2  Plant Taxonomy and Molecular Systematics

In the realm of plant science, there are several key terms to understand:

In 2023, plant systematics encompasses several crucial tasks. Firstly, scientists work on reconstructing phylogenies, which involves determining the evolutionary relationships among different plant species. By understanding these relationships, researchers gain insights into the shared ancestry and diversification of plants over time. Additionally, plant systematics involves defining groups of plants at various points in the hierarchy through plant taxonomy. This classification process organizes the vast diversity of plant life into manageable categories based on shared characteristics and evolutionary history. Moreover, systematists assign names to these groups using a formal naming system, known as plant nomenclature, ensuring clear communication among scientists and accurate reference to specific plant taxa. Another important aspect of plant systematics is the identification of unknown plants, which aids researchers, conservationists, and individuals in recognizing and understanding the plants they encounter in various environments. Finally, the publication of findings by systematists in scientific journals and other publications contributes to the collective knowledge and understanding of plant diversity and evolution.

Understanding plant systematics is essential for several reasons. Firstly, it enhances our comprehension of the natural world and biodiversity, providing valuable insights into ecosystem dynamics and evolutionary processes. Moreover, systematics plays a crucial role in everyday life, as people constantly classify the plants around them. Whether determining if a plant is edible or hazardous, the principles of plant systematics inform decisions that impact human health and safety. Furthermore, the practice of classifying plants has a rich history spanning thousands of years, reflecting humanity’s innate curiosity about the natural world and our desire to organize and understand it.

2.1 Folk Taxonomy

Folk taxonomy, also known as traditional or vernacular taxonomy, is a classification system used by societies based on the significance of plant groups within their culture. In folk taxonomy, names are often assigned to plants based on their importance or usefulness to the community. Interestingly, some names in folk taxonomy align with modern botanical concepts, such as the use of “grass” to refer to plants in the Poaceae family and “sedge” for those in the Cyperaceae family. However, there’s usually no traditional English name that encompasses all species within most modern plant families.

For particularly important plant groups, vernacular names often reflect their significance. Take, for example, Brassica oleracea, which includes cauliflower, kohlrabi, cabbage, Brussels sprouts, and broccoli. Despite being the same species, the wide variety of names for different cultivars highlights the subtle but essential differences that are valued by society.

These patterns of naming and classification are not unique to English-speaking cultures; similar patterns exist in most languages around the world.

2.1.1 The West

In ancient times, Theophrastus, who lived from 370 to 285 BCE, was the first known European to create a formal plant classification. He organized 480 different taxa and used a wide range of plant features, including morphology and even anatomy, to classify them. Some of the names he coined were later adopted by Linnaeus, the famous botanist, and are still in use today. Linnaeus even referred to Theophrastus as the “father of botany.”

Dioscorides, who lived in the 1st century CE, wrote a significant work called “De Materia Medica,” in which he documented around 600 plant species. He provided detailed information about the practical uses of these plants, especially in medicine. Dioscorides’ work remained the main European herbal text for over a thousand years until the 16th century.

During the European Renaissance, botany and herbalism were closely linked. Herbalists of this time provided the groundwork for plant classification, focusing mainly on the plants’ uses rather than their evolutionary relationships. Their classifications were primarily based on how people used plants, reflecting the practical knowledge of the time.

2.1.2 Ancient China?

In ancient China, herbalism was important for health care. The earliest herbal text is called Shennong’s Materia Medica (神农本草经). It was made by gathering knowledge from stories and traditions between 206 BCE and 220 CE. Shennong’s Materia Medica sorted 365 plants, animals, and minerals into three groups based on how they were thought to affect the body: “upper herbs,” “middle herbs,” and “lower herbs.”

A significant work in Chinese herbalism is the Compendium of Materia Medica (本草纲目), created by Li Shizhen during the Ming dynasty. Over 27 years, Li Shizhen put together this massive book. He fixed mistakes, added new plants, and included lots of illustrations. His book became very famous and was widely read in Asia. It even got translated into other languages by a missionary named Michał Piotr Boym.

Li Shizhen’s Compendium tried to organize plants and animals based on how they looked and behaved, not just on their medical uses. The title of his book shows this attempt at organization. The terms “gāng” (纲) and “mù” (目) in the title later became words used in modern biology to describe different ranks, like “class” and “order.”

2.2 Early Taxonomists

Early taxonomists made significant contributions to the organization and classification of plants:

Gaspard Bauhin published the “Pinax Theatri Botanici” in 1623, listing around 6,000 plant species along with synonyms. He not only identified species but also recognized genera. Bauhin introduced binary nomenclature, a system where each species is given a genus name followed by a specific epithet.

