Classification, Phylogeny and the Diversity of Life

1Overview

Scientists have catalogued about 1.5 million species, and estimates suggest up to 100 million more remain unidentified. Making sense of that many organisms requires a system: a way to name them, group them, and show how they are related. Classification is a human tool, and like every scientific tool it keeps changing as new evidence arrives. This lesson covers the evidence used to work out relationships, the principles of taxonomy, the knowledge systems of First Peoples for classifying animals and plants, and the domains and kingdoms of life.

2Evidence for phylogenetic relationships

A phylogeny is the evolutionary history of a group of organisms. Because the past cannot be observed directly, biologists build hypotheses about relationships from several kinds of evidence. The curriculum names six.

Homologous or analogous?

The first task in building a tree is to decide whether a similarity is homologous (inherited from a common ancestor, with a shared developmental origin) or analogous (independently evolved under similar pressures). Only homologous traits are useful for working out relationships. Complex, multi-part features that overlap are more likely to reflect shared ancestry than simple ones.

The power and limits of molecular data

Molecular systematics uses DNA data to confirm earlier classifications and to reveal past errors. It has limits. A single insertion or deletion can shift a sequence so that closely related organisms seem unrelated, and unrelated organisms can share similar sequences by chance. Combining molecular and anatomical evidence is more reliable than either alone.

3Phylogenetic trees and cladograms

A phylogenetic tree is a diagram of evolutionary relationships. A cladogram is a tree that groups organisms by shared characters. Key terms:

• A branch point (node) is where one lineage splits into distinct new lineages; it represents a common ancestor.
• Sister taxa share a branch point and a most recent common ancestor; neither gave rise to the other.
• A clade is a group that includes an ancestor and all of its descendants (a monophyletic group). A group that spans several branch points is not a clade.
• A shared derived character appears partway through the tree and is found only in some members (the amniotic egg in the Amniota). A shared ancestral character appears in a group's ancestor and is found in all its members.
• A polytomy is a branch with more than two lineages, often where relationships are not yet resolved.
• Branch length usually shows evolutionary order and not elapsed time, unless the diagram says otherwise. Rotating branches at a branch point does not change the information.

The principle of maximum parsimony says that the most likely evolutionary pathway is the simplest, the one needing the fewest major events to explain the evidence. Like hikers who usually stay on established trails, evolution is assumed to avoid unnecessary detours unless evidence says otherwise.

4Taxonomic principles

The hierarchy of taxa

Taxonomy sorts organisms into increasingly inclusive groups called taxa (singular: taxon), in what is often called the Linnaean system. The levels, from broadest to most specific, are domain, kingdom, phylum, class, order, family, genus and species. A common memory aid is "Dear King Philip Came Over For Good Soup". Each level nests inside the one above it, so the system is hierarchical.

Binomial nomenclature

Scientists refer to organisms by a two-word scientific name: the genus followed by the species. This is binomial nomenclature. The rules are: the genus name is capitalized, the species name is not, and both are italicized (or underlined when handwritten). Examples include Homo sapiens (humans) and Canis lupus (wolf). Scientific names are shared worldwide, while common names such as "dog" differ from place to place and may refer to more than one organism. A name may be abbreviated after first use, for example C. lupus.

Dichotomous keys

A dichotomous key is a tool for identifying organisms by their observable traits. It presents a series of numbered steps, each with two choices, and each choice leads either to another step or to an identification. To use a key: make accurate observations, follow the directions carefully, and choose the statement that matches at each step. To build one: use pictures that show the entire organism, base each step on visible traits (not behaviours, such as "hunts at night", which a picture cannot show), and have another student test the key. Keys can be written as numbered couplets or drawn as branching diagrams.

5First Peoples knowledge on classification

Classification is not only a Linnaean activity. First Peoples in British Columbia have long-standing systems for organizing knowledge about animals and plants, grounded in relationships, use and place. The curriculum specifically names two examples: classifying animals based on use (for example traditional clothing, food and hunting seasons) and classifying BC plants based on use (for example food and medicine).

• Hundreds of plant, algae and fungi species have individual names in BC Indigenous languages, showing long familiarity with them. Children in each of the province's language groups once learned many plants and their uses, and trained specialists handled tending, harvesting, weaving, carving and healing.
• Plant knowledge is recorded in the context of daily life: materials for fuel, shelter, transportation, clothing, nets, cordage and containers, as well as foods and medicines. One ethnobotanist's reference describes more than 100 plants used in First Nations material culture.
• Animals are known by when and how they can be hunted, what they provide (food, hides, materials for clothing), and how they relate to other species and seasons, as in the salmon and salmonberry relationship described in the first lesson.

