The rise of modern Population Genetics in the second half of the twentieth century allowed geneticists to endeavour to define the origins and relatedness of Jewish people (Ostrer and Skorecki, 2013). Some of the questions put forward by researchers were: a) Do all contemporary Jews come from the ancient Israelites of the Middle East of three thousand years ago? b) Does DNA evidence show that European Jews are mainly comprised of European ancestors from the host populations? c) Were the Ashkenazi Jews descendants of the Khazars (an ancient tribe with roots in central Asia and Russia that converted to Judaism in the 8th century)? (Levy-Coffman 2005) and d) Can what must be a complex system of interrelations between Jewish groups and between Jews and their host peoples be unravelled?
Early studies were based on the so-called classical markers (blood groups, enzymes, serum markers, immunoglobulins and human leukocyte antigen), and provided the first evidence that the most Jewish diaspora groups originated in the Middle East and were more similar amongst themselves than compared with their corresponding host non-Jewish populations (e.g. Bonné-Tamir et al., 1978; Carmelli and Cavalli-Sforza, 1979; Karlin et al., 1979;
Kobyliansky et al., 1982; Livshits et al., 1991; Nevo et al., 1996). Subsequent studies in DNA autosomal markers, based on STRs (Rosenberg et al., 2001; Picornell et al., 2002;
Kopelman et al., 2009; Listman et al., 2010) also anchored the origin of different Jewish populations to the Middle East. However, the different studies inferred a variable component of Middle Eastern ancestry, with varying degrees of admixture and introgression from the corresponding Diaspora host populations (Ostrer and Skorecki, 2013).
More recent studies based on genome-wide SNP arrays have been performed on several populations with Jewish origin (e.g. Atzmon et al., 2010; Behar et al., 2010; 2013;
Campbell et al., 2012; Waldman et al., 2016). The combined analysis of millions of polymorphism markers along the genome have led to greater precision in the clustering of different Jewish groups and in the estimate of the Middle Eastern, European, and African components in each group. These new analyses reflect that Jews are a mosaic of people (Levy-Coffman, 2005). In spite of the close genetic interrelatedness of many groups, modern Jews exhibit a diversity of genetic profiles. Each of today’s Jewish populations is the result of the blending of Middle Eastern and host population (European, Asian or African) heritage to which its particular history has led through the centuries.
Genome-wide studies have also been carried out in an attempt to discover new genes for susceptibility to diseases in Jewish populations (Ostrer, 2001). It is well known that some genetic disorders are more prevalent in particular Jewish populations. This fact has been especially well-studied in Ashkenazi Jews (Rosner et al., 2009), where bottlenecks through their history (Behar et al., 2004b) could explain the relatively high frequency found in more than 20 recessive disorders, such as Gaucher or Tay-Sachs diseases (Jorde, 1992). The aim
in Clinical Genetics in the current genomic era is whole exome sequencing to address personalized medicine in the future (Ostrer, 2011).
In order to delve further into the origins of Jewish people and the demographic events that have contributed to the current make-up of the different Jewish groups settled in a vast geographic span after the Diaspora, haploid marker studies have been actively used. These research studies make it possible to focus attention on the paternal (Y-chromosome) and maternal (mtDNA) history of each population studied.
Concerning the Y-chromosome, early studies were based on Restriction Fragment Length Polymorphisms (RFLPs) (Lucotte and David, 1992; Lucotte et al., 1993; Santachiara Benerecetti et al., 1993) and searched for a common origin of modern Jewish male lineages.
They also attempted to estimate the contribution of males from the host populations to the gene pool of the different Jewish groups. Subsequent studies (Hammer et al., 2000; Thomas et al., 2000; Nebel et al., 2001; Picornell et al., 2002; 2004) indicate that European, North African and Middle Eastern Jewish populations are more similar between them and other Middle Eastern populations, than between them and their host populations, suggesting, therefore, that most Jewish communities share an ancestral common Middle Eastern origin, and that they remained relatively isolated from neighbouring non-Jewish communities during the Diaspora.
