Taxonomy and Systematics

Systematics

• It integrates taxonomy (description, identification etc) with phylogeny (evolutionary history) to understand life's diversity and evolution.
• Systematics identifies unique evolutionary modifications and patterns.
• It connects taxonomy, phylogenetics, and evolutionary biology, foundational for understanding the natural world.
• Taxonomy and Systematics may be seen as separate but related fields.
• Systematics operate under the idea that all life has a unique phylogeny.
• Evolution is defined as change, or "descent with modification" by Darwin
• Descent is the transfer of genetic information from parent to offspring
• Modification involves changes to DNA over time.

Mechanisms of Descent

• Clonal reproduction: Simple, like bacterial fission.
• Sexual reproduction: Needs meiosis and gamete fusion from two parents.
• Used to identify unique modifications resulting from evolution

Taxonomy

• It is a major part of Systematics involving Description, Identification, Nomenclature, and Classification (DINC).
• Taxonomy studies taxa, defined groups of organisms.

Four Components of Taxonomy

• Description: Assigning attributes to a taxon.
• Character states are different forms of a character (e.g., "petal color").
• Identification: Associates unknown and known taxa, also recognizing the unknown taxon as new, by noting unique characteristics
• Nomenclature: Giving taxa formal names using standardized systems such as the International Code of Botanical Nomenclature
• Classification: Organizing taxa to show relationships.
• Uses hierarchical system, where each rank includes all lower ranks

Phylogeny

• Involves studying the evolutionary history of groups, figuring out how species relates and evolve.
• It is visualized using a cladogram (or phylogenetic tree).
• The tree represents a pattern of descent, showing how lineages have evolved over time.

Cladogram Lines

• Lines represent lineages (groups of organisms that share a common ancestor).
• These show evolution over time as populations pass down traits.
• Branching points indicate lineage divergence, as related species become different.
• The time scale indicates which groups diverged earlier versus later.
• Distance shows how recently species shared a common ancestor

Cladogram details

• Branching diagrams show evolutionary patterns of descent.
• Lines trace populations over time
• Branching indicates lineage divergence
• Time scale indicates relative sequence of events

Cladogram Importance

• It provides an endgoal and is used for understanding phylogeny
• Aids in creating a classification system (taxonomy).
• The tree enables exploration of biogeographic or ecological origin, speciation and evolution of adaptations

Phylogeny vs Taxonomy

• Phylogeny focus is based on evolutionary relationships whereas Taxonomy focus is based on grouping into categories
• Phylogeny purpose is to explain how organisms evolved whereas taxonomy's purpose is to name and classify
• Phylogeny visual output is phylogenetic trees, whereas Taxonomy outputs are hierarchical lists
• Phylogeny uses genetic, fossil, and data whereas taxonomy is based on observable traits Taxonomy supplies names and groups. Phylogeny explains the relationships through evolution.

Importance of Systematics

• It provides a foundation of information about the tremendous diversity of life
• Allows for correct determination of a given study organism based on description, identification, naming, and classification.
• Builds a research foundation for acquiring, cataloging, and retrieving information about life's diversity through specimen collection and data entry.

Goals of Systematics

• The discipline aims to provide an inventory of the world with the flora and fauna
• Provides a easy method of identification
• Systemize a method of classification that shows the evolution inside of the groups.
• Integrate available information and apply it to statistical analysis to provide a classification depending on overall similarity
• Understand and highlight relationships between organisms in an evolutionary view
• Create hierarchical classifications to reflect the evolutionary relationships
• Look for evolution throughout the plant kingdom

Fields of Systematics

• Biodiversity – number and kinds of organisms
• Taxonomy - art & science of describing organisms
• Classification - methods of grouping organisms
• Nomenclature -science of naming organisms
• Biogeography - studies the distribution of organisms and location that they live and abundance
• Evolutionary Biology - classifies organisms using phylogenetic relationship and overall similarity
• Phylogenetics - study of evolutionary relatedness among groups

Pre-Linnaean Taxonomy

• Began with identifying edible plants
• Shen Nung (3000 BC) was the Father of Chinese medicine
• Egyptian medicine was documented in the Ebers Papyrus (1500 BC)

Greeks and Romans

• Aristotle (384-322 BC): created animal classification diving them by with and without blood, still used today
• Theophrastus (370-285 BC): wrote De Historia Plantarum (480 species), provided basis for plant classification
• Dioscorides (40-90 AD): wrote De Materia Medica (600 species), used medicinally for centuries
• Plinius (23-79 AD): wrote Naturalis Historiam with 160 volumes describing plants

The Herbalists

• The printing revolution allowed for mass production of books and in turn botanical knowledge spread
• Brunfels, Bock, Fuchs, Mattioli, Turner, L'Obel, Gerard, L'Ecluse are some herbalists
• Some notable herbs are Brunfelsia, Mattiolia, Turnera

The Herbalists (cont.)

