Lecture 31

Lecture Overview

Introduction to Genetics Class

  • Update on course assignments and expectations for engagement.

  • Chapter 10 Achieve assignment due Monday; encourages students to review all materials thoroughly.

  • Note on assessment frequency: less frequent assignments moving forward, allowing for deeper learning.

Clouded Leopard Research

Overview of Clouded Leopard

  • An endangered species found in two distinct species: the mainland clouded leopard populating areas in southern China, Nepal, and India, and the Sunda clouded leopard residing on islands like Sumatra and Borneo.

  • Current population estimates range from 4,000 to 5,000 individuals, with both species experiencing critical endangerment.

  • Habitat loss is significant, with approximately 30% of their natural habitat deteriorating over the last 20 years due to deforestation and human encroachment.

Adaptations for Arboreal Life

  • Clouded leopards possess unique adaptations for life in trees:

    • Their coat features a modelled pattern that provides effective camouflage among the foliage of forests, aiding in hunting and predator avoidance.

    • They have the longest tail of any cat species, which aids in balance while navigating tree branches. Their ankles are rotatable, providing versatility in climbing.

    • Adapted with long canine teeth designed specifically for their hunting method, which involves biting the nape of their prey to subdue it swiftly.

Genomic Research Findings

Whole Genome Sequencing

  • Conducted whole genome sequencing of 20 mainland clouded leopards to understand genetic diversity and evolutionary history.

  • Utilized a molecular clock to date the divergence within the genus Neofelis, revealing:

    • A divergence of approximately 2 million years ago from the mainland clouded leopard to the Sunda clouded leopard and approximately 6 million years from other cat species.

    • Divergence aligns with historical glacial epochs that initiated environmental changes influencing species adaptations.

    • Evidence of incomplete lineage sorting: some alleles remain in a shared state rather than sorting into distinct lineages.

Genes Under Selection

  • Identified genes in the clouded leopard that are under selection, highlighting how these genetic changes have evolved:

    • Positive Selection: 153 genes related to survival traits.

    • Rapid Evolution: 386 genes indicating swift evolutionary changes.

    • Convergent Evolution: 21 genes that have adapted to similar functions across different species.

    • These genes are primarily concentrated in areas related to tooth development, pigmentation (affecting coat color), muscle development, and olfaction (sense of smell).

Gene Specifics

  • Tail Length Genes:

    • lnl28 and TBXT: both genes associated with determining mammalian tail length, with specific mutations identified in both clouded leopards and certain primates, suggesting a shared evolutionary pathway.

  • Canine Teeth Genes:

    • APC gene: known to influence tooth size across various mammalian species, including humans, indicating a genetic correlation in morphological traits.

  • Coat Color Variations:

    • MC1R gene: critical for pigmentation in several species, having specific mutations linked to the distinct coat colors of clouded leopards and their relatives such as marbled cats.

Reproductive Challenges

  • Clouded leopards face significant reproductive hurdles, with high rates of abnormal sperm observed (75-80% abnormality), posing risks for successful mating.

  • Genetic analysis has identified 289 deleterious mutations affecting sperm development, which complicates breeding.

  • A deletion in MHC (Major Histocompatibility Complex) genes has been linked to sterility issues, raising concerns about genetic health and reproduction.

  • Additionally, low heterozygosity rates coupled with high inbreeding coefficients suggest a decreasing genetic diversity that may threaten the long-term survival of the species.

Applications and Conservation Efforts

  • Emphasizes the critical role of genomic technology in conserving endangered species and understanding genetic health risks.

  • Necessity for hybridization practices or genetic interventions is highlighted to promote increased genetic diversity within clouded leopard populations.

  • Acknowledgment of the risks clouded leopards face from potential inbreeding depression, which can diminish overall fitness and adaptability.