Even though most of the studies focus on Ashkenazim (e.g. Behar et al., 2003; 2004a; Nebel et al., 2005) other Jewish communities have also been studied in the last decades, for example Middle Eastern, Sephardic Jews, Yemenite or Ethiopian Jews (e.g. Ritte et al., 1993; Nebel et al., 2001; Semino et al., 2004; Shen et al., 2004; Adams et al., 2008; Oefner et al., 2013). Furthermore, the male lineages of the Lemba, black Jews of Southern Africa (Spurdle and Jenkins 1996; Thomas et al., 2000; Soodyall, 2013) and Indian Jews (Chaubey et al., 2016) have been analysed. Although a specific Middle Eastern ancestry component is found in most of the studies, more distant geographical groups (such as Ethiopian, Lemba or Indian Jews) have a very important admixture with local populations in accordance with their history.
Other studies have concentrated on the Jewish priestly lineages, Cohanim and Levites.
Cohanim (both Ashkenazi and Sephardic) reveal very high frequencies of a haplotype called CMH (Cohen Modal Haplotype) (Skorecki et al., 1997). The origin of CMH has been estimated at 3190±1090 years, supporting the hypothesis that the majority of contemporary Jewish priests descend from a limited number of paternal lineages with their origin in the Middle East before the dispersion of the Jewish people into separate communities (Hammer et al., 2009). Meanwhile, Levites show greater diversity, suggesting multiple origins in their paternal lines (Behar et al., 2003). This study claimed a founder effect for the haplogroup R1a-M17, and they suggested that it was an introgression by an Eastern European male or small group of males. Posterior studies performed with whole
sequences of Y-chromosomes (Rootsi et al., 2013) indicated that in fact there exists a founder effect by the R1a haplotype, but the Levite one comes from the Near East and not from Eastern Europe as thought at the beginning, since this haplotype is present in Hebrew populations pre-Diaspora. A recent study (Tofanelli et al., 2014) questions the previous results of Jewish Priestly lineages and indicates the need to look further into Y-chromosome typing to refine the phylogeny of this marker and ultimately clarify their role in the study of the Jewish groups’ ancestry.
Regarding mitochondrial DNA, although the first studies were performed with RFLPs (e.g.
Bonné-Tamir et al., 1986; Zoosmann-Diskin et al., 1991; Ritte et al., 1993), subsequent analyses were based on sequencing, first by means of fragments of the Control Region, later on expanded to the complete D-loop, and more recently to the whole mtDNA genome.
Early studies in Jewish populations (Thomas et al., 2002; Picornell et al., 2006) indicated that each of the different Jewish communities is composed of descendants of a relatively small group of maternal founders, that the process was independent and different in each geographical area, and that inward gene flow from the host populations has probably been very limited on the female side.
Like in the Y-chromosome, many studies focus on Ashkenazi Jews (Behar et al., 2004b;
2006; Brandstätter et al., 2008; Costa et al., 2013; Tian et al., 2015). Mitochondrial DNA reveals a genetic bottleneck in the early history of the Ashkenazi Jewry. In fact, current variation in this Jewish group can be traced back to only 4 women, who would be the major founders, and several minor contributors. It is a matter of controversy where these 4 main contributors came from, some studies claim the Near East, while others suggest the Caucasus or Europe. A recent study (Tian et al., 2015) even suggests that there is a contribution to the Ashkenazi population that comes from the Far East through the Silk Road. Behar et al. (2008b) studied non-Ashkenazi communities to compare how these were founded. Contrary to the Ashkenazim, no evidence for narrow founder effects was found in these populations. For Indian and Ethiopian communities, an important local female contribution was detected, while mtDNAs in all other communities studied belong to a well-characterized West Eurasian maternal pool. In North African and Iberian Exile Jewish communities, a putative Iberian admixture has been shown. These results led them to conclude that there are striking differences in the demographic history of the widespread Jewish Diaspora communities.
