Bio Phylogeny and Evolution Notes

VISTA: Variation, Inheritance, Selection, Time, and Adaptation
- Used to identify if natural selection has occurred
Inbreeding Practices:
  - Description: Inbreeding practices include breeding siblings, cousins, or using line breeding (parent x offspring) to maintain specific traits that arise from unique mutations.
  - Impact on Disease: This information supports the idea that certain ailments are more prevalent in some breeds over others because:
    - The gene pool is significantly narrowed when relatives interbreed.
    - Shared recent ancestry results in highly similar DNA among individuals, increasing susceptibility to diseases that could be survived by a more genetically diverse population.
Comparison of Selection Types:
  - Artificial Selection vs. Natural Selection:
    - Both processes result in organisms that are "better fit" for their environments.
    - Artificial Selection: Involves human intervention where an external organism selects preferred traits.
    - Natural Selection: Driven by environmental pressures that confer advantages to certain traits.
- Requirements for Natural Selection to Occur:
  - Variation in traits within a population.
  - Competition for resources and mates.
  - Heritable traits that confer advantages in survival and reproduction.

Students will be able to communicate scientific information that common ancestry and biological evolution are supported by multiple lines of empirical evidence.
Phylogenetic Trees:
  - Information Representation: Phylogenetic trees can convey extensive information and can be depicted in various formats.
  - Components:
    - Each line represents a lineage.
    - Each branching point is designated as a node.
    - Nodes signify the common ancestors of species.
    - Collectively, nodes and all branches stemming from them are known as clades.
    - Species within a clade exhibit shared derived characteristics.

Tree Representation:
- The tree showcases relationships between various dog breeds by analyzing SNPs (Single Nucleotide Polymorphisms) in DNA to ascertain genetic relationships.
- Notable dog breeds listed include: Bru, Papillon, Miniature Pinscher, American Cocker Spaniel, English Springer Spaniel, and many others spanning various geographical regions and lineage classifications.

Cladogram:
- Shows evolutionary relationships but does not imply a timescale.
- All branch points are equidistant.
Phylogram:
- Implies different branch lengths representing time.
- Example labeled with specific branch lengths and evolutionary time frames (e.g., millions of years before present - mya).

DNA Sequencing:
  - The advent of DNA sequencing technologies has significantly enhanced the understanding of relationships among species, leading to more accurate phylogenetic trees.
  - Branch Points (Nodes):
    - Nodes depict recent common ancestors.
      - For instance, a box can designate the node for all fox species, while a triangle can represent the node for all Canis species.
Species Name Formation:
  - BINOMIAL NOMENCLATURE: A species name consists of two parts
    - The first part signifies the genus. E.g., wolves, coyotes, and dogs belong to the genus CANIS.
    - The genus for the foxes is Vulpes.
    - Subspecies Identification:
      - The domestic dog is identified as Canis lupus familiaris and is classified as a subspecies.

Comparative Analysis:
  - A question arises: Is a dog more closely related to a coyote or a wolf?
    - According to the phylogenetic tree, dogs share a more recent common ancestor with wolves than with coyotes.
    - Evidence:
      - Direct lineage shows that the ancestor of wolves and dogs is more recent than that of coyotes and dogs, making wolves and dogs more closely related.

Homologous Structures: Indicate a shared common ancestor.
- Definition: Structures that are similar in form but serve different functions.
- Example: The wings of birds and the forelimbs of mammals are considered homologous.
Convergent Evolution: Happens when species develop similar features due to similar selective pressures, not shared ancestry.
- Analogous Structures: Show similarities due to convergent evolution, such as the wings of insects versus the wings of birds.
- Definition: Structures that arose independently in different species and do not share a recent common ancestor.

Key Topics:
  - What constitutes a species?
  - Understanding phylogenetic trees.
  - Differentiate homologous structures from convergent structures.
  - Practice labeling a phylogenetic tree.
  - Identify homologous and analogous structures and the factors leading to their development.