Arab dna map

Arab dna map DEFAULT

Genetic history of the Middle East

The genetic history of the Middle East is the subject of research within the fields of human population genetics, archaeogenetics and Middle Eastern studies. Researchers use Y-DNA, mtDNA, and other autosomal DNAs to identify haplogroups and haplotypes in ancient populations of Egypt, Persia, Mesopotamia, Anatolia, Arabia, the Levant, and other areas.

History[edit]

See also: Fertile Crescent § Cosmopolitan diffusion

Developments in DNA sequencing in the 1970s and 1980s provided researchers with the tools needed to study human genetic variation and the genetics of human populations to discover founder populations of modern people groups and human migrations.[citation needed]

In 2005, National Geographic launched The Genographic Project, led by 12 prominent scientists and researchers, to study and map historical human migration patterns by collecting and analyzing DNA samples from hundreds of thousands of people from around the world.[citation needed]

Regions[edit]

Egypt[edit]

Further information: DNA history of Egypt

Contamination from handling and intrusion from microbes create obstacles to the recovery of Ancient DNA.[1] Consequently, most DNA studies have been carried out on modern Egyptian populations with the intent of learning about the influences of historical migrations on the population of Egypt.[2][3][4][5]

In general, various DNA studies have found that the genetic variant frequencies of North African populations are intermediate between those of the Near East, the Horn of Africa, southern Europe and Sub Saharan Africa,[6] though Egypt's NRY frequency distributions appear to be much more similar to those of the Middle East than to any sub-Saharan African population, suggesting a much larger Eurasian genetic component in samples examined .[7][8][9][10][11]

A recent genetic study published in the "European Journal of Human Genetics" (2019) showed that Northern Africans (including Egyptians) are closely related to Europeans and West Asians as well as to Southwest Asians. Northern Africans can clearly be distinguished from West Africans and other African populations dwelling south of the Sahara.[12]

Blood groups[edit]

Blood typing and DNA sampling on ancient Egyptian mummies is scant; however, a 1982 study of blood typing of dynastic mummies found ABO frequencies to be most similar to modern Egyptians[13] and some also to Northern Haratin populations. ABO blood group distribution shows that the Egyptians form a sister group to North African populations, including Berbers, Nubians and Canary Islanders.[14]

Ancient Egyptians[edit]

In 2013, Nature announced the publication of the first genetic study utilizing next-generation sequencing to ascertain the ancestral lineage of an Ancient Egyptian individual. The research was led by Carsten Pusch of the University of Tübingen in Germany and Rabab Khairat, who released their findings in the Journal of Applied Genetics. DNA was extracted from the heads of five Egyptian mummies that were housed at the institution. All the specimens were dated between 806 BC and 124 AD, a timeframe corresponding with the late Dynastic period. The researchers observed that one of the mummified individuals likely belonged to the mtDNA haplogroup I2, a maternal clade that is believed to have originated in Western Asia.[15]

In a 2017 study published in Nature, three Egyptian mummies were obtained spanning around 1,300 years of Egyptian history from the New Kingdom to the Roman period. Analyses revealed that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times, around 750 years ago.[16]

Iran[edit]

Further information: Iranian peoples § Genetics

Genetic links to neolithic Anatolia[edit]

A 2017 study analyzed the autosomal DNA and genome of an Iron Age Iranian sample taken from Teppe Hasanlu (F38_Hasanlu, dated to 971-832 BCE) and revealed it had close affinities to a neolithic North-West Anatolian individual from Kumtepe even closer than Neolithic Iranians.[17]

Gilaks and Mazandaranis[edit]

Further information: Gilaks § Genetics, and Mazanderani people § Genetics

A 2006 genetic research was made by Nasidze et al. on the North Iranian populations on the Gilaks and Mazandaranis, spanning the southwestern coast of the Caspian Sea, up to the border with neighbouring Azerbaijan. The Gilaks and Mazandaranis comprise 7% of the Iranian population. The study suggested that their ancestors came from the Caucasus region, perhaps displacing an earlier group in the South Caspian.[18] Linguistic evidence supports this scenario, in that the Gilaki and Mazandarani languages (but not other Iranian languages) share certain typological features with Caucasian languages, and specifically South Caucasian languages.[18] There have been patterns analyzed of mtDNA and Y chromosome variation in the Gilaki and Mazandarani.

Based on mtDNA HV1 sequences tested by Nasidze et al., the Gilaks and Mazandarani most closely resemble their geographic and linguistic neighbors, namely other Iranian groups. However, their Y chromosome types most closely resemble those found in groups from the South Caucasus.[18] A scenario that explains these differences is a south Caucasian origin for the ancestors of the Gilani and Mazandarani, followed by introgression of women (but not men) from local Iranian groups, possibly because of patrilocality.[18] Given that both mtDNA and language are maternally transmitted, the incorporation of local Iranian women would have resulted in the concomitant replacement of the ancestral Caucasian language and mtDNA types of the Gilani and Mazandarani with their current Iranian language and mtDNA types. Concomitant replacement of language and mtDNA may be a more general phenomenon than previously recognized.

The Mazandarani and Gilani groups fall inside a major cluster consisting of populations from the Caucasus and West Asia and are particularly close to the South Caucasus groups—Georgians, Armenians, and Azerbaijanis. Iranians from Tehran and Isfahan are situated more distantly from these groups.[18]

Iranian Azeris[edit]

The 2013 comparative study on the complete mitochondrial DNA diversity in Iranians has indicated that Iranian Azerbaijanis are more related to the people of Georgia, than they are to other Iranians (Like Persians), while the Persians, Armenians and Qashqai on the other hand were more related to each other.[19] It furthermore showed that overall, the complete mtDNA sequence analysis revealed an extremely high level of genetic diversity in the Iranian populations studied which is comparable to the other groups from the South Caucasus, Anatolia and Europe.[19] The same 2013 research further noted that "the results of AMOVA and MDS analyses did not associate any regional and/or linguistic group of populations in the Anatolia, Caucasus and Iran region pointing to strong genetic affinity of Indo-European speaking Persians and Turkic-speaking Qashqais, thus suggesting their origin from a common maternal ancestral gene pool.[19] The pronounced influence of the South Caucasus populations on the maternal diversity of Iranian Azeris is also evident from the MDS analysis results."[19] The study also notes that "It is worth pointing out the position of Azeris from the Caucasus region, who despite their supposed common origin with Iranian Azeris, cluster quite separately and occupy an intermediate position between the Azeris/Georgians and Turks/Iranians grouping".[19] The MtDNA results from the samples overall on average closely resemble those found in the neighbouring regions of the Caucasus, Anatolia, and to a lesser extent (Northern) Mesopotamia.[19]

