Prokaryotes and Protists

How does speciation happen?
- A critical process in the evolution of new species through the cessation of gene flow between populations.
Gene Flow
- The transfer of genetic material between populations of the same species.
- Cutting off gene flow is essential to allow populations to diverge genetically leading to the development of separate species.

Geographic Barrier
- Example: The Grand Canyon serves as a geographic barrier separating two squirrel species.
- Not all species will diverge despite barriers, such as birds and other animals on either side of the Grand Canyon.
Reproductive Isolation
  - Refers to mechanisms that prevent different species from interbreeding.
  - Types of Reproductive Isolation:
    1. Temporal Isolation:
       - Species breed at different times (seasonal or daily).
    2. Habitat/Ecological Isolation:
       - Species occupy different habitats within the same geographic area.

Types of Reproductive Isolation Continued:
  3. Behavioral Isolation:
     - Differences in courtship or mating behaviors.
  4. Mechanical Isolation:
     - Physical differences prevent mating (e.g., anatomy undesired fit).
     - Example: "Jeremy" the left-spiraled snail, who faced difficulty in mating due to mechanical isolation as the genital structures did not fit together.
  5. Gametic Isolation:
     - Sperm and egg are incompatible; fertilization is unsuccessful.
Examples of Mechanisms:
- When communication cues are not understood between species.
- Discuss the case of the left-spiraled snail and why it couldn’t find mating partners.

Types:
  6. Hybrid Inviability or Infertility:
     - Offspring of two different species do not survive or produce viable offspring.
     - Reduced Hybrid Viability:
       - Example: Some salamanders can hybridize, but their offspring are frail and do not survive long enough to reproduce.
       - Examples of hybrids include:
         - Horse + Donkey = Mule (sterile)
         - Rice hybrids, where the first generation is fertile but shrinks to sterility in subsequent generations.

Examining why certain organisms thrive in specific habitats;
- Example: The dependency of organisms on moisture, such as being common in redwood forests.
- The need for moist decaying logs and leaves for food and rodent burrows for shelter.

California's Ensatina Salamanders:
- Investigate the type of reproductive isolation that might be occurring.

Definition:
  - A process where two species influence each other's evolution.
  - Examples of Coevolution:
    - Parasites and hosts (e.g., body lice and their primate hosts).
    - Brood parasites and their host birds.
    - Predators and prey dynamics.
    - Orchids and their pollinators, with specialization occurring across different species of bee orchids.

Discussion on the implications of origins and extinction in relationships like the orchids and their pollinators.
Example:
- Oprhys apifera, an orchid that mimics female bees leading to pollination but lacking the necessary pollinators due to extinction.
- The extinction of the bee highlights issues of ecological dependencies that can lead to further species declines.

Timeline of Earth Formation:
   - Earth: 4.6 billion years ago
   - Oldest known rocks formed: 3.85 billion years ago
   - Prokaryotes appeared: 3.5 billion years ago
   - Eukaryotes appeared: 1.8 billion years ago
Discuss the atmospheric oxygen origins through the process of photosynthesis as shown in the equation:
$6 CO_2 + 6 H_2O <br>ightarrow C_6H_{12}O_6 + 6 O_2$

Three Domains:
  - Domain Bacteria
  - Domain Archaea
  - Domain Eukarya
    - Kingdom Plantae, Kingdom Fungi, Kingdom Animalia
  - Different shapes and arrangements observed in bacteria (e.g., Streptococcus pneumoniae, Clostridium tetani).

An exploration of specific bacteria shapes, e.g., cocci, bacilli, and their significance.
Discussion on how archaea are distinguished from bacteria, such as the presence of pseudomurein.

How Plants and Animals Acquire Nitrogen:
- Nitrogen fixation through bacteria in root nodules.
- Role of nitrifying and denitrifying bacteria in maintaining ecosystem balance.

Beneficial bacterial strains (e.g., Bifidobacteria, Lactobacilli) vs. harmful strains (e.g., Clostridium difficile).

Endosymbiotic Theory:
- Explanation of how eukaryotic cells evolved from ancestral prokaryotes by engulfing aerobic prokaryotes leading to mitochondria and chloroplasts.

Discussion on protists as eukaryotes that do not fall within the domains of fungi, plants, or animals, with examples such as Euglena, Amoeba, and Paramecium.

Definition:
- Unicellular organisms that lack a nucleus and membrane-bound organelles.
Types:
  - Domain Bacteria:
    - Includes a vast range of organisms, from pathogenic bacteria to beneficial bacteria involved in processes like nitrogen fixation.
  - Domain Archaea:
    - Similar to bacteria in appearance but differ biochemically and genetically; often found in extreme environments.
Shapes and Arrangements:
- Bacteria exhibit diverse shapes such as cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped).

Prokaryotes do not have membrane-bound organelles, which distinguishes them from eukaryotes.
The presence of peptidoglycan in bacterial cell walls is a key feature that helps identify them.
Archaea have unique biochemical pathways and structures, such as pseudomurein in some species.

Definition:
- Eukaryotic microorganisms that do not fall into the categories of fungi, plants, or animals.
Examples of Protists:
- Euglena (flagellated photosynthetic organism), Amoeba (protozoan with the ability to change shape), Paramecium (ciliated organism).
Significance:
- Protists play critical roles in ecological systems, acting as primary producers, decomposers, and as part of complex food webs.

Protists can provide insights into the evolution of eukaryotic cells and their transition from prokaryotic ancestors.
Understanding protists helps clarify the evolutionary relationships among various living organisms in the tree of life.