Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci

Abstract

BackgroundThere is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region.ResultWe report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia.ConclusionWe show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.

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

“…The mean I n across the markers (and standard deviation) I n was 0.078 (0.035). This is lower than the average I n found for the Sudanese populations at 0.167 (0.070) 38 . These low I n values indicate that individually these markers are not best suited for the inference of ancestry.…”

The genetic variation of lactase persistence alleles in northeast Africa

“…Bifurcation plots for the Beja populations. The topmost plot is centered around position -13907 and contains only haplotypes that have non of the derived LP-associated alleles.The genetic di↵erentiation, that has been identified previously between the Arabs of central/north Sudan and the Messiria(Babiker et al, 2011;Hollfelder et al, 2017), is also seen in the frequency of the LP alleles. The derived allele for -14009 is found in the Bataheen, Gaalienand Shaigia at 0.125-0.167 frequency but not in the Messiria (site specific F M essiria;X ST =0.062167 to 0.113881, where X is one of the other Sudanese Arab populations).…”

Population Identifiability from Forensic Genetic Markers: Ancestry Variation in Latin America

“…In particular, research on human genetic variation has utilized the extensive CODIS data available for analysis in public, private and federal/state databases, and also used the manufactured and validated kits for multiplex STR genotyping to amass new data. A major application of the CODIS STR variation in recent research is the estimation of ancestry proportions from forensic STRs (Pritchard et al, 2000;Wang, 2003;Alexander et al, 2009), and is well-represented in anthropological and population genetics literature for both modern and ancient populations (Barnholtz-Sloan et al, 2005;Sahoo and Kashyap 2005;Montinaro et al, 2012;Pereira et al, 2011;Phillips et al, 2011;Silva et al, 2012;Babiker et al, 2011;Mohammad et al, 2009, Callegari-Jacques et al, 2011Rubicz et al, Pre-print version. Visit http://digitalcommons.wayne.edu/humbiol/ after publication to acquire the final version.…”