Among the most common MtDNA lineages in the nation, namely U3b3, appears to be restricted to populations of Iran and the Caucasus, while the sub-cluster U3b1a is common in the whole Near East region.[19]

Iraq[edit]

Further information: Iraqis § Genetics

Ancient genetic links to South Asia[edit]

Further information: Genetics and archaeogenetics of South Asia

A 2013 study based on DNA extracted from the dental remains of four individuals from different time eras (200–300 CE, 2650-2450 BCE, 2200–1900 BCE) unearthed at Tell Ashara (ancient Terqa, in modern Syria) and Tell Masaikh (ancient Kar-Assurnasirpal) suggested a possible genetic link between the people of Bronze Age Mesopotamia and Northern India. According to the study, "We anticipate that the analysed remains from [northern] Mesopotamia belonged to people with genetic affinity to the Indian subcontinent since the distribution of identified ancient haplotypes indicates solid link with populations from the region of South Asia-Tibet (Trans-Himalaya). They may have been descendants of migrants from much earlier times, spreading the clades of the macrohaplogroup M throughout Eurasia and founding regional Mesopotamian groups like that of Terqa or just merchants moving along trade routes passing near or through the region."[20] A 2014 study expanding on the 2013 study and based on analysis of 15751 DNA samples arrives at the conclusion, that "M65a, M49 and/or M61 haplogroups carrying ancient Mesopotamians might have been the merchants from India".[21]

Assyrians[edit]

Further information: Assyrian people § Genetics

In the 1995 book The History and Geography of Human Genes the authors wrote that: "The Assyrians are a fairly homogeneous group of people, believed to originate from the land of old Assyria in northern Iraq [..] they are Christians and are bona fide descendants of their ancient namesakes."[22] In a 2006 study of the Y chromosome DNA of six regional populations, including, for comparison, Assyrians and Syrians, researchers found that, "the two Semitic populations (Assyrians and Syrians) are very distinct from each other according to both [comparative] axes. This difference supported also by other methods of comparison points out the weak genetic affinity between the two populations with different historical destinies."[23]

A 2008 study on the genetics of "old ethnic groups in Mesopotamia," including 340 subjects from seven ethnic communities ("These populations included Assyrians, Jews, Zoroastrians, Armenians, Arabs and Turkmen (representing ethnic groups from Iran, restricted by rules of their religion), and the Iraqi and Kuwaiti populations from Iraq and Kuwait.") found that Assyrians were homogeneous with respect to all other ethnic groups sampled in the study, regardless of religious affiliation.[24]

Marsh Arabs[edit]

Further information: Marsh Arabs § Genetics

A study published in 2011 looking at the relationship between Iraq's Marsh Arabs and ancient Sumerians concluded "the modern Marsh Arabs of Iraq harbour mtDNAs and Y chromosomes that are predominantly of Middle Eastern origin. Therefore, certain cultural features of the area such as water buffalo breeding and rice farming, which were most likely introduced from the Indian sub-continent, only marginally affected the gene pool of the autochthonous people of the region. Moreover, a Middle Eastern ancestral origin of the modern population of the marshes of southern Iraq implies that, if the Marsh Arabs are descendants of the ancient Sumerians, also Sumerians were not of Indian or Southern Asian ancestry."[25] The same 2011 study, when focusing on the genetics of the Maʻdān people of Iraq, identified Y chromosome haplotypes shared by Marsh Arabs, Arabic speaking Iraqis, Assyrians and Mandeans "supporting a common local background."[25]

Levant[edit]

Further information: Druze § Genetics, Palestinians § DNA and genetic studies, Samaritans § Genetic studies, and Syrians § Genetics

Chalcolithic and Bronze Age periods[edit]

From a 2020 study published in Cell: "Understanding the nature of this movement was the primary motivation behind this study. Here, we present a large-scale analysis of genome-wide data from key sites of prehistoric Anatolia, the Northern Levant, and the Southern Caucasian lowlands ... In the Northern Levant, we identified a major genetic shift between the Chalcolithic and Bronze Age periods. During this transition, Northern Levantine populations experienced gene flow from new groups harboring ancestries related to both Zagros/Caucasus and the Southern Levant. This suggests a shift in social orientation, perhaps in response to the rise of urban centers in Mesopotamia, which to date remain genetically unsampled." They further add: "This expansion is recorded in the region of the Northern Levant ca. 2800 BCE and could be associated with the movement/ migration of people from Eastern Anatolia and the Southern Caucasian highlands. However, our results do not support this scenario for a number of reasons". "There are extensive textual references from the end of the EBA through the LBA referring to groups of people arriving into the area of the Amuq Valley. Although these groups were named, likely based on designations (e.g., Amorites, Hurrians), the formative context of their (cultural) identity and their geographic origins remain debated. One recent hypothesis (Weiss, 2014, 2017; Akar and Kara, 2020) associates the arrival of these groups with climate-forced population movement during the ‘‘4.2k BP event,’’ a Mega Drought that led to the abandonment of the entire Khabur river valley in Northern Mesopotamia and the search of nearby habitable areas."[26]

The study also suggested a substantial genetic continuity from the Levantine Bronze Age both in modern-day Arabic-speaking Levantine populations (such as Syrians, Druze, Lebanese, and Palestinians) and Jewish groups (such as Moroccan, Ashkenazi, and Mizrahi Jews), who are all suggested to derive a majority (about half or more) of their ancestry from Canaanite-related or Bronze Age Levantine populations (with differering variables for different communities, and with Ashkenazi Jews deriving just over half of their ancestry from Bronze-Age Levantines/Canaanite-related peoples and the rest from Europeans, and Arabic-speaking Levantines, Moroccan Jews, and Mizrahi Jews deriving a larger majority of their ancestry from Bronze Age Canaanite-related peoples). The study concludes that this does not mean that any of these present-day groups bear direct ancestry from people who lived in the Middle-to-Late Bronze Age Levant or in Chalco-lithic Zagros; rather, it indicates that they have ancestries from populations whose ancient proxy can be related to the Middle East.[27]

