STR-based genetic structure of the Berber population of Bejaia (Northern Algeria) and its relationships to various ethnic groups

Abstract

Patterns of genetic variation in human populations have been described for decades. However, North Africa has received little attention and Algeria, in particular, is poorly studied, Here we genotyped a Berber-speaking population from Algeria using 15 short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA from the commercially available AmpF/STR Identifiler kit. Altogether 150 unrelated North Algerian individuals were sampled across 10 administrative regions or towns from the Bejaia Wilaya (administrative district). We found that all of the STR loci met Hardy-Weinberg equilibrium expectations, after Bonferroni correction and that the Berber-speaking population of Bejaia presented a high level of observed heterozygosity for the 15 STR system (>0.7). Genetic parameters of forensic interest such as combined power of discrimination (PD) and combined probability of exclusion (PE) showed values higher than 0.999, suggesting that this set of STRs can be used for forensic studies. Our results were also compared to those published for 42 other human populations analyzed with the same set. We found that the Bejaia sample clustered with several North African populations but that some geographically close populations, including the Berber-speaking Mozabite from Algeria were closer to Near-Eastern populations. While we were able to detect some genetic structure among samples, we found that it was not correlated to language (Berber-speaking versus Arab-speaking) or to geography (east versus west). In other words, no significant genetic differences were found between the Berber-speaking and the Arab-speaking populations of North Africa. The genetic closeness of European, North African and Near-Eastern populations suggest that North Africa should be integrated in models aiming at reconstructing the demographic history of Europe. Similarly, the genetic proximity with sub-Saharan Africa is a reminder of the links that connect all African regions.

The Orientalisation of North Africa: New hints from the study of autosomal STRs in an Arab population

“…Expected average heterozygosity across 13 STR loci was Tunisian Arabs are genetically more homogeneous and less differentiated than Berbers, a finding that can be explained by the recent shared ancestry between the Tunisian Arabs and the nonBerber neighbouring populations. Our results reinforce previous studies with autosomal STR loci (Amir et al, 2015;Bosch et al, 2000;ElOssmani et al, 2010;Khodjet-El-Khil et al, 2008), revealing the heterogeneity of Berbers in North Africa, as was further supported by patterns of mtDNA (Fadhlaoui-Zid et al, 2004, Frigi et al, 2010Kefi et al, 2015), and Y chromosome (Cherni et al, 2005b;Frigi et al, 2006b;Khodjet-El-Khil et al, 2001, 2005 …”

“…In the cloud of North African and Near Eastern populations, Tunisian Berbers remain in a relative outsider position, confirming previous observations based on autosomal STR loci (Amir et al, 2015;Henn et al, 2012;Khodjet-El-Khil et al, 2008), which have been assumed to be a consequence of genetic drift, founder effects and high level of endogamy due to geographic isolation and/or cultural…”

“…For the comparative analyses, data on 13 autosomal STRs (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, VWA, TPOX, D18S51, FGA, D5S818, D16S539) in a total of 32 populations were selected from previous studies in which raw genotypic data were available or were provided by the authors (Amir et al, 2015;Gaibar et al, 2012) or downloaded from the STR database http://cracs.fc.up.pt/popaffiliator/str_db.html. Out of those populations, sixteen were from North Africa, five from Europe, three from sub-Saharan Africa, six from the Middle East, and two from Eastern Asia.…”

“…In addition, owing to the autosomal mode of inheritance, these markers are not especially sensitive to genetic drift and founder effects, which make them useful for population genetic studies, being able to provide valuable insights into past evolutionary events including isolation by distance or genetic admixture, among others (Amir et al, 2015;Bertrand et al, 2014;Eaaswarkhanth et al, 2009;ElOssmani et al, 2009;Gaibar et al, 2012;GarciaBertrand et al, 2014;Khodjet-El-Khil et al, 2008;Kutanan et al, 2014;Lopes et al, 2009).…”

“…Still higher values were observed for Libyans (0.790) (Khodjet-El-Khil et al, 2012), Egyptians (0.792) (Coudray et al, 2007b) and Algerian Berbers from Bejaia (0.795)(Amir et al, 2015) pointing to a high level of genetic diversity in North African populations that likely reflects their rich demographic history. In the exact tests of population differentiation performed locus by locus, Tunisian Arabs showed less significant differences than Tunisian Berbers(Khodjet-El- Khil et al, 2008) compared to other North African populations including Egyptians, Moroccans, Sahrawi, Algerians and Libyans(Coudray et al, 2007a; Coudray et al, 2007b; Gaibar et al, et al, 2001;Amir et al, 2015; Khodjet-El-Khil et al, 2012). Thus, based upon average heterozygosity and exact tests of population differentiation, there are indications that…”