DNA Identification of Human Remains

Introduction

  • Jeremy Austin, an Evolutionary Biologist and Forensic Scientist, discusses DNA identification methods for human remains, focusing on missing persons and war dead.
  • The lecture will cover technology, biological and genetic aspects, challenges, and applications.

The Global Problem of Missing Persons

  • Missing persons are a significant global issue.
  • Statistics:
    • 40,000 sets of human remains are in police stations and mortuaries in the United States.
    • Australia has approximately 1,600 long-term missing persons.
  • Forced disappearances occur in over 80 countries, with more than 50,000 people missing, often due to government actions.
  • Natural disasters, such as the Boxing Day tsunami (over 200,000 deaths), create substantial identification challenges.
  • Wars result in highly dismembered and fragmented bodies, complicating identification.
    • Australia has over 25,000 missing service personnel since World War I.
    • The United States has over 80,000 missing service personnel.
  • Terrorist attacks, such as the World Trade Center attack (almost 3,000 deaths, over 15,000 body parts recovered), also pose major identification problems.

Methods for Forensic Human Identification

  • Three primary methods:
    • Fingerprints: Commonly used in criminal investigations and for police checks/passports.
    • Dental Records: Effective due to most people having dental records in countries like Australia.
    • DNA: Requires DNA from the remains and a reference sample for comparison.
      • Reference samples can be antemortem (hairbrushes, toothbrushes, mouthguards) or from family members.

Limitations of Fingerprints and Dental Records

  • Fingerprints are impossible to obtain from skeletonized remains.
  • Dental records are unavailable if a person never visited a dentist.
  • Criminals may attempt to prevent identification by destroying fingerprints and dental records (example: Queensland case of dismemberment and burning).

DNA Identification Requirements

  • Two essentials for successful DNA identification:
    • Ability to extract and sequence DNA from remains (bones, teeth, tissue).
    • A reference DNA sample for comparison (antemortem records, family members, DNA databases).
  • In cases where the identity is completely unknown, DNA can guide investigations.
    • Example: Identifying the sex of a child from remains found in a suitcase in Wanaka, South Australia.

Uses of DNA Beyond Direct Identification

  • Determining the number of individuals present at a site.
  • Identifying sex (male or female).
  • Predicting physical characteristics like hair and eye color.
  • Differentiating between historical and recent remains.
    • Example: Identifying traditional Aboriginal burials for repatriation using DNA and radiocarbon dating.
  • Determining biogeographic ancestry or ethnicity.

Types of DNA Used in Human Identification

  • Focus on different types of DNA found in human cells:
    • Autosomes: Inherited half from each parent, located in the nucleus.
    • Sex Chromosomes: X and Y chromosomes (males: XY, females: XX), located in the nucleus.
    • Mitochondrial DNA: Circular DNA found outside the nucleus in mitochondria (energy-producing organelles) present in hundreds or thousands of copies per cell.

Inheritance Patterns

  • Mitochondrial DNA: Passed on only by daughters; traces the maternal line (mother, maternal grandmother, etc.).
  • Y Chromosome: Inherited from the father and passed on only by males; traces the paternal line.
  • Autosomes: Biparental inheritance; approximately 25% from each grandparent, 12.5% from each great-grandparent, etc.

DNA Markers

  • Types of DNA used vary depending on the application.

Short Tandem Repeats (STRs) or Microsatellites

  • Autosomal DNA in the nucleus.
  • High power for individualization.
  • Relatively simple lab process, allowing for high throughput.
  • Measures the length of DNA.
  • Good for analyzing mixtures of DNA from multiple individuals.
  • Used for blood stains, fingerprints, saliva, skin, and hair.
  • Limitation: Requires relatively good quality DNA.
  • Requires a reference sample for comparison (family member, antemortem sample, DNA database).

STR Profile Example

  • Collecting an STR profile to identify samples.
  • Measurements are taken at different regions of the DNA called loci (Locus 1, Locus 2, Locus 3, Locus 4).
  • Measuring the length of the allele
  • Comparison of STR profiles from a bone to antemortem samples (toothbrush, hairbrush, mouth guard) to find a match.
  • The profile from mouthguard three has the same number of repeat units for each locus as the bone, supporting a match between person three and the bone itself.

Mitochondrial DNA

  • Used when DNA is degraded, or the person has been deceased for a long period.
  • Maternally inherited.
  • Cannot be used for individual identification since maternal relatives share the same mitochondrial DNA (e.g., siblings, maternal aunts).
  • Can be compared across distant relatives.
  • Useful for degraded DNA due to shorter fragment lengths.
  • Samples used: bones, teeth, and hair shafts.
  • Measures DNA sequence (As, Cs, Gs, and Ts) rather than length.

Mitochondrial DNA Sequence Example

  • Comparing the DNA sequence from a bone to family reference samples of missing persons.
  • Looking for a match between a family reference sample and the sequence from the bone.
  • In family reference two and four, there are some mismatches, therefore they can be excluded.
  • The family reference three has exactly the same mitochondrial sequence as the bone, which gives evidence to support that missing person and family reference three are maternally related.