Canaanites and Phoenicians[edit]

Further information: Phoenicia § Genetic studies

Zalloua and Wells (2004), under the auspices of a grant from National Geographic Magazine, examined the origins of the CanaanitePhoenicians. The debate between Wells and Zalloua was whether haplogroupJ2 (M172) should be identified as that of the Phoenicians or that of its "parent" haplogroup M89 on the YDNA phylogenetic tree.[28] Initial consensus suggested that J2 be identified with the Canaanite-Phoenician (North Levantine) population, with avenues open for future research.[29] As Wells commented, "The Phoenicians were the Canaanites"[29] It was reported in the PBS description of the National Geographic TV Special on this study entitled "Quest for the Phoenicians" that ancient DNA was included in this study as extracted from the tooth of a 2500-year-old Phoenician mummy.[30]

Wells identified the haplogroup of the Canaanites as haplogroup J2 which originated from Anatolia and the Caucasus.[29] The National Geographic Genographic Project linked haplogroup J2 to the site of Jericho, Tel el-Sultan, ca. 8500 BCE and indicated that in modern populations, haplogroup J2 is found primarily in the Middle East, but also along the coasts of North Africa and Southern Europe, with especially high distribution among present-day Jewish populations (30%), Southern Italians (20%), and lower frequencies in Southern Spain (10%).[31]

Cyprus[edit]

Cruciani in 2007 found E1b1b1a2 (E-V13) [one from Sub Clades of E1b1b1a1 (E-M78)] in high levels (>10% of the male population) in Cypriot and Druze lineages. Recent genetic clustering analyses of ethnic groups are consistent with the close ancestral relationship between the Druze and Cypriots, and also identified similarity to the general Syrian and Lebanese populations, as well as a variety of Jewish lineages (Ashkenazi, Sephardi, Iraqi Jewish, and Moroccan Jews).[32]

A 2016 study on 600 Cypriot males asserts that "genome-wide studies indicate that the genetic affinity of Cyprus is nearest to current populations of the Levant". Analyses of Cypriot haplogroup data are consistent with two stages of prehistoric settlement. E-V13 and E-M34 are widespread, and PCA suggests sourcing them to the Balkans and Levant/Anatolia, respectively. Contrasting haplogroups in the PCA were used as surrogates of parental populations. Admixture analyses suggested that the majority of G2a-P15 and R1b-M269 components were contributed by Anatolia and Levant sources, respectively, while Greece/Balkans supplied the majority of E-V13 and J2a-M67. Haplotype-based expansion times were at historical levels suggestive of recent demography.[33] On the other hand, more recent Principal Component Analyses based on autosomal DNA, have placed Cypriots clearly separate from Levantine and Middle Eastern groups, either at the easternmost flank of the south European cluster,[34] or in an intermediate position between southern Europeans and northern Levantines.[35][36][37] In a study by Harvard geneticist Iosif Lazarides and colleagues investigating the genetic origins of the Minoans and Mycenaeans, Cypriots were found to be the second least differentiated population from Bronze Age Mycenaeans based on FST index and also genetically differentiated from Levantines.[38]

Israel[edit]

Further information: Genetic studies on Jews

A study published by the National Academy of Sciences found that "the paternal gene pools of Jewish communities from Europe, North Africa, and the Middle East descended from a common Middle Eastern ancestral population", and suggested that "most Jewish communities have remained relatively isolated from neighbouring non-Jewish communities during and after the Diaspora".[39] Researchers expressed surprise at the remarkable genetic uniformity they found among modern Jews, no matter where the diaspora has become dispersed around the world.[39] Skorecki and colleague wrote that "the extremely close affinity of Jewish and non-Jewish Middle Eastern populations observed ... supports the hypothesis of a common Middle Eastern origin".[40]

This research has suggested that, in addition to Israelite male, significant female founder ancestry might also derive from the Middle East-with 40% of Ashkenazim descended from four women who lived about 2000–3000 years ago in the Middle East.[41] In addition, Behar (2006) suggested that the rest of Ashkenazi mtDNA is originated from about 150 women; most of those were probably of Middle Eastern origin.[42] A 2013 genetic study suggested that the four founding maternal lineages of Ashkenazi Jews originate in Europe and that only ~8% of Ashkenazi mtDNA can confidently be assigned a Near Eastern origin, while >80% of Ashkenazi maternal lineages have a likely European origin (with most Ashkenazi paternal lineages having a Middle Eastern origin),[43] while a 2014 study carried out by Spanish geneticists suggested an ancient Near Eastern origin of the four founding maternal lineages of Ashkenazi Jews.[44]

In 2004, a team of geneticists from Stanford University, the Hebrew University of Jerusalem, Tartu University (Estonia), Barzilai Medical Center (Ashkelon, Israel), and the Assaf Harofeh Medical Center (Zerifin, Israel), studied the modern Samaritan ethnic community living in Israel in comparison with modern Israeli populations to explore the ancient genetic history of these people groups. The Samaritans or Shomronim (singular: Shomroni; Hebrew: שומרוני) trace their origins to the Assyrian province of Shomron (Samaria) in ancient Israel in the period after the Assyrian conquest circa 722 BCE. Shomron was the capital of the Northern Kingdom of Israel when it was conquered by the Assyrians and gave the name to the ancient province of Samaria and the Samaritan people group. Jewish tradition holds that the Samaritans were a mixed group of Israelites who were not exiled or were sent back or returned from exile and non-Israelites relocated to the region by the Assyrians. The modern-day Samaritans are believed to be the direct descendants of the ancient Samaritans.

