Genetic variation and population structure of Botswana populations as identified with AmpFLSTR Identifiler short tandem repeat (STR) loci

Abstract

Population structure was investigated in 990 Botswana individuals according to ethno-linguistics, Bantu and Khoisan, and geography (the nine administrative districts) using the Identifiler autosomal microsatellite markers. Genetic diversity and forensic parameters were calculated for the overall population, and according to ethno-linguistics and geography. The overall combined power of exclusion (CPE) was 0.9999965412 and the combined match probability 6,28 × 10−19. CPE was highest for the Khoisan Tuu ethnolinguistic group and the Northeast District at 0.9999582029 and 0.9999922652 respectively. CMP ranged from 6.28 × 10−19 (Khoisan Tuu) to 1,02 × 10−18 (Northwest district). Using pairwise genetic distances (FST), analysis of molecular variance (AMOVA), factorial correspondence analysis (FCA), and the unsupervised Bayesian clustering method found in STRUCTURE and TESS, ethno-linguistics were found to have a greater influence on population structure than geography. FCA showed clustering between Bantu and Khoisan, and within the Bantu. This Bantu sub-structuring was not seen with STRUCTURE and TESS, which detected clustering only between Bantu and Khoisan. The patterns of population structure revealed highlight the need for regional reference databases that include ethno-linguistic and geographic location information. These markers have important potential for bio-anthropological studies as well as for forensic applications.

Whole-Exome Sequencing Reveals Uncaptured Variation and Distinct Ancestry in the Southern African Population of Botswana

“…22,24 These anthropological groups have since merged within modern-day Gaborone, a populous, urban city in which current marriage and mating practices 17 mean that self-reported ethnic affiliations are more social constructs than reflective of the highly stratified genetic ancestry found in more rural Botswana. 33 This separates our work from previous genetic surveys.…”

“…[30][31][32] Therefore, the broader genetic variation and substructure among the Batswana remains largely undescribed. 33 The Collaborative African Genomics Network (CAfGEN), under the auspices of the Human Heredity and Health in Africa (H3Africa) Consortium (Web Resources), 34,35 has among its primary goals the use of genomics to study pediatric HIV and TB disease progression in the sub-Saharan countries of Uganda, Botswana, and, more recently, Swaziland. The ability to utilize the wealth of genetic diversity within these countries to better understand phenotypic variability in HIV and other prevalent diseases is highly desirable; 1,3,16 however, the present dearth of available population-level genomic data [30][31][32] makes attaining such a goal challenging.…”

Population Structure and Implications on the Genetic Architecture of HIV-1 Phenotypes Within Southern Africa

“…Moreover, a strong signal of selection was found around the human leukocyte antigen (HLA) complex in several genes that are known to protect against infectious diseases in the ‡Khomani and Karretjie, this effect probably owing to early and extensive contact with European colonists and novel infectious diseases such as smallpox (Schlebusch et al, 2012). Likewise, Tau and colleagues also reported significant genetic differences between the Khoe-San and Bantu-speaking groups through analysis of short tandem repeats (STRs) (Tau et al, 2017).…”

Genetic structure of the ethnic Lao groups from mainland Southeast Asia revealed by forensic microsatellites

“…Additionally, modeling of mtDNA genome and Y chromosomal sequences of Lao Isan indicates contrasting paternal and maternal genetic histories that show paternal admixture with the Khmer but not on the maternal side, which possibly occurred after the exit of the Lao Isan from Laos (Kutanan et al., 2017, 2019). Although mtDNA and the Y chromosomal sequences have proven to be powerful sources for the study of genetic lineages and relationships, here we extend the investigation using 15 loci of biparentally inherited autosomal short tandem repeats (STRs) in the AmpFLSTR Identifiler panel (Applied Biosystems, Foster City, CA), which are commonly used for forensic studies (Eaaswarkhanth et al., 2009; Rajkumar & Kashyap, 2004; Silva, Pereira, Poloni, & Currat, 2012) because, in recent years, this set of markers has proven equally as informative in the reconstruction of recent human evolutionary history (Chantakot et al., 2017; Eaaswarkhanth et al., 2009; Kang et al., 2010; Kutanan et al., 2011; Rajkumar & Kashyap, 2004; Silva et al., 2012; Srithawong et al., 2015; Tau et al., 2017; Yao, Xing, Xuan, & Wang, 2017). So far, the Laotian population has not been genetically studied using this set of markers.…”