Uses of Mitochondrial DNA

  • Analysis of shorter DNA fragments makes it useful if bones, teeth, or human tissue are degraded.
  • Higher copy number per cell means it lasts longer.
  • Comparison across distant relatives is possible.
  • Example:
    • Identification of King Richard III (died in 1485) using mitochondrial DNA.
    • Comparison to Michael Ipsen and Wendy Dooldig, who share an unbroken chain of female ancestors back to Richard III's sister, Anne of York.
    • Matching mitochondrial DNA supported the identification.
  • Another Example:
    • Analysis of remains thought to be Ned Kelly, an Australian bushranger.
    • Comparison of mitochondrial DNA from a skull and a headless skeleton to Lee Oliver, the great-grandnephew of Ned Kelly.
    • The skeleton matched Lee Oliver, but the skull did not, indicating it was someone else.

Preventing DNA Contamination

  • Critical to avoid contaminating remains with external human DNA.
  • Protective clothing is worn to prevent skin, hair, sweat, and breath from contaminating samples.
  • The goal is to prevent DNA from the scientist to contaminate the sample.
  • The precautions are similar to protection worn for COVID sample collection.

Challenges in Working with Skeletonized Remains

  • Typical challenges:
    • Broken bone ends.
    • Prolonged exposure to soil.
    • Lack of fingerprints and dental records.
    • Mass casualty events complicating matching.
    • Deliberate attempts to destroy DNA (e.g., burning).
    • Limited bone availability (e.g., small fragments).
    • Commingling of remains.

DNA Degradation

  • Well-structured DNA degrades after death.
  • Long chromosomes are fragmented into smaller pieces (30-40 base pairs long).
  • This complicates gathering genetic information.
  • Ideal samples: fresh-looking teeth and bones.
  • Typical samples: fragmented bones heavily contaminated with soil and microbial DNA.

Contamination Issues

  • Human handling can transfer DNA to bones and teeth.
    • Example: Study of museum dog skulls showed three times more human DNA than dog DNA due to handling.
  • Laboratory contamination can occur.
    • Example: The "Phantom of Heilbronn" case, where DNA from cotton swabs contaminated in the factory was found at 40 crime scenes over 16 years.

Characteristics of DNA from Degraded Remains

  • Degraded (chopped into small pieces).
  • Low concentration.
  • Chemically damaged.
  • Contaminated with human and environmental DNA (bacteria, fungi).
  • Resembles ancient DNA.

Ancient DNA Lab Techniques

  • Utilizing ancient DNA lab techniques to maximize success in extracting DNA.
  • Clean room laboratory with positive air pressure to exclude dust and bugs.
  • Use of UV light and personal protection equipment (PPE).
  • The aim of the lab is to create an enviroment that resembles conditions used for extracting DNA from extinct animals such as Mammoths to prevent contamination.

Applications of DNA Identification

Daniel Morcombe Case

  • Abducted and murdered in the early 2000s in South East Queensland.
  • DNA analysis on a bone fragment was extracted.
  • Mitochondrial DNA sequencing and comparison to Daniel's mother and brothers.
  • Matching sequences confirmed the remains were Daniel's.
  • Led to the conviction of the abductor and murderer.

HMA Sydney Unknown Sailor Case

  • HMA Sydney sunk in World War II with 645 Australians lost.
  • Three months later, a life raft with decayed remains was found off Christmas Island.
  • Gravesite was lost but recovered in 2006.
  • DNA identification was attempted using mitochondrial DNA.
  • Mitochondrial DNA is maternally inherited, so samples must be collected from maternal relatives.
  • Dental records excluded about 300 sailors, and age/height predictions excluded another 200.
  • Clothing suggested the man might have been an officer.

Maternal Relative Identification for Comparison

  • Explanation of how to identify living maternal relatives.
  • The process involves:
    • Building family trees for each missing sailor
    • Identifying maternally related individuals
    • Tracking down those people
    • Getting consent to acquire DNA samples
  • Samples aren't appropriate from sons and daughters and also deceased relatives cannot be used.

DNA Analysis and HiRisPlex Test

  • DNA was extracted from teeth and found to have J1C12 mitochondrial DNA.
  • Testing confirmed there was no contamination from the forensic team.
  • The Navy had an initial three sailors that they belived the remains may have been and sent samples for mitochondrial DNA testing, however these were excluded.
  • HiRisPlex test predicted red hair and blue eyes, indicating Celtic ancestry (Scottish and Irish).
  • This narrowed the search for family reference samples.

Identification of Thomas Wellsby Clarke

  • Continued testing over five to six years without a match.
  • A breakthrough occurred when giving a talk at a local genealogy society.
  • A Woman linked him to someone by the name of Abel Seaman Thomas Wellsby Clarke.
  • In 2019, a contact at the Navy linked a person with that mitochondrial DNA type to a Scottish woman born in 1810 who was related to Abel Seaman Thomas Wellsby Clarke (who was on the HMA Sydney)..
  • On the eightieth anniversary of the sinking of the HMA Sydney, the unknown sailor was identified as Thomas Clarke.
  • The grave will receive a new headstone with his name.
  • The project took fourteen years from start to finish.

Conclusion

  • DNA is an effective tool for Identification of missing persons remains.
  • The lecturer is happy to answer questions about the presentation via email.
  • Research group activities can be checked out on their website.