Founder mutations in Tunisia: implications for diagnosis in North Africa and Middle East

Tunisia has approximately 10 million inhabitants. It is three times as much as in 1956 at the end of the French protectorate, and twice as much as in the seventies (Figure 1) [8, 9]. This growth is mainly attributed to the decrease of infantile mortality rates and the improvement of life expectancy; which are indicators of improvements in health status and medical management [9]. African, Near Eastern and European influences have shaped the Tunisian cultural identity. The overwhelming majority of the population is Muslim (98%) . Christian and Jewish communities also contribute to the Tunisian cultural diversity [10]. Like the other North African and Middle Eastern countries, Tunisia has kept the consanguineous and endogamous marriages as a social habit. Indeed, the frequencies of unions between relatives range from 20.1% to 39.33% [11‐14] and those of endogamous marriages could reach more than 96% in some specific groups like those of Douiret in Southern Tunisia [Ben Halim, Unpublished data]. The Tunisian family structure is generally extended and often associated with inbreeding. Tunisia is classified as a middle-income country [15].

Tunisia has been inhabited since the Paleolithic period. Remainders of Acheulean industry (700,000 to 100,000 years BCE) have been discovered on several sites in the layer of Sidi Zin in the north west, Gafsa and Redayef in the south. The 100,000 last years of Paleolithic were characterized by the presence of Homo sapiens archaic contemporary of Homo neanderthalensis in Europe. Between 60,000 and 20,000 years BCE, the Mediterranean coast stretching over from Cap Bon to Monastir was occupied by Homo sapiens sapiens. In the Epipaleolithic period (23,000 years to 10,000 years BCE), the Mechta El Arbi Man, Homo sapiens sapiens specific to North Africa succeeded to the Aterian population. Around 8,000 years BCE, the Capsian civilization first identified in the eponymous city of Gafsa covered a broad area of Central and Southern Tunisia and could be considered as the ancestor of the Berber population. Berbers occupied the North African region including Tunisia. They have been for long self-identified as “Imazighen” which means “free people” [17, 18].

The Punic era initiated with the arrival of Phoenician traders from the eastern Mediterranean Sea and was marked by the founding of the City of Carthage on 814 BC (present Tunis). For many centuries, the Punic civilization either displaced the native Berbers to the city periphery or integrated them. Phoenicians expanded their dominance to the western Mediterranean and had settled in what are now Sardinia, Sicily, Spain, Morocco and Algeria. The emergence of the Roman Republic led to sustained rivalry with the more anciently established Carthage for dominion over the western Mediterranean. Carthage lost its influence over the Berbers leading to the defeat of Carthage during the Third Punic War (149–146 BC), therefore, marking the end of the Phoenician reign. Tunisia became the Roman Province of Africa. After the dissolution of the Roman Empire during the 5^th century, the Germanic nation of the Wisigoths migrating downward to south Western Europe (the so called Vandals) took control of the coastal part of North Africa for nearly a hundred years. The Byzantine Empire re-established its dominion in 533 AD, which lasted till the Islamic conquest in the 7^th century. This era started with the arrival of Arabs from the Arab Peninsula who brought their language, their culture and Islam [19]. They founded Kairouan in 670 AD, the first Arab-Muslim city in “Ifriqya” (nowadays: Tunisia, Eastern Algeria and Western Libya). Successive Arab dynasties were established in the region. The 11^th century was marked by a breaking event: the invasion of Bedouins of Banu Hilal and Banu Sulaym originating from the Banu’Amir tribe from the southwest Arabia. These Arab newcomers (up to 200,000 individuals) represented the second large Arab immigration into Ifriqiya [19].

In 1135 AD, Ifriqiya was attacked by Normands and Sicilians who occupied four coastal cities of Tunisia. They were then expelled under the reign of the Almohad dynasty (1147–1269 AD) [19]. The arrival of Béni Soulaim in Tunisia had accelerated the administrative desagregation of the country and the dissolution of the Almohad dynasty [19]. Under the Hafsids (1230–1574 AD), the Black Death has caused extensive devastation from Tunis to Tanger. Since then it had hit every 10 years in addition to droughts and starvations [20, 21]. Spain had occupied a series of positions in North Africa including Tunis (1534 AD) until their incorporation in the Ottoman Empire. The population size of the region had evolved from 4.7 millions around 1500 AD, to 5.4 millions in 1620 AD after the mass migration of hundreds of thousands of Morrish Andalusian Muslims and Jews expelled from Spain to North Africa [19‐21]. The 16^th and the 17^th centuries were characterised by successive epidemic waves, cricket invasions and starvations leading to severe human losss that reached hundreds of thousands [20, 21]. The beginning of the 18^th century was hallmarked by the decline of the Ottoman Empire and the reemergence of plague that hit the entire Maghreb until the first half of the 19^th century [20]. The Tunisian population growth was periodically slowed by successive and prolonged epidemics of plague, cholera and typhus during the 19^th century as nearly one thousand individuals had died in the city of Tunis in 1918 [21]. In 1881, French forces established a protectorate. In 1936, the European population (French, Italian and Maltese) in Tunisia was of more than 213 thousands inhabitants [16]. The French protectorate ended in 1956 AD [19].