This knowledge belongs to the Nations and communities who hold it. The Curricular Competencies suggest inviting a local First Peoples Elder to talk with the class about the traditional use of plants and animals, which is the appropriate way to learn it; the summaries here describe only what has been published.

6Domains and kingdoms: the largest groups

The broadest level of classification currently in common use is the domain. Three domains are recognized: Bacteria, Archaea and Eukarya. The first two are prokaryotes (no nucleus); the Eukarya are organisms with a nucleus and organelles. Within Eukarya, the kingdoms are usually taught as:

Fungi are not plants. Molecular analysis indicates that fungi are more closely related to animals than to plants, and fungi and animals share traits such as chitin, melanin and glycogen storage.

Unifying criteria for classification

Groups are defined by a set of unifying criteria. The most useful are: cell type (prokaryotic or eukaryotic), number of cells (unicellular or multicellular), cell wall composition (peptidoglycan, cellulose or chitin), how energy and carbon are obtained (photosynthesis, absorption or ingestion), and genetic evidence such as DNA similarity. Notice that no single criterion works for every group. A plant and a cyanobacterium both photosynthesize but fall in different domains, while a mushroom and a bacterium both absorb nutrients but also fall in different domains. Classification therefore combines several criteria.

The hierarchical nature of diversity

Living diversity is organized as nested groups: species within genera, genera within families, and so on up to domains. This nesting fits what evolution predicts, because each species descends from an earlier one, and groups of related species share an ancestor. Hierarchy is therefore a consequence of branching descent, not simply a filing convenience.

7Changing models based on emerging knowledge

Classification is a model, and models change when new evidence arrives. Several examples show this clearly.

• From appearance to DNA. Earlier classifications relied mainly on shared characteristics. DNA technology revealed more precise phylogenies, and some older classifications were revised, as with the hippopotamus and the whale.
• From simple kingdoms to domains. The three-domain system places Bacteria, Archaea and Eukarya at the top, based largely on molecular comparisons. It reflects the finding that some eukaryotic genes resemble archaeal genes and others resemble bacterial genes.
• From a tree to a web. Darwin sketched the first phylogenetic tree in 1837, with a single trunk and branches diverging. Horizontal gene transfer, the movement of genes between unrelated species by transformation, transduction, conjugation or gene transfer agents, complicates this picture. Estimates suggest it transfers only about 2% of the prokaryotic genome, though some researchers consider that estimate premature. It also occurs in eukaryotes, for example aphids that acquired fungal genes for carotenoid production. Some biologists propose a "web of life" with multiple trunks and cross-connections. Another proposal, the "ring of life", suggests that all three domains arose from a pool of gene-swapping prokaryotes, but many phylogeneticists remain skeptical.
• Endosymbiosis. The origin of mitochondria and chloroplasts from engulfed prokaryotes means that the eukaryotic cell is itself a merger of lineages (see lesson two).

Applying classification: a short project outline

1. Collect photographs or specimens of ten local plants (leaf shape, arrangement, cones or flowers).
2. List observable features that differ between them, avoiding features that need behaviour or special equipment.
3. Write the key as numbered couplets with two choices each, and have another student test it.
4. Build a cladogram using shared derived characters such as vascular tissue, seeds, cones and flowers.
5. Compare the key and the cladogram: the key aims to identify quickly, the cladogram to show relationships.
6. Where possible, include knowledge of traditional uses learned from a local Elder or community resource, and acknowledge the source.

8Summary

• Phylogenetic relationships are inferred from DNA, biochemistry, anatomy, embryology, fossils and biogeography; homologous traits are informative and analogous traits are not.
• Cladograms show clades defined by shared derived characters; parsimony favours the simplest explanation.
• Taxa run domain, kingdom, phylum, class, order, family, genus, species; binomial nomenclature uses genus and species.
• Dichotomous keys identify organisms using paired choices based on observable traits.
• First Peoples classify animals and BC plants by use and relationship, a knowledge system held by communities.
• Three domains (Bacteria, Archaea, Eukarya) and kingdoms are defined by cell type, cell number, cell wall, nutrition and DNA; models change as new knowledge emerges.

?Quick check

Try each question first, then reveal the answer.