Genetic Linkage and Recombination

  • Reviewed key concepts of genetic linkage and the applications of Punnett squares:

    • Dihybrid crosses illustrate phenotypic ratios (9:3:3:1) for unlinked genes, whereas linked genes modify these ratios closer to 3:1.

  • Estimations of recombination frequency are crucial, with test crosses serving as an effective method for determining genetic linkage.

Genetic Mapping with Centimorgans

  • Centimorgan: a unit used to express the probability of recombination occurring between two loci on a chromosome; 1 centimorgan equals a 1% chance.

  • Recognition of variations in recombinant frequencies across different chromosomes that can influence mapping strategies in genetic research.

Jargon and Genetic Configuration

  • Discussion of terms related to chromosomal arrangements:

    • Cis configuration: alleles located on the same chromosome.

    • Trans configuration: alleles located on different chromosomes.

  • Overview of Genome-Wide Association Studies (GWAS) that utilize the concept of linkage to associate single nucleotide polymorphisms (SNPs) with specific traits, noting how recombinations can break these associations over generations.

  • Importance of the proximity of SNPs to the causal trait genes for accurate association discovery.

Chromosome Variation (Brief Overview)

  • Types of chromosomal mutations are noted:

    • Duplications and deletions resulting from unequal crossing over.

    • Inversions can create challenges for proper alignment during meiosis, potentially leading to reproductive isolation.

    • Instances of inversions in species demonstrate significant evolutionary impacts, referencing human-chimpanzee relationships.

Conclusion

  • Concludes with a reflection on the complexity and interconnectedness of genetics with conservation strategies.

  • Reinforces the necessity of integrating new technologies in the ongoing study of genetic health in endangered species, particularly to inform effective conservation and management practices.


Study Questions for Lecture 31 (11/4/2024)

1. Molecular Clock and Clouded Leopard Species

Question 1:

  • Based on the molecular clock, how long ago did the two clouded leopard species (genus Neofelis) part ways (last share a common ancestor) with the other big cats? The vast majority of the genome supports a phylogeny where Neofelis forms one clade, and the tigers, leopards, and lions a separate (sister) clade. A small % of the genome does not support this tree. Is this likely due to introgression or incomplete lineage sorting? What is incomplete lineage sorting?

Answer 1:

  • The two clouded leopard species diverged from other big cats approximately 6 million years ago. The minority of the genome not supporting this tree is likely due to incomplete lineage sorting, which occurs when gene lineages separate at a slower rate than the species divergence, leading to some gene alleles being shared among species.

Question 2:

  • In what phenotypic traits did they find evidence of rapid evolution/strong selection?

Answer 2:

  • The study found evidence of rapid evolution or strong selection in phenotypic traits such as tooth development, pigmentation, and aspects of musculoskeletal structure related to locomotion.

Question 3:

  • What did the authors of the paper discover at a couple of pigmentation genes that indicates that the color resemblance is not just superficial? What do we call it when the same change occurs in different lineages independently?

Answer 3:

  • The authors discovered mutations in pigmentation genes indicating that the color resemblance between clouded leopards and marbled cats is not superficial, establishing an example of convergent evolution since similar traits evolved independently in different lineages.

Question 4:

  • Does the clouded leopard have low, medium, or high levels of heterozygosity in its genome? What evidence is there that the species has, in its evolutionary past, suffered from small Ne and inbreeding depression?

Answer 4:

  • The clouded leopard exhibits low levels of heterozygosity. Despite having a population of around 5,000, evidence suggests historical inbreeding depression due to past population bottlenecks or changes in effective population size (Ne) leading to increased genetic drift.

2. Cucumber Traits and Crossbreeding

Question 1:

  • In the F1s, are the T and D alleles in cis or trans configuration?

Answer 1:

  • In the F1 generation (TtDd), the T and D alleles are in cis configuration.

Question 2:

  • What is the name of this type of cross (crossing back to a homozygous recessive)?

