Biology 3594A Study Guide - Final Guide: Thylacine, Historical Demography, Morphometrics
13 May 2018
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Lecture 17 Flashcards
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Evidence that specific substitutions lead to
drivers of hypermutation other
substitutions do not
Sensitivity to amino acid changes - not just the codon but
the nature of the substitution matters
Sensitive codon
Same codon, different substitution, different mutation
burden
2 major events contributing to the
extinction of the Tasmanian Tiger
(historical demography)
1. Humans arrive - kill animals and move them out of
their natural habitat
2. Tasmania became an island, restricted the population
size
- they also like to be in demes (small pops, less migration)
-> smaller diversity
- contributed to their decline and extinction
- decline in genetic diversity arose prior to arrival of
humans and isolation of Tasmania
3D landmark-based geometric
morphometrics
- why the thylacine has a skull that looks
like a mammal (dog)
Diet is the same as the mammal but it's also striking
because their ancient ancestor probably did not have the
same skull
Phenotypic convergence based on morphometry and
metrics
Genomic convergence through analysis of
homoplasious amino acids
Not enough evidence for genomic convergence
- increased genetic distance with decreased
homoplasious amino acid substitutions
- results are consistent with neutral evolution and not
genomic convergence
- no evidence for strong selection
Thylacine is grouped with other mammals and
vertebrates
- clustered in the same area, can't distinguish between
relation with mammals vs other vertebrates
- if there was some genomic contributor you would
expect some separation
Alternate hypothesis for convergent
evolution (mechanism)
Perhaps a result of mutations affecting gene expression
- next steps are to look at how much protein we have,
regulation of proteins, timing and location of gene
expression
- look at CREs (promoters, enhancers)
find more resources at oneclass.com
find more resources at oneclass.com
Resurrection experiment
Take an ancient gene and resurrect it by putting it into
cells or a mouse model
- figure out why that protein allows for adaptations
Challenges associated with the study of
aDNA (4)
pG. 8 of the reading
1. Expensive lab required: positive pressure, cleaned
daily, hoods for certain reactions, UV radiated agents,
suits/hairnets/masks/gloves
2. Controls: positive control is cave bear bone, negative
control is water
3. Need to avoid contamination, careful you don't
sequence the technician's DNA
4. Potential contamination with microbes, people, putting
the same thing back into the reaction
Challenges in studying population of extinct
species
You need a lot of individuals, and sometimes with aDNA
you only have 1
Population genetics is about the DNA of multiple
individuals
Studying population genetics:
matrilineal/patrilineal/whole population
Matrilineal: study mitochondrial DNA
Patrilineal: study the Y chromosome DNA
Whole population dynamics: nuclear DNA, mitochondrial
DNA, Y chromosome DNA
Advantages to mitochondrial DNA
Easy to study because it's small (16k bp)
Only need the small hypervariable region (D loop) to have
survived to gather information on the variability between
animals
- the rest of the genes are highly conserved
DNA decay
Most frequent is cytosine to thymine substitutions
(deamination)
- most often at the ends of a molecule
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Evidence that specific substitutions lead to drivers of hypermutation other substitutions do not. 2 major events contributing to the extinction of the tasmanian tiger (historical demography) Why the thylacine has a skull that looks like a mammal (dog) Genomic convergence through analysis of homoplasious amino acids. Sensitivity to amino acid changes - not just the codon but the nature of the substitution matters. Same codon, different substitution, different mutation burden: humans arrive - kill animals and move them out of their natural habitat, tasmania became an island, restricted the population size. They also like to be in demes (small pops, less migration) Decline in genetic diversity arose prior to arrival of humans and isolation of tasmania. Diet is the same as the mammal but it"s also striking because their ancient ancestor probably did not have the same skull. Increased genetic distance with decreased homoplasious amino acid substitutions. Results are consistent with neutral evolution and not genomic convergence.