Their findings reported on four family lineages among the Samaritans: the Tsdaka family (tradition: tribe of Menasseh), the Joshua-Marhiv and Danfi families (tradition: tribe of Ephraim), and the Cohen family (tradition: tribe of Levi). All Samaritan families were found in haplogroupsJ1 and J2, except the Cohen family which was found in haplogroupE3b1a-M78.[45] This article predated the E3b1a subclades based on the research of Cruciani, et al.[46]

A 2018 study conducted by scholars from Tel-Aviv University, the Israel Antiquities Authority and Harvard University had discovered that 22 out of the 600 people who were buried in Peki'in cave from the Chalcolithic Period were of both local Levantine and Persian and Zagros[47] area ancestries, or as phrased in the paper itself: "Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation," the scientists concluded that the homogeneous community found in the cave could source ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~26% from groups related to those of the Anatolian Neolithic, and ~17% from groups related to those of the Iran Chalcolithic.[48] The scholars noted that the Zagros genetic material held "Certain characteristics, such as genetic mutations contributing to blue eye color, were not seen in the DNA test results of earlier Levantine human remains"...The blue-eyed, fair-skinned community didn’t continue, but at least now researchers have an idea why. "These findings suggest that the rise and fall of the Chalcolithic culture are probably due to demographic changes in the region".[48][49]

In a 2005 study of ASPM gene variants, Mekel-Bobrov et al. found that the IsraeliDruze people of the Carmel region have among the highest rate of the newly evolved ASPM haplogroup D, at 52.2% occurrence of the approximately 6,000-year-old allele.[50] While it is not yet known exactly what selective advantage is provided by this gene variant, the haplogroup D allele is thought to be positively selected in populations and to confer some substantial advantage that has caused its frequency to rapidly increase. According to DNA testing, Druze are remarkable for the high frequency (35%) of males who carry the Y-chromosomalhaplogroup L, which is otherwise uncommon in the Mideast.[45] This haplogroup originates from prehistoric South Asia and has spread from Pakistan into southern Iran.

Lebanon[edit]

Further information: Lebanese people § Genetics

In a 2011 genetic study by Haber et al which analyzed the male-line Y-chromosome genetics of the different religious groups of Lebanon, revealed no noticeable or significant genetic differentiation between the Maronites, Greek Orthodox Christians, Greek Catholic Christians, Sunni Muslims, Shiite Muslims, and Druze of the region on the more frequent haplogroups. Major differences between Lebanese groups were found among the less frequent haplogroups.[51] In 1965, Ruffié and Taleb found significant differences of blood markers between ethno-religious groups.[52] A 2005 study by Makhoul et al on Beta Thalassemia Heterogeneity in Lebanon[53] found out that the thalassemia mutations in some Lebanese Christians are similar to the ones observed in Macedonia which "may confirm the presumed Macedonian origin of certain Lebanese Christians".

A 2013 genetic study carried out by Haber at al found "all Jews (Sephardi and Ashkenazi) cluster in one branch; Druze from Mount Lebanon and Druze from Mount Carmel are depicted on a private branch; and Lebanese Christians form a private branch with the Christian populations of Armenia and Cyprus placing the Lebanese Muslims as an outer group. Lebanese Muslims cluster towards the predominant Muslim populations of Syrians, Palestinians, and Jordanians, which in turn cluster on branches with other Muslim populations as distant as Morocco and Yemen."[54]

The authors explained that "In particular, conversion of the region's populations to Islam appears to have introduced major rearrangements in populations' relations through admixture with culturally similar but geographically remote populations, leading to genetic similarities between remarkably distant populations like Jordanians, Moroccans, and Yemenis. Conversely, Christians, Jews and Druze became genetically isolated in the new cultural environment." In conclusions, the authors reconstructed the genetic structure of ancient Levantines and found that a pre-Islamic expansion Levant was more genetically similar to Europeans than to Arabians.[54]

A 2017 study published by the American Journal of Human Genetics, concluded that present-day Lebanese derive most of their ancestry from a Canaanite-related population (Canaanite being a pre-Phoenician name), which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. More specifically, according to Chris Tyler-Smith, a geneticist and his colleagues at the Sanger Institute in Britain, who compared "sampled ancient DNA from five Canaanite people who lived 3,750 and 3,650 years ago" to modern people. "The comparison revealed that 93 percent of the genetic ancestry of people in Lebanon came from the Canaanites and the other 7 percent was of a Eurasian steppe population"[55]

A 2019 study, carried out by the Wellcome Sanger Institute, United Kingdom, after analyzing the "DNA evidence from the remains of nine Crusaders found at a burial site in Lebanon", concludes that contrary to the popular belief, the Crusaders did not leave "a lasting effect on the genetics of modern-day Lebanese. Instead, today’s Lebanese Christians in particular are more genetically similar to locals from the Roman period, which preceded the Crusades by more than four centuries."[56][57]

Turkey[edit]

Further information: Genetic studies on Turkish people

Turkish genomic variation, along with several other Western Asian populations, looks most similar to genomic variation of South European populations such as southern Italians.[58] Data from ancient DNA – covering the Paleolithic, the Neolithic, and the Bronze Age periods – showed that Western Asian genomes, including Turkish ones, have been greatly influenced by early agricultural populations in the area; later population movements, such as those of Turkic speakers, also contributed.[58] The first and only (as of 2017) whole genome sequencing study in Turkey was done in 2014.[58] Moreover, the genetic variation of various populations in Central Asia "has been poorly characterized"; Western Asian populations may also be "closely related to populations in the east".[58] An earlier 2011 review had suggested that "small-scale, irregular punctuated migration events" caused changes in language and culture "among Anatolia's diverse autochthonous inhabitants," which explains Anatolian populations' profile today.[59]

See also[edit]

References[edit]

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Sours: https://en.wikipedia.org/wiki/Genetic_history_of_the_Middle_East

Population genetic diversity in an Iraqi population and gene flow across the Arabian Peninsula

Abstract

Y-STRs have emerged as important forensic and population genetic markers for human identification and population differentiation studies. Therefore, population databases for these markers have been developed for almost all major populations around the world. The Iraqi population encompasses several ethnic groups that need to be genetically characterised and evaluated for possible substructures. Previous studies on the Iraqi population based on Y-STR markers were limited by a restricted number of markers. A larger database for Iraqi Arab population needed to be developed to help study and compare the population with other Middle Eastern populations. Twenty-three Y-STR loci included in the PowerPlex Y23 (Promega, Madison, WI, USA) were typed in 254 males from the Iraqi Arab population. Global and regional Y-STR analysis demonstrated regional genetic continuity among the populations of Iraq, the Arabian Peninsula and the Middle East. The Iraqi Arab haplotypes were used to allocate samples to their most likely haplogroups using Athey’s Haplogroup Predictor tool. Prediction indicated predominance (36.6%) of haplogroup J1 in Iraqi Arabs. The migration rate between other populations and the Iraqis was inferred using coalescence theory in the Migrate-n program. Y-STR data were used to test different out-of-Africa migration models as well as more recent migrations within the Arabian Peninsula. The migration models demonstrated that gene flow to Iraq began from East Africa, with the Levantine corridor the most probable passageway out of Africa. The data presented here will enrich our understanding of genetic diversity in the region and introduce a PowerPlex Y23 database to the forensic community.