• Early herbals were copies from Theophrastus with no classification
• Over time, herbals became original and included detailed images
• Herbalists played a part in retaining all the botanical knowledge

Early Taxonomists

• 16th century, thanks to optical lenses and the focus shifting, works began to move beyond ancient Greek classifications with shifted focus from collection to focus from specimen to taxonomic classification
• Caesalpino (1519-1603): known to be Italy's oldest taxonomist
• Wrote De Plantis, which classified 1500 species based on growth and fruit form.
• Recognized plant families such as Brassicaceae and Asteraceae, still acknowledged today.
• Bauhin Brothers (1541–1631; 1560-1624): Published Pinax Theatri Botanici in 1623, with 6000 species shown
• Introduced synonyms

John Ray

• John Ray (1627-1705) emphasized the importance of specific taxonomic properties
• In Methodus Plantarum Nova, listing 18,000 plant species based
• Developed into entomology

Joseph Pitton de Tournefort

• Joseph Pitton de Tournefort (1656–1708) developed classification depend on floral characters
• In 1700, Institutiones Rei Herbariae, listed 9000 species in 698 genera which influenced Linnaeus by including sexual reproduction

Linnaean Era

• Carl Linnaeus (1707–1778) showed modern taxonomy as the father of taxonomy
• With publications in Species Plantarum of Systema Naturae
• Introduced nomenclature system where a species has a trivial name
• In 1753 he did identify around 8530 flowering plants
• By showing these species, he introduced modern approach, which is still used today

Carl Linnaeus' Early Career

• Sexual system introduced in 1735 and classified by the stamen-pistol
• Introduced rules for generic names through the Critica Botanica and provided instructions through the Fundamenta Botanica
• Revolutionized botony and zoology by coining terms

Post-Linnaean Taxonomy

• French scientists resisted the Linnaeus System and preferred a natural system
• Georges-Louis Leclerc de Buffon was a strong outspoken critic that influenced species development
• Criticized Linnaeus and was a wide range supporter that created a evolution theories, and a natural comprehensive approach

Development of Botanical and Zoological

• Augustin Pyramus de Candolle (1778-1841) proposed botanical taxonomy theories
• Introduced date priority
• Alphons de Candolle (1806-1873) adopting naming rules
• Botanists introduced concepts like type specimens
• Rules were set in the 1900's for the Zoological Nomenclature

Introduction of Evolutionary Theory

Charles Darwin (1809-1882) and Alfred Russel Wallace (1823-1913) showed the early traits through evolutionary trees

• Pioneers of trees were Ernst Haeckel and August Wilhelm Eichler
• Systematics focused on comparing anatomy and biochemisty

Phenetics vs. Cladistics

• Plant and Animals grew over 250K species

Cladistics and the Rise of Phylogenetics

• Willi Hennig (1913–1976), used derived traits and taxa from a single ancestor
• By the 1980's Cladistics gained traction
• PCR made phylogenetic studies better

The PhyloCode Emergence

• In the 1990s, Kevin de Queiroz and Jacques Gauthier introduced to the modern world
• Philosophical shift made taxonomy unique
• Controversal but aimed on stability

Contributions of Systematics to Biology

• Evolutionary studies
• Revolutionized how we look at diversity by introducing concepts
• Introduced applications Biology and made it available for evolution studies

The History of Life on Earth

• Introduced origins where first life forms had stromatolites ( layered structures formed by cyanobacteria)
• Great Oxygenation Event (2.4-2.5 Billion Years Ago) enabled evolution for oxygen species
• Rise of Eukaryotes (2 Billion Years Ago) origin where eukayrotes had endosymbiosis
• Multicellularity (1 Billion Years Ago) algae grew with different properties
• Cambrian Explosion (541 Million Years) rapid life diversification
• Colonization of Land (500-400 Million Years Ago) early land plants and animal forms Age of Dinosaurs (252-66 Million Years Ago), domination and extinction over the era
• Mammalian and Flowering Plant Evolution enabled more diversity
• Human Emergence occurred 2-3 million years with humans evolving from Apes and making tools and languages
• Genetic species also revealed extinct relatives such a the Neanderthals

Biodiversity and Modern Systematics

• Modern is defined by species of high biodiversity being lossed rapidly
• In that revolution tool, DNA has come into play
• Also databases were a good source

Test your knowledge of taxonomy and systematics. This quiz covers the components of taxonomy, evolutionary relationships among organisms, and the use of cladograms. Explore the principles of nomenclature and phylogenetic trees.