A Jewish minority has existed in Tunisia since the Roman times. In the 7th century, the Jewish population in Tunisia largely increased due to Spanish immigrants fleeing the persecutions of the Visigoth king. They fled to Morocco and settled in the Byzantine cities. These settlers, according to the Arab historians, mixed with the Berber population and converted many tribes [22]. Later, during the Islamic expansion they continued to profess Judaism until the reign of the Idrisid dynasty in Western Maghreb (789–985 AD) though they could maintain their particularism thanks to the permissive Islamic rule of Dhimma. Molecular studies based on the analysis of mitochondrial DNA and Y-chromosome polymorphisms showed a negligible or low level of admixture of the Jewish community with Arab and Berber populations in Tunisia [23, 24]. As a conclusion, the genetic landscape of the Tunisian population has been shaped by successive invasions and migratory flows through its history. Epidemics, droughts and plagues have also impacted the Tunisian population [20, 21]. The new-comers and the local Berbers intermarried and mixed to some extent, although, some Berber groups like the Berbers of Douiret in the South and those of “El Gallala” in the island of Jerba are known to have poorly mixed with new-comers and are still Berber speaking and highly endogamous. Genetic investigations based on mitochondrial DNA analysis of current populations from Berber villages in Tunisia showed the absence of a common genetic Berber profile. Genetic differentiation was observed between Berbers from different localities (Sejnane, Takrouna, Kesra and Jerba Island) and between Berbers and Arabs (Zriba and Jerba Island) as well as among Jews (Jerba Island) [25‐27]. This genetic heterogeneity between these current small groups is due essentially to founder effects and could also be due to their limited size and the variation of Sub-Saharan African traces detected in their gene pool. Nevertheless, when comparing samples from neighboring populations, the general ancient genetic profile of the native North Africans –the Berbers- appears not to be very different from that of the present-day North African populations despite some admixture with other people, particularly Arabs of little genetic contribution. This suggests that the populations of the Maghreb seem to share a substantial genetic background [28‐30].

In a country with limited resources and with other public health and research priorities, the rare genetic diseases remain neglected. As no complete report on founder mutations in the Tunisian population was performed, we have collected data on these mutations in the region and discussed their usefulness for the design of cost effective diagnosis tool in the Tunisian, North African and the Middle Eastern populations.

In the Tunisian population, 22 genetic diseases are due to Tunisian specific founder alleles and likely founder alleles whereas 8 genetic diseases can be due to either Tunisian-specific alleles or non-specific alleles shared with other North African or Middle Eastern populations. Sixty two percent (21/34) mutations are due to common ancestors on the basis of shared haplotypes (Additional file 1, Additional file 3 and Figure 2). For the majority of these Tunisian founder mutations, geographic distribution is limited to a region of the country like mutations responsible for congenital muscular dystrophy 1C [Louhichi N, personal communication] and spastic paraplegia 15 encountered in Southern Tunisia [Boukhris A, personal communication]. The p.L273P founder mutation affecting the TAT gene that leads to Richner–Hanhart Syndrome is restricted to the region of Monastir [Charfeddine C, personal communication]. The p.Ser493ArgfsX11 mutation in LDLR gene causing familial hypercholesterolemia is limited to the village of Souassi [33] and the deletion in IL12p40 gene of disseminated BCGitis is restricted to the village of Akouda [34] and several other examples (Figure 2).

Some other founder mutations are specific to an ethnic and religious group such as the c.890_893del mutation in FANCA gene that underlies Fanconi anemia specifically among the Tunisian Jews [35]. They could be also specific to both an ethnic group and a geographic region. This is illustrated by the Jewish community living on the Island of Jerba who is affected with combined factor V and factor VIII deficiency due to the c.IVS9+2T>G mutation in LMAN1 gene [36].