Introduction

The location of ancient Iraq corresponds to an area known as Mesopotamia1,2. This fertile land witnessed probably the first human settlement and cultural shift processes. It attracted the ancient hunter-gatherer people to settle down around 10,000 BC and initiate the agricultural society, which then developed to become a trading society3.

The Arabs were tribal people who inhabited the central Arabian Peninsula under the protection of many empires (Assyrian, Babylonian and others).

Modern Iraq is an Arabian country with a population of ~ 40 million, bordered by the Arabian Gulf, Kuwait, and Saudi Arabia to the south, Jordan and Syria to the west, Turkey to the north, and Iran to the east4. Supplementary Figure S1 shows the political borders of Iraq and its position in the Middle East5. There are five ethnic groups in Iraq but there is little published data about the diversity of the Iraqi population. In this context the major ethnic groups are Arabs and Kurds6. Our data represents the Arabs, the largest ethnic group.

SNP-markers are stable due to low mutation rates7; SNPs therefore have little diversity and weak discrimination for individual identification (unless used in large multiplexes). Therefore, in forensic practice, a combination of SNPs is used to determine haplogroups. This information also aids in studying human migration and evolutionary patterns8. In comparison, Y-STRs have an average mutation frequency of 0.2% per generation, with high levels of diversity and strong powers of discrimination between unrelated males, and can aid individual identification as well as our understanding of population structure and issues of consanguinity.

Recently, alleles at STR loci have been used to generate haplotypes9,10 and these haplotypes can then be used to predict a haplogroup and the population of origin11,12. Using this approach, Y-STRs can address internal diversity in the population by providing information on more recent events in the history of a haplogroup13. There is little published data about genetic diversity in the Iraqi population and its ethnic groups. This study utilises Y-STRs to shed light on the genetic makeup of this population, the relationship to its close neighbours and the effect of its colonisation history.

Results

Y-STR alleles and haplotype diversity within the Iraqi population

The PowerPlex Y23 loci showed more discriminating haplotypes than the Y-Filer kit. Supplementary Table S1 contains a full list of the Iraqi (Arab) haplotypes, as well as other sample information; data are also available from YHRD, release 62 (accession number YA004630).

Allele frequency distributions of the 23-STR loci and the most frequent allele for each locus are presented in Supplementary Table S2 for the 254 males of the population under study. Multiple alleles were observed for each locus ranging from 13 for DYS458 to four for DYS437. Genetic diversity and match probability values for each locus are presented in Supplementary Fig. S2 and Supplementary Table S3. By far the most polymorphic locus was DYS385, with a genetic diversity value of 0.93; the least polymorphic locus was DYS392 with a genetic diversity value of 0.34. The diversity of four of the six newly added markers for the PowerPlex Y23 kit (DYS481, DYS570, DYS576 and DYS643) showed greater diversity than the Y filer loci, as can be inferred from the ranking of these loci (ranks 3, 4, 5 and 7); the other two loci (DYS549 and DYS533) did not show such a high diversity and their ranks were 9 and 11 respectively.

Duplicated alleles were found in three Iraqi individuals at the locus DYS19. The three haplotypes show the same duplicated alleles (15, 16) and were predicted to belong to haplogroup G2a. These duplicated alleles were found in the same haplotypes that contain variant alleles at the locus (DYS385a/b). A null allele was found in two Iraqi samples at the locus DYS576 and these were predicted to belong to haplogroup J2.

The 254 Iraqi Arab males carried 244 distinct haplotypes, eight identical pairs, and one trio, providing a discrimination capacity of 96%. However, when the sub-set of Yfiler haplotype was considered, the shared haplotypes increased to 25, with a discrimination capacity of 85%. The summary statistics of diversity for PowerPlex Y-23 and Y-Filer kits for the 254 haplotypes of the Iraqi Arab population in this study are listed in Supplementary Table S4. The full list of haplotypes and their predicted haplogroups is presented in Supplementary Table S1.

Microvariant alleles in the Arabian Peninsula

To study the microvariant alleles at the locus DYS458 in the Middle Eastern populations, the Middle Eastern data were compared to African, European, and southeast Asian countries. The presence of the microvariant alleles at the locus DYS458 was highest in the Middle Eastern populations (Table 1).

Full size table

The total percentage of microvariant alleles in the Iraqi population was 36.6% (93/254). Most were observed at the locus DYS458 (88/254; 34.6%); 87 of these are predicted to belong to haplogroup J1, in particular the 0.2 variant which, was observed for alleles 17, 18, 19, 20 and 21. One individual with microvariant 15.1 was predicted to belong to haplogroup N. The rest of the microvariant alleles were distributed as follows: one copy of the duplicated STR DYS385a/b carrying a 0.2 variant (allele 13/14.2) was observed in four haplotypes and predicted to belong to haplogroup G2a. One haplotype carrying a 0.4 variant for allele 17 at locus DYS448 was predicted to belong to haplogroup J2a1b.

Comparison with other populations

We compared the Iraqi population with other populations using Arlequin 3.5.2.223 with the use of 10,000 permutations and 0.05 as the significance level. The population pairwise genetic distances (Rst) were calculated between the Iraqi population and neighbouring Arab, Asian, African and European populations. The results are shown in Supplementary Table S5. The pairwise matric plot is shown in Supplementary Fig. S3.

The Rst pairwise differences were significant between the compared populations. The closest populations to the Iraqi Arabs were the Iraqi (Kurds) (Rst = 0.01081), then the Yemeni (Rst = 0.01215) and the Kuwaiti (Rst = 0.03986). The furthest were the Djiboutian (Rst = 0.24004), the Ethiopian (Rst = 0.22156) and the Turkish (Rst = 0.16422). Among the Middle Eastern populations Lebanon showed the highest genetic difference from the Iraqi Arabs (Rst = 0.14748).

