensuring the exchange and integration of biological data across the internet.” The agronomist of the future will work with digital tools of systematics as naturally as we work with a smartphone today.

Systematics is becoming increasingly interdisciplinary. It is closely connected with ecology, evolutionary biology, genetics, bioinformatics, and agricultural sciences. An agronomist who possesses systematic thinking will be able to work effectively at the intersection of these disciplines.

6.5. Final Points

Allow me to formulate several final points that I ask you to remember.

1. Systematics is the language of agricultural science. It provides universal communication, predictive power, and a basis for decision-making.

2. Systematics is a tool. It provides methods for identifying, classifying, and studying organisms.

3. Systematics is a developing field. Classifications change, names are revised, but fundamental principles remain stable.

4. Systematics is the foundation of an agronomist’s professional identity. It forms precision of thinking, breadth of outlook, a critical attitude toward information, and responsibility.

5. Key principle: taxon ≠ organism ≠ species ≠ name. Confusing these concepts is a source of errors. Distinguishing them is the path to precision.

6. A species is a hypothesis. Do not trust a name blindly. Clarify the taxonomic concept. Follow changes.

7. The future of systematics lies in integration. Molecular methods, digital technologies, and interdisciplinarity — these determine the development of science in the 21st century.