Answer 2:

  • The cross between TtDd and ttdd is known as a test cross. This type helps estimate recombination frequency because crossing TtDd with ttdd provides a clear phenotype distribution and separates parental types from recombinant types.

Question 3:

  • When you do this, you observe the following frequencies. What do you estimate the number of map units (cM) these two loci are apart?

  • Phenotype Frequency

    • Warty dull 0.40

    • Warty shiny 0.10

    • Smooth dull 0.10

    • Smooth shiny 0.40

Answer 3:

  • The number of map units (cM) can be estimated based on the observed phenotype frequencies, giving a calculation that reflects the recombination frequency derived from these percentages.

3. Alternate Test Cross and Phenotype Frequencies

Question 1:

  • Suppose that someone gives you heterozygote seeds (TtDd) where the T and D alleles are in repulsion. What would that look like? Label the chromosome with appropriate letters.

Answer 1:

  • For a heterozygote in trans (TtDd with T and D on different homologs), it would look like: T-D / t-d.

Question 2:

  • Given the trans configuration, what do you expect the frequency of the following 4 phenotypes to be with an 8% recombination frequency?

    • Warty dull

    • Warty shiny

    • Smooth dull

    • Smooth shiny

Answer 2:

  • The expected phenotype frequencies can be calculated based on the 8% recombination frequency affecting the distribution of these phenotypes in the offspring.

4. Chromosome Map and Recombination Frequencies

Question 1:

  • Give the approximate recombination frequency you expect between loci A and C (1) under perfect additivity, and (2) using the figures below.

Answer 1:

  • Under perfect additivity, the A to C recombination frequency would be calculated by adding the cM values between A-B and B-C. According to the data provided, the figure method can provide a more precise recombination frequency based on graphical analysis of distance in cM.

5. Crossing Over and Linkage

Question 1:

  • Why does the probability of recombination between two loci depend on whether there are an odd vs an even number of crossing over events? What happens to the linkage between the loci when there are two crossing-over events?

Answer 1:

  • With an odd number of crossing over events, there is recombination between genes, while an even number usually restores parental combinations, maintaining linkage. This dynamic alters recombination chances based on proximity between loci.

6. Mendel’s Law of Segregation

Question 1:

  • Why is it also true that loci that are sufficiently far apart on the same chromosome also assort independently?

Answer 1:

  • Loci that are farther apart on the same chromosome appear to assort independently due to a higher likelihood of recombination occurring between them, making their inheritance patterns resemble those of loci located on different chromosomes.

7. GWAS and SNPs

Question 1:

  • What does GWAS stand for?

Answer 1:

  • GWAS stands for Genome-Wide Association Studies.

Question 2:

  • What does SNP stand for?

Answer 2:

  • SNP stands for Single Nucleotide Polymorphism.

Question 3:

  • Suppose a mutation that causes a serious disease arises in a gene at the location indicated in yellow. What happens over generations to the association of the disease-causing allele in yellow and that 11100 combination of SNP alleles? Which allele of which SNP locus is the association going to last the longest in?

Answer 3:

  • Over generations, the association between the disease-causing allele and the original haplotype will decrease due to recombination. The allele most likely to be retained is a0 or b0 at SNP loci.

8. Chromosome-Level Variation and BRCA Genes

Question 1:

  • Individuals who are heterozygotes for BRCA1 with one functional and one nonfunctional allele are at elevated risk of what?

Answer 1:

  • Individuals are at elevated risk for breast and ovarian cancer.

Question 2:

  • How many mutational variants are known for BRCA1?

Answer 2:

  • The known mutational variants for BRCA1 can be found on the NIH website under “Health conditions” and therein, “Breast Cancer.”

Question 3:

  • What does this suggest about expression of the gene for individuals who are homozygous for the normal allele vs heterozygotes?

Answer 3:

  • This suggests that heterozygotes may express less functional BRCA1 protein compared to homozygotes for the normal allele, indicating potential complete dominance.