John Ray’s “Methodus Plantarum Nova,” first published in 1682 with a second edition in 1703, expanded the classification with around 18,000 species. Ray opted not to use the binary system due to its complexity, instead developing a detailed system based on various flower and vegetative characteristics.

Joseph Pitton de Tournefort’s “Institutiones Rei Herbariae,” published in 1700, contained approximately 9,000 species organized into 698 genera and 22 classes. Although his classification was largely artificial, it was highly practical and promoted the importance of the genus rank in taxonomy. These early taxonomists laid the groundwork for modern plant classification systems.

2.2.1 Carl Linnaeus

Carl Linnaeus, born in 1707 and passing away in 1778, made significant contributions to the field of taxonomy:

Linnaeus was known for synthesizing a vast amount of botanical literature. He wrote extensively, observed plants keenly, and recorded his observations methodically. He was incredibly passionate about his work and played a crucial role in popularizing the binomial naming system, where each species is given a two-part Latin name comprising the genus and species.

In his work “Systema Naturae” published in 1735, Linnaeus introduced the sexual system of plant classification. He proposed organizing living organisms into three main kingdoms: Animal, Vegetable (or Plant), and Mineral.

Linnaeus’ sexual system of classification primarily relied on the number of stamens and carpels in flowers. It was not designed to depict evolutionary relationships but rather served as a practical means of identifying and categorizing plants.

Linnaeus’ bold discussion of plant reproduction, though focusing on botanical matters, caused some controversy in the conservative society of the 18th century. Nonetheless, his work was groundbreaking.

In Linnaeus’ notable publications “Species Plantarum” (1753) and “Genera Plantarum” (5th Edition, 1754), he cataloged around 7,700 plant species across 1,105 genera. “Species Plantarum” provided numbered lists of species within each genus, along with references to important literature, synonymy, distribution information, and brief descriptions. Each species was assigned a unique specific epithet.

The publication of “Species Plantarum” in 1753 is widely regarded as a landmark moment in modern plant taxonomy, marking the beginning of a more systematic approach to organizing and naming plant species. Linnaeus’ contributions laid the foundation for the structured classification system still used today.

2.2.2 Other Western Taxonomists

Michel Adanson (1727-1806) and Antoine-Laurent de Jussieu (1748-1836) were influential figures in the development of botanical classification:

Adanson’s significant work, “Familles des Plantes” (1763), departed from the methods of Linnaeus. Instead of focusing on predetermined characteristics, Adanson emphasized considering a wide range of plant traits to establish classification. He proposed 58 plant families, many of which remain recognized in modern botanical classification. Adanson was notably critical of Linnaeus’ approaches.

Antoine-Laurent de Jussieu’s “Genera Plantarum” (1789) marked a significant advancement in botanical classification. He categorized the plant kingdom into Acotyledones (cryptogams), Monocotyledones, and Dicotyledones (including gymnosperms). Jussieu introduced 15 classes and 100 natural orders (families), many of which are still recognized today. His work is considered a precursor to modern classification systems and laid the foundation for subsequent developments in botanical taxonomy.

Augustin Pyramus de Candolle (1778-1841) and his son Alphonse Louis Pierre Pyramus de Candolle (1806-1893) made significant contributions to botanical classification. Their monumental work, “Prodromus Systematis Naturalis Regni Vegetabilis,” spanning volumes 1-17 published between 1823 and 1873, is a comprehensive account of plant taxonomy. It cataloged approximately 58,000 plant species classified into 161 families. Remarkably, even today, some plant families are best described in their work, making it a highly influential and enduring contribution to botanical science.

In 1857, Darwin and Wallace presented their groundbreaking joint papers titled “On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection” to the Linnean Society of London. This laid the foundation for evolutionary theory. Darwin’s seminal work, “On the Origin of Species,” published in 1859, presented his comprehensive theory of evolution through natural selection. Despite its monumental significance, initially, evolutionary theory had minimal impact on how taxonomy was practiced. Over time, however, the idea gradually gained acceptance that classification should reflect evolutionary relationships. This shift in perspective led to the development of phylogenetic classification systems, where organisms are classified based on their evolutionary history rather than solely on morphological similarities.

2.3 Natural Systems

A.W. Eichler’s “Syllabus” (1883) and H.G.A. Engler and K.A.E. Prantl’s monumental work “Die Natürlichen Pflanzenfamilien” (1887-1915) were early contributions to natural systems. These systems aimed to classify plants based on their evolutionary relationships rather than just their superficial similarities.

