Lecture 5: Using Phylogenies

Learning Goals

  • At the end of this lecture, you should be able to:

    1. Explain how phylogenies can be used to build classifications of organisms.

    2. Explain how phylogeny was used to track the sale and international trade of whale meat.

    3. Provide examples of how phylogeny is used to inform medical forensics.

Overview

  • Previous Lecture: Building Phylogenies

  • Current Lecture: Using Phylogenies

  • Next Lecture: Assembling the Tree of Life

Key Applications of Phylogenies

A. Taxonomy

  • Phylogenies are employed to construct meaningful classifications of organisms.

  • By assigning scientific names only to monophyletic groups, classifications reflect the evolutionary history.

  • The binomial naming system, established in 1753, is predominantly utilized.

    • Example:

    • Pacific Tree Frog

      • Kingdom: Animalia

      • Phylum: Chordata

      • Class: Amphibia

      • Order: Anura

      • Family: Hylidae

      • Genus: Pseudacris

      • Species: Pseudacris regilla

    • The species designation comprises a genus name followed by a specific epithet, both italicized or underlined (e.g., Homo sapiens).

B. Conservation Biology

  • Phylogenies reveal the connections and classifications of organisms based on shared features, called synapomorphies.

  • Every monophyletic group has a unique common ancestor that is not shared with any other groups.

  • Such classifications are considered “natural,” linked by common ancestry, enhancing their meaning.

  • Polyphyletic Groups Issue:

    • Polyphyletic groups cannot be defined by features stemming from a common ancestor.

    • Example: The term "Homeothermia" suggests that the ability to regulate internal temperature is homologous across different species when it is not.

C. Medical Forensics

  1. The International Whaling Commission prohibited commercial whaling in 1986; however, countries like Japan, Iceland, and Norway continue hunting for "scientific" purposes.

    • Minke whales are hunted in Japan and can be marketed as meat.

    • Trade of endangered whale species (such as fin, gray, humpback, and blue) is illegal.

  2. Case Study: Are You Eating What You Think You’re Eating?

    • In 1994, scientists utilized a genetic database of identified samples to collect whale meat from markets in Japan.

Conservation Efforts

  • Given limited resources, conservation biologists must prioritize areas for management interventions to protect the greatest evolutionary history.

  • Example with Giraffes:

    • Though previously thought to be a single species, new genetic studies indicate at least four distinct giraffe species:

    • West African

    • Reticulated

    • Rothschild's

    • Angolan

    • Masai

    • These findings led to reevaluating conservation priorities and management plans based on evolutionary diversity.

Medical Forensics Scenario

  • Case Study: Kim Bergalis contracted HIV, asserting she was a virgin, had never used IV drugs, or received a blood transfusion.

    • She had two molars extracted by her dentist.

  • Other community members also contracted HIV, all sharing the common factor of being treated by the same dentist.

  • A sequencing of the virus was performed among the dentist’s patients (denoted as Patient A) and included control sequences from the local community (denoted as LC).

  • Important Note: Ignore the duplicated patient sequences, as they are repetitions of the gene used to infer the phylogeny.