Question 4:

  • How likely is a woman who is heterozygous with one nonfunctional copy of the BRCA1 gene to get ovarian cancer? How does this compare to the general population?

Answer 4:

  • Women who are heterozygous for BRCA1 are at a significantly higher risk for ovarian cancer compared to the general population.

9. Duplication Types

Question 1:

  • When a duplication event results in the copy being immediately adjacent to the original, what is this type of duplication called?

Answer 1:

  • This type of duplication is called a tandem duplication.

10. Chromosome Mutations and Crossing Over

Question 1:

  • What is meant by unequal crossing over? What types of chromosome mutations does it tend to generate?

Answer 1:

  • Unequal crossing over results in duplications and deletions of chromosomal regions and is more prone to occur following tandem duplications.

Question 2:

  • Once a region of a chromosome experiences a tandem duplication event, do the chances of unequal crossing over remain the same, go up, or go down?

Answer 2:

  • The chances of unequal crossing over go up after a tandem duplication event.

11. Impact of Deletions

Question 1:

  • What are several reasons why having a deletion usually leads to bad outcomes?

Answer 1:

  • Having a deletion can lead to loss of essential genes, disrupt gene function, cause haploinsufficiency, and may result in dosage imbalances, contributing to negative phenotypic effects.

12. Prader-Willi Syndrome (PWS)

Question 1:

  • What is it called when genes are methylated so as to silence them in the formation of gametes?

Answer 1:

  • This process is called genomic imprinting.

Question 2:

  • Normally, are the maternal genes, or the paternal genes, or both maternal and paternal genes in this region of chromosome 15, expressed?

Answer 2:

  • Normally, the paternal genes in this region of chromosome 15 are expressed.

Question 3:

  • Why would a deletion during spermatogenesis of this region of chromosome 15 lead to PWS?

Answer 3:

  • A deletion of paternal genes in this region during spermatogenesis leads to a lack of expression of critical genes, causing PWS in offspring.

13. Chromosomal Rearrangements

Question 1:

  • Indicate which is (a) deletion, (b) duplication, (c) inversion, and (d) translocation among the given diagrams.

Answer 1:

  • Diagrams should be labeled according to the specified types of chromosomal rearrangements as per the provided visuals.

14. Inversions in Meiosis

Question 1:

  • Do inversions present problems during meiosis when they appear as a homozygote or as a heterozygote?

Answer 1:

  • Inversions complicate meiosis primarily when they appear as heterozygotes, as difficulties arise during crossing-over interactions.

Question 2:

  • Where do things go awry during meiosis—during lining up of homologous chromosomes, or during crossing-over/segregation?

Answer 2:

  • Problems arise during crossing-over/segregation when one homolog has the inversion and the other does not.

Question 3:

  • Why will a significant proportion of the gametes from this heterozygous individual be inviable?

Answer 3:

  • Many gametes from heterozygotes containing inversions may be non-viable due to improper pairings during meiosis, leading to missing critical genes.

15. Evolutionary Role of Inversions

Question 1:

  • What do we call it when, upon secondary contact, mating occurs and offspring are born, but those offspring suffer reduced viability?

Answer 1:

  • This phenomenon is referred to as fitness reduction due to hybridization.

Question 2:

  • Suppose that during allopatry, an inversion has become common or fixed in one population but not the other. Will hybrid offspring tend to be homozygous or heterozygous for the inversion?

Answer 2:

  • Hybrid offspring will tend to be heterozygous for the inversion since they will inherit different genetic backgrounds from each parental population.

Question 3:

  • Would selection tend to favor individuals who mate with those of the same population or those from the other population?

Answer 3:

  • Selection would tend to favor individuals who mate with those of the same population due to adaptation and fitness advantages associated with local conditions.

Question 4:

  • Do you see how this could contribute to speciation?

Answer 4:

  • Yes, this reproductive isolation and preference for local mating can lead to genetic divergence over time,