The Tunisian population shares founder mutations with other North African and Middle Eastern populations for 43 inherited conditions whereas 8 genetic diseases are due to either shared or specific alleles (Additional file 2, Additional file 3). Common haplotypes described in the Tunisian population could also be reported in restricted regions of North Africa. Founder chromosomal segments described in Tunisian patients with Meckel syndrome, mal de Meleda (MDM), sickle cell anemia and Xeroderma pigmentosum (XP) group A are identical to those described in Algerian affected individuals [37‐40]. In addition, the founder mutations leading to adenomatous polyposis of the colon and the hepatocerebral mitochondrial DNA depletion syndrome are reported on the same haplotypes only among Tunisian and Moroccan patients [41, 42].

Founder mutations could be shared in some countries of the Maghreb (defined today as Morroco, Tunisia, Libya, Mauritania and Algeria). In Tunisian, Algerian and Moroccan patients, autosomal recessive non syndromic optic atrophy and Bare lymphocyte syndrome are caused by the p.R2034X and 752delG-25 founder mutations, respectively [43, 44]. Identical haplotypes bearing founder mutations are observed for congenital myasthenia syndrome and XP group C in four North African countries [45, 46].

Founder mutations observed in Tunisia were also reported in populations from the Middle East such as the splice site mutation in the CA II gene responsible for carbonic anhydrase II deficiency in the Arabic peninsula [47] and the p.Q357R molecular defect in the UGT1A1 gene of the Crigler-Najjar type I syndrome in the Kuwaiti population [48]. In other cases, founder mutations are dispersed around the Mediterranean basin as illustrated by the c.744delA mutation in the TTPA gene of ataxia with isolated vitamin E deficiency [49] and the splice site defects in megaloblastic anemia 1 [50] and triple-A syndrome [51]. In other examples, the founder haplotypes are shared with populations from Europe and America, as for the Parkinson disease [52].

Some other founder mutations are reported in specific ethnic and religious groups mainly Jews from North Africa. The p.R35X founder mutation, responsible for ataxia-telangiectasia, is mainly reported in Jews from Tunisia and Morocco [53]. Common haplotype bearing the large CGG repeats on the FMR1 gene, responsible for fragile X, is observed among Tunisian and Sephardic Jewish patients and among Israeli Arabs as well [54]. A common founder mutation responsible for cutaneaous malignant melanoma was also reported only among Jewish patients from Tunisia, Morocco, Spain and France [55].

A same mutation could have arisen on different haplotypes. This could be explained by independent mutational events that could have occurred and have been introduced into the population by different founders during migrations and invasions. This is a possible hypothesis if we take into consideration the rich history of the Tunisian population. This is the case for mutations underlaying beta thalassemia [40], sickle cell anemia [40], familial Mediterranean fever [56], G6PD deficiency [57], 21 hydroxylase deficiency [58, 59], limb-girdle muscular dystrophy type 2C (LGMD2C) [60] and non syndromic hearing loss [61] that show a large distribution arround the Mediterranean basin.

For the same disease and/or the same causing gene, some mutations could be specific to the Tunisian population and others are shared by other populations (Additional file 3). Eight genetic diseases belong to this category. This is the case for 11-β hydroxylase deficiency [62, 63], hereditary breast and ovarian cancer [64, 65], cystic fibrosis [66, 67], glycogen storage disease type III [68, 69], Leber congenital amaurosis [70], leukocyte adhesion deficiency [71, 72] and MDM [Charfeddine C, personal communciation, 37,73]. For some founder mutations, the situation is relatively complex. Indeed, the p.C99Y mutation responsible for MDM is distributed in various geographic areas of the country, while the p.C77R mutation is restricted to the North. On the other hand, the c.82delT mutation is widely encountered in populations from the Mediterranean basin and also in Scottish and Croatian ones [37, 73].

Multiple founder effects are encountered for 4 inherited diseases caused by more than one founder mutation (Additional file 3). This phenomenon could affect the same gene. This is illustrated by the examples of hereditary breast and ovarian cancer [64, 65], leukocyte adhesion deficiency [71, 72] and MDM [Charfeddine C, personal communciation,73]. Another situation is encountered in genetically heterogeneous diseases with founder mutations in different underlying genes as is the case with Bardet-Biedl syndrome where two founder mutations affecting both BBS2 and BBS8 genes were reported [74] (Additional file 1).