C.E. Bessey’s “Outlines of Plant Phyla” (1911) and H. Hallier’s “Provisional scheme of the natural system of flowering plants” (1905) further developed this approach, providing frameworks for organizing plant taxa according to their phylogenetic relationships.

In more recent times, numerous botanical systems have been proposed by notable botanists such as Takhtajan, Cronquist, Thorne, Hutchinson, and Dahlgren. These systems vary in their methodologies, with some focusing on phenetic approaches like Sokal and Sneath’s system (1963), while others adopt phylogenetic methods like the Angiosperm Phylogeny Group.

There has also been a proliferation of botanical classification systems, each contributing to our understanding of plant relationships:

Notable systems have been proposed by renowned botanists such as Takhtajan, Cronquist, Thorne, Hutchinson, and Dahlgren. These systems vary in their approaches and methodologies, providing different perspectives on plant classification.

Some systems, like the one developed by Sokal and Sneath in 1963, follow a phenetic approach. These systems focus on grouping plants based on overall similarity in characteristics, without necessarily considering evolutionary relationships.

On the other hand, there are phylogenetic systems, exemplified by the work of the Angiosperm Phylogeny Group. Phylogenetic systems organize plants based on their evolutionary history, aiming to reflect the true genetic relationships between different plant groups.

2.3.1 Periods

Plant systematics has evolved through several major periods:

  1. Prehistory: This period encompasses early folk classifications, where people categorized plants based on their cultural significance and practical uses.

  2. Ancient Greeks through Linnaeus: During this period, from ancient Greece through the time of Linnaeus, plant systematics was influenced by essentialism. This approach focused on identifying essential characteristics and grouping plants based on perceived similarities. Similar systems emerged in other parts of the world during this time.

  3. Natural systems: In this period, botanists began to emphasize overall resemblance among plants, leading to the development of natural classification systems. These systems aimed to group plants based on their evolutionary relationships rather than just superficial similarities.

  4. Darwin/Wallace: The contributions of Charles Darwin and Alfred Russell Wallace introduced an evolutionary perspective to plant systematics. However, this addition had only a superficial effect initially.

  5. Numerical phenetics: With the advent of computers, numerical phenetics emerged as a method for classifying plants. This approach involved analyzing large datasets of plant characteristics to identify patterns of similarity.

  6. Phylogenetic systematics (cladistics): Phylogenetic systematics, also known as cladistics, became prominent with the use of more advanced computers. This approach focuses on identifying shared derived characteristics, called synapomorphies, to determine evolutionary relationships. Key concepts include monophyly, which refers to a group consisting of an ancestor and all its descendants.

In modern times, there has been a shift towards phylogenetic (cladistic) systems in plant systematics. From the 1980s to the early 2000s, there was a debate between traditionalists, who followed classification systems proposed by Takhtajan, Cronquist, Thorne, Hutchinson, Dahlgren, and others, and phylogeneticists. However, the tussle is now largely resolved in favor of phylogenetic approaches. Nevertheless, plant systematics remains dynamic, and future shifts in philosophical paradigms may lead to further developments in the field.

2.3.2 Features of Taxonomies

A taxonomy, or system of classification for plants, should meet several criteria:

  1. Practical: The names assigned to plants should be easy to use, stable over time, and clear in their meaning. This ensures that botanists and other researchers can accurately identify and communicate about different plant taxa.

  2. Informative: Taxonomic names serve as keys to accessing further information about a plant. Therefore, a taxonomy should provide meaningful and informative names that help users understand the characteristics, relationships, and distribution of the taxa.

  3. Predictive: A taxonomy should enable predictions about plants based on their classification. This means that features of a plant that have not yet been studied should be predictable based on known features of the named group. Predictability facilitates research and understanding of plant biology.

  4. Consistent: A taxonomy should be consistent with the theoretical framework on which it is based. This ensures that the classification system aligns with established principles of plant systematics and evolutionary biology, providing a reliable foundation for further research and study.

2.4 Relationships Between Plants

Our understanding of the relationships between plants is formulated by studying various characteristics:

One approach involves examining the external form or appearance of plants, known as morphology. This includes studying a wide range of features related to both reproduction (such as flowers, fruits, and seeds) and vegetative structures (like roots, stems, and leaves). Morphological characteristics can vary greatly and provide valuable clues about the relationships between different plant groups. Interestingly, the same feature might be useful for classification purposes in very different plant groups.

Another aspect is anatomy, which involves studying the internal structure of plants. This has been a significant area of study for over 150 years. Anatomical studies focus on features like xylem and phloem (the tissues that transport water and nutrients), wood structure, nodal and leaf anatomy, secretory structures, and even the presence of crystals. Understanding the internal anatomy of plants provides insights into their evolutionary relationships.

