Lecture 10: Ancient DNA

Question 1

The ancient DNA revolution

Answer 1

• Next generation sequencing
• Targeting the right part of the skeleton
• Improved extraction methods with a focus on very short fragments
• New library building methods
• DNA hybridization capture

Question 2

What is ancient DNA?

Answer 2

1. No clear definition or age limit
2. Broadly speaking, DNA from samples that have not been stored with the explicit aim of preserving DNA
3. Sometimes distinction between museum (< 200 years), historical (< 500 years) and “true” ancient DNA (> 500 years)

Question 3

What characterizes ancient DNA?

Answer 3

1. Generally small amounts of DNA – kind of
2. Contamination – sometimes
3. Short fragments – still true
4. Miscoding lesions – still true
   -> Often when Uracil accures (not normally in DNA)?

Question 4

Sources for ancient DNA-like DNA

Answer 4

• Palaeontological samples, Museum specimens, Bones, Teeth, Hair, Dried skins/cadavers, Formalin fixed soft tissues
• Needs to be young enough (not older than two million years -> in cold areas) -> covers different climates (shows climate fluctuations)

Question 5

How old can ancient DNA be?

Answer 5

1.Depends on the environment
2. In permafrost: at least 2 million years (rare)
3. Outside the permafrost: at least 370,000 years (also rare)
-> if colder -> aDNA is better preserved

Question 6

What affects ancient DNA survival?

Answer 6

1. Age
2. Temperature
3. General (macro- and micro-) environmental conditions (humidity, pH, stability)
4. Part of the skeleton

Question 7

Assessing authenticity: two different approaches

Answer 7

1. Ancient DNA: Do to right or not at all
2. Assessing ancient DNA studies

Question 8

Four “Laws” of ancient DNA

Answer 8

1. Ancient DNA is only present in trace amounts.
2. Ancient samples are highly contaminated!
3. So remove the outer surface of the sample!
4. Ancient DNA is short.

Which one is true?

Question 9

Law 1: low DNA amounts

Answer 9

Often correct
But… you can obtain large amounts of DNA from some ancient samples

Problem of DNA extraction: losing fragments during extraction

Question 10

Law 2: Ancient samples are highly contaminated!

Answer 10

• Small amounts – high contamination risk -> from storage together
• It is all about the ratio between contamination (reduce) and ancient DNA (increase). Best: Do both!
• Post PCR lab (separation of PCR from other labs) -> suits against contamination
  -Ancient samples are highly contaminated – with environmental DNA
• Just sequence, if you can afford it…
• Hybridisation capture
• Matters which bone you use for extraction (the petrous bone is good to use -> gold fever)
  -> But… some ancient samples have high endogenous DNA and little contamination

Question 11

Law 3: Remove the outer surface of the sample!

Answer 11

• that may actually be the best bit!
• Surface is better and less contaminated
• If you do not have a petrous – use a CT-scan

Question 12

Law 4: Ancient DNA is short

Answer 12

Correct!
But… long stretches of ancient DNA do exist, in the genomes of living individuals

Question 13

Things to do with ancient DNA

Answer 13

Phylogenetics, Paleoecology, Population genetics, Functional genetics, Domestication, Paleoepidemics, Genomics

Question 14

Examples: Elephant evolution

Answer 14

• The choice of outgroup – extinct relatives (living relatives are to different in morphology)
• African elephant is outgroup -> all come from Africa

Question 15

Conclusions

Answer 15

1. Next generation sequencing has transformed ancient DNA research
2. NGS can be used to investigate phylogenetics, population genetics, full genome sequencing and many other questions
3. NGS genome projects are transforming our view of extinct species and the very concept of extinction

Question 16

What is Deamidation?

Answer 16

• chemical reaction in which an amide functional group in the side chain of Asp or Glu is removed or converted to another functional group
• the older the DNA, the more deamidation, more or less linear relation