The Genetic Landscape of Mediterranean North African Populations Through Complete Mtdna Sequences

Annals of Human Biology ISSN: 0301-4460 (Print) 1464-5033 (Online) Journal homepage: http://www.tandfonline.com/loi/iahb20 The genetic landscape of Mediterranean North African populations through complete mtDNA sequences Neus Font-Porterias, Neus Solé-Morata, Gerard Serra-Vidal, Asmahan Bekada, Karima Fadhlaoui-Zid, Pierre Zalloua, Francesc Calafell & David Comas To cite this article: Neus Font-Porterias, Neus Solé-Morata, Gerard Serra-Vidal, Asmahan Bekada, Karima Fadhlaoui-Zid, Pierre Zalloua, Francesc Calafell & David Comas (2018) The genetic landscape of Mediterranean North African populations through complete mtDNA sequences, Annals of Human Biology, 45:1, 98-104, DOI: 10.1080/03014460.2017.1413133 To link to this article: https://doi.org/10.1080/03014460.2017.1413133 View supplementary material Published online: 30 Jan 2018. Submit your article to this journal View related articles View Crossmark data Citing articles: 1 View citing articles Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=iahb20 ANNALS OF HUMAN BIOLOGY, 2018 VOL. 45, NO. 1, 98–104 https://doi.org/10.1080/03014460.2017.1413133 RESEARCH PAPER The genetic landscape of Mediterranean North African populations through complete mtDNA sequences Neus Font-Porteriasa, Neus Sole-Morata a, Gerard Serra-Vidala, Asmahan Bekadab, Karima Fadhlaoui-Zidc, Pierre Zallouad, Francesc Calafella and David Comasa aDepartament de Ciencies Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain; bDepartement de Biotechnologie, Faculte des Sciences de la Nature et de la Vie, Universite Oran 1 (Ahmad Ben Bella), Oran, Algeria; cLaboratoire de Genetique, Immunologie et Pathologies Humaines, Faculte des Sciences de Tunis, Campus Univesritaire El Manar II, Universite El Manar, Tunis, Tunisia; dSchool of Medicine, The Lebanese American University, Chouran, Beirut, Lebanon ABSTRACT ARTICLE HISTORY Background: The genetic composition of human North African populations is an amalgam of different Received 25 July 2017 ancestral components coming from the Middle East, Europe, south-Saharan Africa and autochthonous Revised 23 November 2017 to North Africa. This complex genetic pattern is the result of migrations and admixtures in the region Accepted 30 November 2017 since Palaeolithic times. Aims: The objective of the present study is to refine knowledge of the population history of North KEYWORDS African populations through the analysis of complete mitochondrial sequences. Population genetics; North Subjects and methods: This study has sequenced complete mitochondrial DNAs (mtDNAs) in several Africa; mitochondrial DNA; North African and neighbouring individuals. haplogroups Results: The mtDNA haplogroup classification and phylogeny shows a high genetic diversity in the region as a result of continuous admixture. The phylogenetic analysis allowed us to identify a new haplogroup characterised by positions 10 101 C and 146 C (H1v2), a sub-branch of H1v, which is restricted to North Africa and whose origins are estimated as 4000 years ago. Conclusions: The analysis of the complete mtDNA genome has allowed for the identification of a North African sub-lineage that might be ignored by the analysis of partial mtDNA control region sequences, highlighting the phylogeographic relevance of mtDNA complete sequence analysis. Introduction was one of the last major demographic events that occurred North Africa has traditionally been a geographically strategic in the region (Fadhlaoui-Zid et al., 2011). region surrounded by two natural borders: the Sahara Desert Despite the amount of knowledge about North African in the south and the Mediterranean Sea in the north, which populations obtained from palaeoarchaeological data, more have contributed to the isolation of this area. However, studies are needed to investigate the recent history of this changes in the climate conditions have promoted contacts region (Arauna et al., 2017). Indeed, genetic studies point out with south-Saharan Africa, Europe and the Middle East, that modern North Africans constitute a heterogeneous resulting in complex demographic events (Drake et al., 2011; group, whose ancestry is a result of at least three admixture Osborne et al., 2008). Archaeological studies report the suc- events from populations outside Africa: a “back-to-Africa” cession of different cultures and civilisations: the Aterian gene flow (12,000 ya), a Near East gene flow (1400 ya) and lithic industry from 145,000 to 40,000 years ago (ya) migrations from south-Saharan Africa resulting from the slave (Nespoulet et al., 2008), which was replaced by the trade (1200 ya) (Arauna et al., 2017; Henn et al., 2012). Iberomaurusian