The highest genetic difference was between Djiboutian and Iraqi (Kurds) (Rst = 0.25351) and the lowest was between Moroccan and Eritrean populations (Rst = 0.00714).

Arlequin 3.5.2.2 was also used to calculate the average pairwise differences between (PiXY) and within populations (PiX), in addition to the corrected average pairwise difference between populations (PiXY − (PiX + PiY)/2). The results are shown in Supplementary Table S6. The population average pairwise differences is shown in Supplementary Fig. S4.

Different groupings of Iraqis were compared with other populations and are shown in Supplementary Table S7. As expected, most of the variation occurs within populations, but variable values of the among-population variation were observed depending on the population groups targeted. This analysis suggested that Iraqis grouped best with Middle Eastern populations and all others as individual groups. The highest among-group difference was 3.52% and the lowest among-population within-groups variance was 6.75%; both of these values were noted when the Iraqi Arabs were grouped with the Middle Eastern populations. The P-values were significant for all among-group variance in various groupings.

Dendrogram clustering was illustrated based on Rst values using the R statistical software24, to display the relationships among the 23 populations; see Supplementary Fig. S5. Four clusters were created. Iraq (Arab), Iraq (Kurd), Yemen and Kuwait fell into one cluster. The rest of the Middle Eastern populations, including UAE, Qatar, Saudi Arabia, and Lebanon, fell into one cluster with Eritrea, Egypt, Morocco, South Korea and Japan. Three European countries, Sweden, Belgium and Finland, were clustered with China and India. The last cluster contained the three populations from African countries, Germany and Turkey.

The Iraqi and several Middle Eastern populations Y-STR data was analysed, using multi-dimensional scaling based on Rst distances using the R statistical software24. Supplementary Figure S6 shows the Multidimensional Scaling (MDS) plot of the Middle Eastern populations.

In the first dimension of the plot, four Middle Eastern populations lie in the lower left quadrant (Iraq (Arab), Iraq (Kurd), Yemen and Kuwait). Three European countries (Belgium, Finland and Sweden) are clustered with India and China in the upper left quadrant of the plot. All the other populations are clustered on the left side of the plot. The second dimension of the plot shows two clusters: the Middle Eastern occupies the lower two quadrants with some of the African countries and two Far Eastern countries (Japan and South Korea). All the European countries are clustered with some African and the South East Asian countries in the upper quadrants.

Analysis of diversity via network analysis and haplogroup prediction

Whit Athey’s tool analysis showed that the Iraqi Arab population had seven major haplogroups; J1, E1b1b, J2a1b, J2, R1a, R1b and J2b. The most common haplogroup was J1 which represented 36.6% (93/254) of the population. The complete haplogroups for Iraqi Arabs are shown in Supplementary Table S8.

Median-joining Y-STR network was calculated for Iraqi Arab haplotypes with NETWORK v5.0.1.0. and edited using NETWORK Publisher v2.1.1.2 (Fluxus Technology Ltd)25,26. Based on Whit Athey’s Haplogroup Predictor, haplogroups were assigned to the Arab haplotypes within the network (see Supplementary Fig. S7).

The complete Iraqi Arab median-joining tree contains seven major clusters, each corresponding to a major haplogroup found in the Iraqi Arab population. All the predicted haplogroups form coherent clusters and create an accurate picture of the Y-STR dataset’s relation to the haplogroups. The most coherent clusters are J1, E1b1b and R1a, followed by J2, J2a, J2b and R1b which are the most spread-out.

HapMap analysis for the Kidd Ancestry Informative SNPs (AISNPs) and the Y-STR data

Two HapMaps were generated using the program STRUCTURE which allows individuals to be clustered by their genetic information. The Kidd Ancestry Informative SNPs (AISNPs) using 55 SNPs from 140 populations (8,148 individuals)27 showed 10 clusters; and the HapMap of the Y-STR using 19 STR markers from 134 populations (21,323 individuals)14,15,16,17 showed 9 clusters.

The HapMap of the Kidd Ancestry Informative SNPs (AISNPs) showed an overlap between the North African and the South West Asian populations which include the Middle Eastern populations; and there was another overlap between the South West Asian and European populations. There was, however, poor sub-grouping of the countries within each population (see Supplementary Fig. S8). The HapMap of the Y-STR, the worldwide populations and the identified clusters of individuals corresponded to specific geographical regions without any overlap, with the Middle Eastern populations forming their own cluster. The HapMap of the Y-STR also showed a stronger sub-grouping of countries within each population (see Supplementary Fig. S9).

Estimation of migration rate in the Iraqi population

The gene flow was studied at three levels. At level one, the out-of-Africa migration to the Arabian Peninsula, three routes were investigated: Morocco → Egypt → Iraq; Africa → Egypt → Iraq; and Africa → Yemen → Iraq. Published data were used to design the migration models: Moroccan21, Egyptian18 and Yemeni (YHRD accession number YA003764). The African pool comprised populations from Eritrea, Ethiopia, Djibouti and Kenya17,19. Figure 1 shows the three level one out-of-Africa migration routes.

Level one migration routes: Morocco → Egypt → Iraq, Africa → Egypt → Iraq and Africa → Yemen → Iraq. The African populations were represented by one pool formed by four populations: Eritrean, Ethiopian, Djiboutian and Kenyan. The most probable migration route is represented by the red arrows. This figure was prepared by the author using Microsoft Word 2016.

Full size image

The Y chromosome migration pattern analysis showed that the best model was model 2 (the divergence model) for the route Africa → Egypt → Iraq; it has the highest log marginal likelihood (− 4,341.57), Bayes factor (0) and a probability of 1. The results are shown in Table 2. The least likely route was Africa → Yemen → Iraq in all three models.

Full size table

Level two examined population movements inside the Arabian Peninsula. Four routes were investigated, two from Yemen to Iraq, through Saudi Arabia and vice versa, and two from Yemen to Iraq through the UAE and vice versa. The most probable migration route was from Yemen to Iraq through the UAE (model 2) which shows the highest log marginal likelihood (− 5,618.94), Bayes factor (0) and probability of 1. The least probable route was from Yemen to Iraq, models 1 and 3. Level two results are shown in Table 3 and Fig. 2.