Other methods include examining characteristics such as chromosomes, embryology, palynology (the study of pollen grains), secondary plant compounds, and gene sequencing. Each of these approaches contributes to our understanding of plant relationships by providing different types of data and insights into the evolutionary history of plants.

Embryology focuses on the development of gametophytes and embryos in plants, which reveals significant evolutionary trends. For instance, the evolution of heterospory, where plants produce different types of spores (microspores and megaspores), is a crucial development. This leads to the development of micro- and megagametophytes with distinct functions. In some cases, these gametophytes may rely on the sporophyte for nutrition. Additionally, features like the shape of ovules and the process of embryo development provide insights into plant relationships and evolutionary history.

Chromosomes play a vital role in plant systematics, with variation in chromosome number and structure providing valuable information. For example, some plant species have a chromosome number of 2n=4, while others, like Ophioglossum reticulatum, have a chromosome number of 2n=1260. Studying chromosome structure helps botanists understand genetic relationships among plant taxa.

Palynology is the study of pollen and spores, which serve as crucial markers for understanding plant relationships. Spores mark the beginning of the gametophyte generation, while pollen grains represent mature microgametophytes. Palynologists examine structural features of pollen and spores, such as apertures and outer walls, to gather information about plant evolution and relationships.

2.4.1 Secondary Plant Compounds

Secondary plant compounds have been utilized indirectly for centuries through their tastes, smells, and medicinal properties. However, their taxonomic use began approximately 100 years ago. These compounds, known as secondary plant metabolites, include various groups such as alkaloids, betalains, anthocyanins, glucosinolates, cyanogenic glycosides, polyacetylenes, terpenoids, and flavonoids. Each group is structurally diverse and may have specific distributions among plant taxa. For instance, betalains are found exclusively in the order Caryophyllales, while glucosinolates are a synapomorphy for the order Brassicales. Secondary plant metabolites provide valuable information for understanding plant relationships and evolutionary history.

2.4.2 Sequencing

Gene sequencing has become increasingly important in plant systematics, with its application spanning all levels of the taxonomic hierarchy. Initially focusing on chloroplast and nuclear genes, gene sequencing techniques have advanced to include Whole Genome Sequencing (WGS). Gene sequencing provides significant insights into higher-level relationships among plant taxa, offering a powerful tool for studying evolution and phylogeny. Despite the advancements in gene sequencing, morphological data remain critical for phylogenetic studies, species delimitation, and plant identification, highlighting the importance of integrating different types of data in plant systematics.

2.5 Classification

In plant taxonomy, organisms are classified into hierarchical ranks:

  1. Kingdom: The highest rank, representing broad groups of organisms sharing fundamental characteristics. For plants, the kingdom is Plants.

  2. Division (or Phylum): Subdivisions within the kingdom, grouping together related classes of organisms. For example, Angiosperms represent one division within the plant kingdom, encompassing flowering plants.

  3. Class: Further subdivisions within divisions, categorizing organisms based on shared characteristics. An example is Magnoliopsida, which includes dicotyledonous flowering plants.

  4. Order: Orders consist of families of organisms that share similar characteristics and evolutionary history. For instance, Gentianales includes various families of flowering plants like Gentianaceae.

  5. Family: Families group together genera with similar features and evolutionary relationships. An example is Gentianaceae, a family of flowering plants within the order Gentianales.

  6. Genus: Genera are groups of closely related species sharing common characteristics. Cyrtophyllum is an example of a genus.

  7. Species: The lowest and most specific rank, representing individual organisms with similar characteristics that can interbreed and produce fertile offspring. Cyrtophyllum fragrans, for instance, refers to a specific species within the genus Cyrtophyllum.

2.6 Nomenclature

Taxonomy/Systematics focuses on the scientific classification of organisms into taxonomic groups based on their similarities and evolutionary relationships. It involves identifying and analyzing various characteristics of organisms to understand their evolutionary history and relationships with other organisms. Taxonomy/Systematics aims to organize and categorize the diversity of life on Earth systematically.

Nomenclature, on the other hand, is the process of assigning scientific names to taxonomic groups for reference and communication. It involves the creation and application of standardized names for organisms, ensuring clarity and consistency in scientific communication. Nomenclature follows a set of internationally agreed rules and recommendations, such as the International Code of Nomenclature for algae, fungi, and plants (ICN) and the International Code of Zoological Nomenclature (ICZN), to ensure uniformity and stability in naming organisms.