culture during the Last Glacial Maximum Genome-wide autosomal studies reveal a gradient of likely (22,000–9000 ya) (Newman & Rogers, 1995); and the Capsian autochthonous Maghrebi ancestry that is reduced from West culture (10,000–6000 ya) (Rahmani, 2004). The Neolithic tran- to East and an opposite cline of Near East ancestry with a sition, 5500 ya, progressively spread from the Near East to westward decrease (Henn et al., 2012). However, geographic North Africa, favouring the increase of social complexity, distance and genetic diversity were not found to be corre- which may have ultimately led to the formation of the ances- lated in North African populations, probably because of tors of the autochthonous Berber groups (Fadhlaoui-Zid heterogeneous or unbalanced admixture (Arauna et al., et al., 2011). In historic times, different populations succes- 2017). Y-chromosome data show an east–west cline from the sively settled in North Africa: Phoenicians (Zalloua et al., Near East compatible with a Neolithic demic expansion 2008), Romans, Vandals and Byzantines. Finally, the Arabic (Arredi et al., 2004), as well as a bidirectional gene flow from expansion linked to the spread of Islam in the 7th century North Africa to Iberia (Bosch et al., 2001). CONTACT David Comas [email protected] Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, 08003, Barcelona, Catalonia, Spain Supplemental data for this article can be accessed here. ß 2017 Informa UK Limited, trading as Taylor & Francis Group ANNALS OF HUMAN BIOLOGY 99 Previous mtDNA studies report an extensively heteroge- mtDNA sequence analysis neous haplogroup distribution in North Africa, which sug- The quality of the sequences was assessed using the soft- gests that it is a highly admixed region (Fadhlaoui-Zid fastqc et al., 2011). Although the frequency of south-Saharan L ware and, then, to optimise the mapping process, haplogroups in North Africa is not negligible, most mtDNA each sample was split in multiple breaks every 1,000,000 fastqbreak lineages in North Africa have a Eurasian origin. U5, V, R0a, base pairs with . Sequenced paired-end reads were J1b and U3 haplogroups have been recently brought from mapped to the reference genome using the Burrows-Wheeler Europe and the Middle East. However, U6 and M1b are Alignment (BWA) tool with the non-default parameter -q 15 estimated to have existed in the region since Palaeolithic (Li & Durbin, 2009). The Cambridge Reference Sequence times (Gonzalez et al., 2007) and are found in high fre- (rCRS) revised by Andrews et al. (1999) was used as the mito- quencies, hence they are considered specific North African chondrial reference in the mapping step. To avoid the erro- lineages, even though they originated elsewhere. Moreover, neous increase of coverage, PCR duplicates were removed Genome Analysis Tool kit these two mtDNA haplogroups have an opposite frequency with the (GATK) software package. gradient in North Africa: U6 is more frequent in the West In addition, the average sequence coverage was also com- and M1 in the East (Olivieri et al., 2006; Pennarun et al., puted with the GATK software (McKenna et al., 2010) 2012). (Supplementary Figure 1, Supplementary Table 1). Initially, most mtDNA studies were based on a few restric- Once the reads were mapped, Samtools 1.3.1 (mpileup tion sites along the molecule and/or a few hundred bp of and vcfutils software) (Li et al., 2009) were used, with the sequence in the hypervariable segment 1 of the control non-default parameters -B, -A and -Q 30, only considering region. Recently, whole mtDNA genome sequencing has minimum base qualities of 30, to obtain the variant call for- become feasible and increasingly popular; it prevents ascer- mat (vcf) file and the FASTA file of each sample. tainment bias and provides a new source of genetic variants Finally, to identify the mitochondrial haplogroups of each to identify novel lineages (Richards & Macaulay, 2001). Taking sample, as well as their local and private mutations, hotspots into account the genetic heterogeneity present in North and expected variants, the FASTA files were uploaded to Africa, the present study aims to describe the maternal lin- Haplogrep (Kloss-Brandst€atter et al., 2011). Haplogroup call- eage landscape and diversity of this region. ing was based on phylotree build 17 (http://www.phylotree. org, 18 February 2016) (van Oven & Kayser, 2008) (Supplementary Table 2). The 19 complete mtDNA sequences Materials and methods have been deposited in Genbank with accession numbers MG182024-MG182042 (Supplementary Table 1). Sample collection and genome sequencing Additionally, a neighbour-joining tree containing all the We collected samples from 19

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