Converted Jews have also been subject of study, either due to their contribution to the host population genetic pool (e.g. Carvajal-Carmona et al., 2000; Maca-Meyer et al., 2003;
Gonçalves et al., 2005; Sutton et al., 2006; Adams et al., 2008; Santos et al., 2010; Velez et al., 2012; Bedford et al., 2013; Marques et al., 2016), or owing to their isolation and differentiation from their neighbours, such as the Portuguese Crypto-Jew communities in Belmonte and Bragança (Gerber et al., 2000; Behar et al., 2008b; Teixeira et al., 2011;
Nogueiro et al., 2010; 2015a; 2015b) or the Chuetas in Majorca.
Regarding the subject of study in the present work, the Chueta population, it has previously been studied using classical markers (Picornell et al., 1990; 1991; 1992; 1994; 1997; Nevo
et al., 1996); autosomal STRs (Tomàs et al., 2000); HLA (Crespi et al., 2002; Cambra et al., 2009); and genetic illnesses (Buades et al., 1995; Domingo et al., 2000; Guix et al., 2002; Matas et al., 2006). The main points of this genetic research were: a) to investigate whether this group was a genetically differentiated population with respect to their neighbours; b) to test to what extent they have kept their genetic make-up, keeping evidence of their historical Middle Eastern origin; c) to estimate the extent of admixture with the host Majorcan population; and d) to investigate possible impoverishment of genetic diversity due to isolation and inbreeding.
In summary, the results of the studies conducted to date on the one hand demonstrate that Chuetas are a differentiated population that has kept a considerable proportion of its original genetic make-up. It was especially clear in some markers, where Chuetas showed polymorphic frequencies of alleles that are very rare in neighbour populations, but not in Middle Eastern populations. Considering their well-documented Jewish origin, the most probable reason for these findings is their ancestral genetic patrimony due to their Middle Eastern origin (Picornell et al., 1994; 2005; Nevo et al., 1996). On the other hand, a certain degree of introgression from and admixture with the host population was also detected. The extent of this admixture was estimated at approximately 50% using present-day Sephardim and Majorcans as parental populations (Tomàs et al., 2000). Lastly, despite being a small, isolated, endogamous group, Chuetas seem not to have suffered a significant loss of diversity, although the observed singular frequency in some mutations seems to point to genetic drift as the most probable cause (Matas et al., 2006).
Haploid markers, data from the X-chromosome and new autosomal approaches would contribute to produce a more detailed genetic landscape of Chuetas, the only current Spanish population whose ancestors can be traced to Sephardic Jewish populations, because of their peculiar history which has kept the memory of their Jewish origin for centuries, along with their genetic heritage.
The main goal of this PhD thesis was to better characterise the Chueta gene pool and to answer unsolved questions, especially regarding their maternal and paternal lineages, since previous studies in autosomal markers have demonstrated that they are a genetically differentiated population. In order to do this, we have studied in depth the Genetics of this community through new autosomal markers (Indels), X-chromosome, Y-chromosome, and mtDNA mitochondrial analyses.
To achieve this main purpose, specific aims were proposed:
• Characterization of a 38-plex panel of autosomal Indels in Chuetas, their host population (Majorca), and other populations with Jewish origin.
• To examine different X-markers (9 Alu insertion polymorphisms, 12 STRs, and 32 Indels) in these populations.
• To evaluate the usefulness of these markers in both Population and Forensic genetics, and establish specific frequency databases for forensic casework.
• To investigate the ancestry and demographic history of the maternal and paternal founding lineages of the Chueta population.
• To analyse whether cultural isolation has led to the impoverishment of genetic diversity in mtDNA and Y-chromosome lineages in Chuetas.
• Through a comparison with other populations in the literature, to attempt to estimate the amount of Sephardic and Majorcan contribution to the Chueta population
• To find out, based on data of X-chromosome, mtDNA, and Y-chromosome in Chuetas, their host population and Jewish populations with whom they share origin, whether there has been an asymmetrical sex-biased contribution from the Sephardic and Majorcan populations to the Chuetas’ gene pool.