Full size table

Level two migration routes: gene flow from Egypt across the Sinai Peninsula, to the east towards Iraq and to the south towards Yemen. Four migration routes were tested from Yemen to Iraq, two from Yemen to Iraq, through Saudi Arabia and vice versa, and two from Yemen to Iraq through Emirate and vice versa. The most probable migration routes represented by the red arrows. This figure was prepared by the author using Microsoft Word 2016.

Full size image

The gene flow from Egypt across the Sinai Peninsula was examined in two directions, to the east towards Iraq and to the south towards Yemen. The results show that the most probable route was from Egypt to Yemen with the highest log marginal likelihood (− 3,398.33), Bayes factor (0) and probability of 1 (Table 4, Fig. 2).

Full size table

The final picture combining the outcomes of levels one and two and according to the most probable routes show that the gene flow to Iraq began from East Africa to Egypt then around the Arabian Peninsula to the south reaching Yemen, and then to the north through the UAE before reaching Iraq. Figure 3 shows the final picture of gene flow from Africa to Iraq. This final picture supports and agrees with the findings of other studies which proposed that the Levantine corridor is the most probable passageway out of Africa28,29,30.

Out-of-Africa gene flow combined with the gene flow inside the Arabian Peninsula. From East Africa to Egypt then around the coast of the Arabian Peninsula to the south reaching Yemen and then to the north through Oman and UAE to reach Iraq. This figure was prepared by the author using Microsoft Word 2016.

Full size image

The level three gene flow examined the effect of Iraq and Saudi Arabia on Kuwait. All four migration models in Supplementary Fig. S10 were applied. We found that model 2 dominates this level with the Saudi population having slightly more influence, log marginal likelihood (− 4,536.15), Bayes factor (0) and probability of 1, than the Iraqis on the Kuwaiti population, log marginal likelihood (− 4,701.61). The fourth model which assumed that two populations belong to the same panmictic population is the least probable, indicating that each of the three populations has its own genetic identity. Level three results are shown in Table 5.

Full size table

Discussion

The inclusion of a larger number of Y-STR loci such as those included in the PowerPlex Y-23 kit31 was intended to increase the discriminative power and therefore it is a popular kit in forensic casework and population studies. Y-STR haplotypes comprising the Y STRs included in the PowerPlex Y-23 kit were evaluated for their diversity in Iraqi Arab population.

Each population has its own unique genetic structure that can be characterised by its Y-STR haplotype databases for studying variation within, and between, population groups. Such databases are of great value in ascertaining the forensic value of Y-STR evidence. This study shows that the Iraqi Arab population has its own distinctive characteristics which differ from other populations17. The comparison of the databases revealed that two loci (DYS389I and DYS392) were less variable in the Iraqi population than in the other populations. Another characteristic feature of the Iraqi database was that the highest genetic diversities were for the dual marker DYS385a/b and a single-locus marker DYS458 at 0.93 and 0.85 respectively, unlike the other populations which showed the highest genetic diversities for the markers DYS385a/b and DYS48117.

Four of the six newly introduced markers, namely DYS481, DYS570, DYS576 and DYS643, ranked near the top in terms of genetic diversity, with GD values exceeding 0.70. This observation was consistent with a published global study17. PowerPlex Y-23 with its 23 loci proved to be more forensically informative and discriminating for the Iraqi population than the Y-Filer kit, which contained fewer loci.

It is notable that, the high incidence of microvariant alleles, in particular as reported at DYS458 (34.6%), is characteristic of the Middle Eastern populations. Microvariant alleles add to the discriminatory power and the evidential value of a DNA profile, and can further aid in determining haplogroups. We noticed that 98.8% of the Y-chromosomes carrying these DYS458 microvariants were located within haplogroup J1. This agrees with another study32 that showed this microvariant allele to overlap with the M267 marker; this has arisen as result of a combination of drift and founder effects, followed by rapid population expansion, in North Africa and the Middle East during human evolution.

In this study we noted two null alleles at the locus DYS576; both samples belonged to haplogroup J2. DYS576 has been reported17 as having the second-highest level of null alleles following DYS448 in an Asian population: 28% of the total reported null allele cases. The YHRD (release 62) contained a total of 31 null allele observations in the locus DYS576 out of a total 126,443 haplotypes (0.024%).

In this study, the duplication of 15, 16 at locus DYS19 was observed in three individuals (1.16%). In the YHRD (release 62) this duplication was at a frequency of 0.053%. Many studies have reviewed and addressed such duplications10,33 and it is thought to be because the duplicated region, mutating at a rate of approximately 10−3 times per generation in a single-step fashion, gives rise to a new allele usually different from the original by a single repeated unit34. The three haplotypes that show duplicated alleles 15, 16 were predicted to belong to haplogroup G2a35.

Y-haplogroups were inferred through using Whit Athey’s Haplogroup Predictor; the results showed that the most common haplogroup (34.6%) in Iraqi Arabs was J1 as detected earlier6,36. Haplogroup J1 (M267) is one of two major sub-haplogroups from the major haplogroup J (M304) found among modern West Asian, North African, Horn of Africa, Southern European, Central Asian and South Asian populations, essentially delineating the Middle East and associated with speakers of Semitic languages, especially Arabic37,38. The frequency of the J1 haplogroup is directly proportional to aridity in the Middle East and it increases toward the periphery of the Arabian Peninsula39.

A comparison of the accuracy of three haplogroup prediction software packages found that the precision was 98.80% in Whit Athey’s Haplogroup Predictor, 98.19% in Y Predictor by Vadim Urasin 1.5.0, and 97.59% in Jim Cullen’s Haplogroup Predictor40. Furthermore, Whit Athey’s Haplogroup Predictor and the median-joining tree complement each other.

The global Y-STR HapMap generated in this study not only showed a stronger geographical proximity of the population samples, but also a stronger sub-grouping of the corresponding populations than the Kidd Ancestry Informative SNPs HapMap, which shows overlapping genotypes of some regions of the world. This can be explained by STRUCTURE handling autosomal markers differently from the haploid markers, since in autosomal analysis STRUCTURE will define clusters by finding Mendelian populations of individuals. Another factor could be the number of individuals in each input population, with more in the Y-STR than the SNPs analysis27. Increasing the number of the Kidd Ancestry Informative SNP markers might improve its HapMap discriminatory power between the overlapping populations.

