6 - Tree of Life

Biodiversity

refers to the variety and variability of life on Earth, encompassing the diversity within species, between species, and of ecosystems

crucial for ecosystem resilience

Importance of biodiversity

Genetic diversity
Species diversity
Ecosystem diversity

3 different focus of biodiversity

Archaea
Bacteria
Eukarya

Three Domains of LIfe

Tree of Life

is a fundamental concept in biology that illustrates the evolutionary relationships among all living organisms. It is divided into three primary domains

Tree of life

visual representation of relationships

evolutionary relationship

holistic traits used to depict between groups

domain

largest most inclusive category in taxonomic grouping

artificial taxonomic category
natural taxonomic category

two systems of classification based on taxonomic groupings

artificial taxonomic category

• no scientific name

• experiential, shallow inclusions

  • ex: all green plants

natural taxonomic category

-there is basis
- there is existing scientific information that supports these categories
ex: Arecaceae and Felis catus - distinct species based on literature

bacteria

-domain is natural
- genetic diversity: Genomes range from <1 million to >10 million base pairs
•Mutations are expressed resulting to variability in phenotypes
- species diversity:
•~1 trillion bacterial species may exist, with only ~50,000 formally described.
•16S rRNA gene sequencing is commonly used to distinguish bacterial
taxa.

Proteobacteria
Firmicutes
Actinobacteria
Cyanobacteria
Bacteroidetes

species diversity of bacteria (types)

Proteobacteria

Includes E. coli, Salmonella, Rhizobium

Firmicutes

Gram-positive bacteria like Bacillus, Clostridium

Actinobacteria

Streptomyces (antibiotic producers)

Cyanobacteria

Photosynthetic, oxygen-producing microbes

Bacteroidetes

Common in the human gut

Aquatic
Soil
Host-associated
Extreme environments

Ecosystem Diversity of bacteria

Thermophiles
Halophiles
Acidophiles
Psychrophiles

Types of bacteria in extreme environments

Thermophiles

Hot springs. Thermus aquaticus

Halophiles

Salty lakes. Halomonas spp.

Acidophiles

Acidic environments. Helicobacter pylori

Psychrophiles

Arctic/Antarctic ice. Psychrobacter spp.

Archaea

• hyperextermophiles

• can survive 100 Celsius, pH 1-12, anoxic conditions

  • obligate anaerobes

Archaea

•Genetic Diversity
•Many have specialized genes that allow survival in extreme conditions—such
as thermotolerance, halotolerance, or acid resistance

Unique Chaperonins: Cpn60

This gene codes for a type of chaperonin specifically adapted for protein folding under extreme heat, differing from bacterial chaperonins.

Thermophilic DNA Polymerases:: Pfu DNA polymerase

Found in Pyrococcus furiosus, this enzyme is adapted for high-temperature DNA replication and is distinct from bacterial polymerases.

Euryarchaeota
Crenarchaeota
Thaumarchaeota
Asgard Archaea

Known groups of archaea

Euryarchaeota

Methanogens, halophiles, thermophiles

Crenarchaeota

Mostly thermophilic or acidophilic Archaea

Thaumarchaeota

Ammonia-oxidizing Archaea found in soil and oceans

Asgard Archaea

Promethearchaeati. A recently discovered superphylum with genes linking them closely to Eukaryotes

Thermophiles
Halophiles
Acidophiles and Alkaliphiles
Methanogens

Ecosystem Diversity of Archaea

Extreme Environments:

Thermophiles

•Ecosystem Diversity (archaea)

•Extreme Environments:

- Hot springs, hydrothermal vents (e.g., Sulfolobus)

Halophiles

•Ecosystem Diversity (archaea)

•Extreme Environments:

- High-salt environments like salt lakes and salt mines (e.g., Halobacterium).

Acidophiles and Alkaliphiles

•Ecosystem Diversity (archaea)

•Extreme Environments:

- pH extremes. (e.g., Aciduliprofundum)

Methanogens

•Ecosystem Diversity (archaea)

•Extreme Environments:

- Anaerobic environments like swamps, cow guts, and deep-sea sediments. (e.g., Methanobacterium formicicum)

Large Genomes
Introns and Exons
Gene Regulation
Endosymbiotic Genes

•Genetic Diversity (eukarya)

• _________: Eukaryotic genomes vary dramatically in

size and gene content (e.g., humans ~3 billion base pairs;

some plants and amphibians much more).

• ___________: Genes are split by introns, allowing

for alternative splicing and multiple protein products from

one gene.

• _________: Complex regulatory networks involving

enhancers, silencers, epigenetic modifications, etc.

• __________: Organelles like mitochondria and

chloroplasts have their own genomes—remnants of

ancestral prokaryotic symbionts.

Animals
Plants
Fungi
Protists

Eukarya

•Species Diversity

•______ (Metazoa): Vertebrates,

invertebrates, insects, etc.

•_______: From mosses and ferns to

flowering plants.

•_______: Yeasts, molds,

mushrooms—important

decomposers and symbionts.

•_______: Diverse single-celled

eukaryotes like Paramecium,

Plasmodium, and algae

Ecosystem function
Ecosystem services

The Value of Biodiversity

Ecosystem Services

benefits that humans derive from natural ecosystems

Conservation

A crisis-oriented discipline aimed at protecting species, habitats, and ecosystems

Document
Understand
Develop strategies

Core Goals: (conservation)

1. ______ biodiversity

2. _______ human impacts on

biodiversity

3. ________ to prevent

extinction and restore

ecosystems