D'Amato Maria Eugenia, Ristow Peter, Livesey Michelle, Heynes Kirsty, Huber Nicole, Bravi Claudio, Hansen Anders J, Parson Walther
Forensic DNA Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa.
Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
Ann Hum Genet. 2025 Jul;89(4):195-207. doi: 10.1111/ahg.12589. Epub 2025 Jan 7.
Southern Africa has been inhabited by hunter-gatherers for at least 20,000 years and has received diverse immigration flows in the last 2000 years. The original inhabitants have interacted with the pastoralist migrants from Eastern Africa (∼2000 ybp), followed by the southern Bantu migration arriving some 1000 ybp, and more recently with the European and Asian settlers after the 17th century. Many of the original Khoekhoe and San inhabitants have either become extinct or have disappeared through admixture in South Africa (SA), in a sex-biased manner involving KhoeSan women.
In this study, we generated mitochondrial DNA (mtDNA) control region (CR) sequences for 247 South African individuals. The sampling effort was concentrated in regions and populations with historical links to the KhoeSan population groups: admixed (Coloured, Griqua), Nama (Khoekhoe) and Bantu in three provinces. Here we evaluate the composition and extent of connectivity between population groups and regions, and to assess the distribution of haplotypes for the practical application of mtDNA CR data in forensic identifications.
The analysis of the newly generated sequences revealed 142 distinct haplotypes, of which 122 were unique. Haplogroup L0 was predominant (overall 71.7%). A high-frequency L0d2a haplotype dominated the pool of the admixed groups with 10%-12.5% incidence overall or per region. Comparative analysis with 545 extant mtDNA CR sequences from South African KhoeSan and admixed descendants revealed extensive population structure and high within-group haplotype sharing.
The observed population and regional variations, combined with the prevalence of high-frequency haplotypes, align with patterns of matrilocality. These findings highlight the limitations of using mtDNA control region analysis for forensic applications in South Africa.
南部非洲至少在2万年前就有狩猎采集者居住，在过去2000年里接收了不同的移民潮。最初的居民与来自东非的牧民移民（约2000年前）进行了互动，随后约1000年前南部班图人开始迁移，最近在17世纪后又与欧洲和亚洲定居者有了接触。在南非，许多最初的科伊科伊人和桑人要么已经灭绝，要么通过混血消失，这种混血以涉及科伊桑女性的性别偏向方式发生。
在本研究中，我们为247名南非个体生成了线粒体DNA（mtDNA）控制区（CR）序列。采样工作集中在与科伊桑人群体有历史联系的地区和人群：三个省份的混血人群（有色人种、格里夸人）、纳马人（科伊科伊人）和班图人。在此，我们评估人群组和地区之间的构成及连通程度，并评估单倍型的分布，以便将mtDNA CR数据实际应用于法医鉴定。
对新生成序列的分析揭示了142种不同的单倍型，其中122种是独特的。单倍群L0占主导地位（总体占71.7%）。一种高频L0d2a单倍型在混血群体中占主导，总体或每个地区的发生率为10% - 12.5%。与来自南非科伊桑人和混血后裔的545条现存mtDNA CR序列进行的比较分析显示，存在广泛的人群结构和群体内高单倍型共享情况。
观察到的人群和地区差异，加上高频单倍型的普遍存在，与母系居住模式相符。这些发现凸显了在南非将mtDNA控制区分析用于法医应用的局限性。
