Dire Wolf Discussions and GWAS

Dire Wolf Discussions

Historical vs. De-Extinct Dire Wolves

• Historical Dire Wolf: Refers to the original, extinct species.
• De-Extinct Dire Wolf: The "new one," brought back by Colossal, which is somewhat subjective.

Species Concepts

Three Species Concepts:

1. Biological:
   • Test by mating the "new" dire wolf with a gray wolf.
   • Observe offspring for:
     • Fertilization
     • Ability to carry to term
     • Ability to breathe
   • Limitations: Scientists often can't perform all tests due to resource constraints. They must justify their methods and acknowledge limitations.
2. **Genetic (Biogenetic):
   • Compare the DNA sequences of both species.
     • Threshold for differences is subjective (e.g., 20%, 50%, 100%). There is no objective cutoff.
   • Historical dire wolf genomes exist, enabling comparison.
   • Comparing DNA sequences of both, using the existing genome data for the historical dire wolf.
3. Phylogenetic:
   • Assess the tree of life to see how closely related they are.
   • Dire wolves and gray wolves diverged approximately 5,000,000 years ago. This suggests they don't share a recent branch of ancestry.
   • Data collection involves sequencing data.

Morphological and Phenotypical traits

• Morphological refers to what something looks like
• Behavior is also a phenotype. This can be harder to categorize,requiring observation.

Applying Species Concepts to the De-Extinct Dire Wolf

The Crux of the Debate:

• Is the de-extinct dire wolf a gray wolf, a historical dire wolf, or something new?

Testing with Species Concepts:

• Biological: Mate the new dire wolf with a gray wolf and observe offspring.

  • If mating is possible and offspring are viable, it suggests they may be the same species.

• If the new wolf can breed with gray wolves and produce fertile offspring.

• Historical Dire Wolf: Biological testing is impossible because historical dire wolves are extinct.

• Genetic: compare the new dire wolf to a gray wolf. Compare the DNA sequences of both, and then applying a subjective cutoff.

  • If the new wolf have large genetic differences that would suggests they are different species.

• Phylogenetic: Analyze sequenced data to see if they're really different.

   **Sister to the Gray Wolf**: The dire wolf being described as sister to the gray wolf.
  

• Morphological: Like the new wolf look, that supports if it is a historical direwolf the most.

Limitations and Subjectivity in Science

• Scientific papers always discuss the limits of their study.
• Applied research must be careful about how results are used and interpreted.
• Science rarely has absolute answers.
• There is often a "more right" answer, justified with evidence.

Phylogenetic Relationships

• Dire wolf is sister to the gray wolf and everything else.
• A more justified "sister" relationship involves sharing a recent common ancestor.
• The common ancestor of a sister group is what matters, not individual species within the group.

Genetic Similarity

• Gray wolves have around 19,000 genes.
• Dire wolves have 99.5\% genetic similarity, equating to approximately 95 gene differences.
• The de-extinct dire wolf had only approximately 14 genes changed.

Ethical Considerations

• Genes were altered in gray wolves rather than directly inserting dire wolf genes.
• Concerns about health consequences (e.g., blindness) in gray wolves, based on prior research with dogs.

Morphological Comparison

• Dire wolves and gray wolves are morphologically similar (dire wolves are slightly larger).

Population Viability of De-Extinct Dire Wolves

Concerns:

• Small population size (only three).
• Lack of gene flow and genetic diversity.
• Risk of inbreeding depression.
• Unknown environmental reactions.

Counterarguments:

• Genetic engineering could introduce diversity.

GWAS (Genome-Wide Association Study)

Overview:

• Method to find loci linked to a trait (SNPs are evidence).
• SNPs (single nucleotide polymorphisms) are single nucleotide differences.

Steps:

1. Sample Collection: Get a sample of individuals with the trait and sample without the trait. Need a group with black hair and a group with white hair.
2. Sequencing: Sequence all the DNA from each group.
3. Comparison: compare the sequences, looking for overlaps and differences.
   • Line up sequences from all individuals and find differences.
   • Identify locations with many differences; plot along the genome.
   • It's super important to think about the groups, because you can have variation within just a group.

Example: Dog Hair Color

• Compare DNA sequences of black-haired and white-haired dogs.
• Look for sequence variations consistently different between the two groups.

Setting up the Experiment

• Crucial to define treatment groups and experimental groups.
• GWAS facilitates statistical comparison.

Manhattan Plot Interpretation

• The greater the p-value, the greater the association between the two groups, difference in their groups that we compare is really high.