Notes: Biodiversity, Cladistics, and Taxonomy

Life on Earth

• Life shares a common origin evidenced by the same core biochemistry (e.g., nucleic acids, amino acids, ribosomes, polymerases).

• Divergence occurred via random mutation, filtered by reproductive fitness.

• Climate change threatens many forms of life; understanding loss requires defining what remains.

What is biodiversity

• Common definition: number of species.

• Extreme definition: number of genetically unique, independently living organisms.

• Google definition: variety of plant and animal life in world or a habitat; high diversity is valuable.

Genetics vs Genomic

• Clones are not automatically good for biodiversity.

• Genetically identical clones may still differ genomically due to epigenetics.

Current biodiversity on Earth

• Currently catalogued: ≈ $1.2\times 10^6$ species.

• Predicted total eukaryotes: ≈ $8.7\times 10^6$ (± $1.3\times 10^6$).

• Of these, marine eukaryotes: ≈ $2.2\times 10^6$ (± $0.18\times 10^6$).

Timeline of life on Earth

• Life on Earth: ≈ $4\times 10^9$ years ago.

• Multicellular plants and animals: ≈ $1\times 10^9$ years ago.

• Unicellular biodiversity is vast; focus often on visible multicellular life.

Historical biodiversity on Earth

• Marine biodiversity by genera since the Cambrian is incomplete due to fossil gaps.

Cambrian explosion/radiation

• Beginning of animals: ≈ $541\times 10^6$ years ago.

• Resulted in formation of most animal phyla; major body-plan diversification.

• Early multicellular life expanded, with hard shells and skeletons aiding defense and support.

Cambrian fossil highlights

• Notable taxa appearing in Cambrian fossil record (e.g., Opabinia, Hallucigenia).

Earlier animal origins

• First undisputed animal fossils: ≈ $580\times 10^6$ years ago, but genetic roots trace back to ≈ $700-800\times 10^6$ years ago.

When life sped up (oxygen and metabolism)

• End of Ediacaran, rise in oceanic oxygen → metabolic capabilities accelerate.

• Key time points:

  • 800 Myr: Oxygen rises from <0.1% to ~1–2% of modern levels.

  • 700–635 Myr: Glacial events with possible oxygen spikes.

  • 580 Myr: Appearance of large Ediacaran animals.

  • 542 Myr: Start of Cambrian explosion.

• Gradual rise toward modern ocean oxygen levels continued.

(Common) Tree of Life

• Based on 16S ribosomal RNA sequences; viruses are not included because they lack metabolic activity and independent protein synthesis.

Major clades and the Tree of Life (concepts)

• Three domains: Bacteria, Archaea, Eukaryotes.

• Archaea are prokaryotes; closest relatives to eukaryotes genetically.

• Eukaryotes include Opisthokonta (animals, fungi, related kingdoms).

Cladistics: core concepts

• Cladistics: method to infer evolutionary relationships (family tree) using shared derived characteristics.

• Clades: groups containing all descendants of a common ancestor (monophyletic).

• Taxon: any named group, not necessarily a clade.

Terminology in Cladistics

• Monophyly: all descendants of a single common ancestor form a group.

• Paraphyly: excludes some descendants.

• Polyphyly: group composed of members from multiple ancestors.

• Example: a primate cladogram highlighting true clades vs non-clades.

Clade vs Taxon: examples

• Reptilia is a taxon but NOT a clade (as traditionally defined) because birds are descended from reptiles.

• Whales debate: “Whales” can be treated as a taxon; as a clade they are paraphyletic unless Modern grouping includes all descendants.

• Whale example: Whales form a taxon, not a clade; often discussed as paraphyletic depending on grouping.

Naming the clades

• Cladistics reveals relatedness, but there is no universal method to name clades.

• Linnaean hierarchy is used to name clades and nested groups (e.g., genus, family, order).

Classical vs Modern Taxonomy

• Classical taxonomy: species as fixed units, defined by external morphology and qualitative traits.

• Modern taxonomy: species/populations are dynamic, defined by ancestry; emphasis on genetic markers (DNA, proteins) and computational algorithms.

The Central Dogma of genetics

• Transcription: DNA → RNA

• Translation: RNA → proteins

Zooxanthellae reclassification (coral symbionts)

• Originally Symbiodinium microadriaticum (one species with many strains).

• Genomic data split into several species (e.g., S. minutum, S. trenchi, S. kawagutii, etc.).

• Later reorganized into family Symbiodiniaceae; clade distinctions A, B, C, D retained for strains.

This lecture's topics

• Life on Earth

• Cladistics vs Taxonomy

• Relevance to modern biology: dynamic nature of classification and its implications for biodiversity research