A population genetic analysis of forensic identity and ancestry markers in Indonesia

Abstract

Population sub-structure and remote inbreeding cause individuals to become more genetically related. Since related individuals are more likely to share a DNA profile than unrelated individuals, the presence of population sub-structure causes inaccuracies in the match probability calculations that are presented in court by forensic biologists. Frequently, a co-ancestry (θ) correction is applied to match probability calculations to accommodate the variations that exist between subpopulations. Population sub-structure within Indonesia is highly probable given that the colonisation history of the archipelago has ensured the co-existence of numerous distinct traditional cultural and linguistic groups. The geography of Indonesia could also contribute to the formation of population sub-structure, with the 240 million residents spread across 6,000 inhabited islands some of which possess significant mountain ranges. However, the population genetic features of Indonesia have not been examined thoroughly and adequate allele frequency data for forensic identity markers in Indonesia does not exist. The aims of this project were to; a) genotype an extensive Indonesian sample set, covering many geographic locations and representing numerous linguistic and cultural groups, using forensic identity markers (autosomal STRs) and ancestry markers (autosomal SNPs) and identify genetically distinct subpopulations; b)compare the genetic subpopulation boundaries revealed through forensic STR and autosomal SNP genotyping and assess the efficacy of each marker type for detecting population differentiation and defining the genetic subpopulations within Indonesia; and c) construct defensible DNA databases for the genetic subpopulations discovered within Indonesia and determine appropriate sub-structure correction factors for use in forensic casework match probability assessments. In total,15 forensic identity markers (Identifiler® kit) and 13 autosomal ancestry SNPs were genotyped in an extensive sample set from the Indonesian archipelago. Population genetic analyses revealed that both forensic identity and autosomal ancestry markers were able to discern population sub-structure within Indonesia and that the overarching patterns of population differentiation were the same. It was determined that island based subpopulations were the most suitable for the purposes of creating forensic population databases. Appropriate values for the co-ancestry (θ) correction factor were determined to be θ=0.03 (3%) for Island Sumatra (N=129),θ=0.02 (2%) for Flores (N=245) and Sumba (N=174) and θ=0.01 (1%) for Mainland Sumatra (N=294),Sulawesi (N=419) and Java and Bali (N=484). The island-based subpopulations of Kalimantan (N=26) and Papua (N=57) are currently too small to make informed decisions about the appropriate value of θ. If desired by the Indonesian jurisdictions, each population database could be used with a θ=0.03 (3%),to assist the implementation of these population databases into routine forensic DNA casework. In summary, this study has generated allele frequency data for 15 forensic identity markers and characterised the levels of population sub-structure present within Indonesia using forensic identity and ancestry markers. Genetically appropriate population databases for the island-based subpopulations (Island Sumatra, Mainland Sumatra, Java & Bali, Kalimantan, Sulawesi, Flores, Sumba and Papua) have been generated and appropriate θ-correction factors are now available for use in the calculation of DNA match statistics.

Date of Award	2012
Original language	English
Supervisor	Dennis McNevin (Supervisor), Stephen Sarre (Supervisor), Runa Daniel (Supervisor) & Roland van Oorschot (Supervisor)