Out-of-Africa migration and peopling of the Middle East has been studied extensively and various routes of migration have been suggested28,29,30.

The Bayesian inference and the coalescence theory in Migrate-n indicated that most of the gene flow of the Y-STR from Africa to Arabia occurred following coastal pathways and crossing the Sinai Peninsula to Arabia. All the migration routes favoured divergence from ancestral populations without an ongoing migration model (model 2) and showed a probability of 1.0.

Two dispersal routes might explain the out-of-Africa model: a northern route through the Sinai Peninsula and the Levant, and a southern route followed the coast around Arabian Peninsula41,42,43.

The southern coastal route crossing the Bab al Mandab Strait (the narrowest point between Africa and Yemen) to Arabia was proposed as an alternative to the northern route in Ice Age because aridity in the Levant was a strong barrier to human expansion44,45. It is also thought that modern humans preferred the southern route because the Bab al Mandab Strait was narrow and shallow at that time; there is no geographical evidence of the existence of an intercontinental bridge 80,000 years ago, when such human intercontinental migrations occurred44,45. This study shows that this migration route is the less probable one.

This study supports the theory that the Levantine corridor served as a migratory route from East Africa through ancient Egypt into Iraq46.

Material and methods

DNA sampling

Blood samples were collected with informed consent from 254 Iraqi males in the Paternity Department of the Medico-Legal Institute in Baghdad using FTA cards. A small disc of 1.2 mm diameter was manually punched out of the card, using a Harris Punch, and used for direct amplification of DNA. Ethical permission for recruitment and analysis was provided by the University of Central Lancashire STEMH Ethics Committee (STEMH 246/June 2014). All methods were performed in accordance with the relevant guidelines and regulations.

DNA amplification

The PowerPlex Y23 System contains 23 loci: DYS576, DYS389I, DYS448, DYS389II, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS643, DYS393, DYS458, DYS385a/b, DYS456 and Y-GATA-H4. PCRs were conducted using one third of the recommended quantities and a total reaction volume of 8 μl. Amplification was performed using the manufacturer’s recommended cycling conditions. Fragments were detected using an ABI3500 Genetic Analyzer (Thermo Fisher Scientific) using the manufacturer’s recommended protocols. GeneMapper IDX software V1.4 was used for allele calling and interpretation.

Forensic and population genetic parameters

The haplotype frequencies were calculated by the counting method. Haplotype diversity was estimated by Nei’s formula47, HD = (1 − Σ pi2) *n/(n − 1) where n is the sample size and pi is the ith’s haplotype frequency. Genetic diversity (GD) was calculated as 1 − Σ pi2, where pi is the allele frequency. The match probability (MP) was calculated as Σ pi2, where pi is the frequency of the ith haplotype. Discriminatory capacity (DC) was calculated by dividing the number of different haplotypes by the total number of samples in a given population; in the formula DC = h/n, h is the number of different haplotypes in the observed population and n is the total number of the population48. The haplotype match probability (HMP) was calculated as HMP = 1 − HD49.

Molecular data were obtained for the Iraqi population using Y-STRs based on the PowerPlex Y 23 System, and subjected to comparative analyses with available data on other close and distant populations. Comparison with other datasets required reduction of the number of STRs to a shared set of 15, so that more Middle Eastern populations could be included in this analysis. Arlequin 3.5.2.2 software23 was used to calculate the average pairwise differences between (PiXY) and within populations (PiX), in addition to the corrected average pairwise difference between populations (PiXY − (PiX + PiY)/2).

Aiming to assess genetic affinity and structuring of the Iraqi sample, AMOVA computations were performed, considering other populations according to their geographical location; Middle Eastern populations were represented by Yemen, Turkey, Kuwait, Saudi Arabia, Iraq (Kurd), UAE, Qatar and Lebanon; African populations by Morocco, Egypt, Eretria, Ethiopia, Djibouti and Kenya, European populations by Germany, Belgium, Finland and Sweden; and East Asian populations by India, China, Japan and South Korea.

Iraqi Y haplogroup assignment

The full Y23 haplotypes were used to allocate haplotypes to their most likely haplogroup using Athey’s Haplogroup Predictor11,12. DYS549, DYS543 and DYS533 were excluded from the data because the first was not included in the program and the last two because no allele frequency data was available12.

The microvariant alleles were truncated to the next lowest integer value since values in the database were treated similarly. Null alleles were simply treated the same as untested markers (T.W. Athey, personal communication).

At GATA-H4, one unit was subtracted from each H4 value to put it on the same basis in the program. There were a number of samples for which the program did not make a prediction (no haplogroup met the criteria), and in those cases the haplotypes were manually examined, with results for some of them (T.W. Athey, personal communication).

Network analysis on Y chromosome haplogroups

Median-joining networks were constructed using the software NETWORK v5.0.1.0.26 and NETWORK Publisher v2.1.1.2 (Fluxus Technology Ltd)25. Following the recommendations of the Network’s authors, the intermediate alleles were rounded to the nearest integer; the locus DYS385a/b was removed for network construction. Missing alleles were coded ‘99′ in input files.

Structure statistical analyses

Population structure was investigated using the program STRUCTURE version 2.3.750 with an admixture model. The HapMap was generated for two panels, the 55 Kidd Ancestry Informative SNPs (AISNPs) genotypes of 140 populations (8,148 individuals)27 and Y-STR data for 19 markers of 134 populations (21,323 individuals)14,15,16,17. Four markers were excluded from the PowerPlex Y23 System, the two rapidly mutating STR (DYS570, DYS576), and the markers (DYS549, DYS643), so that more Middle Eastern populations could be included in this analysis.

For each run, the number of clusters, K, was specified in advance and values in the range 6–11 was used for both Y-STR data and the Kidd AISNPs data. For both tests the program was run with 10,000 burn-ins and 10,000 Markov Chain Monte Carlo (MCMC) iterations.

To assess and visualise likelihood values across multiple values of K and to detect the number of genetic groups that best fit the data, STRUCTURE output was processed with STRUCTURE HARVESTER51. Then the multiple replicate analyses of each data set were aligned using CLUMPP52 and the output files were used to draw the two HapMaps using Distruct53.

Estimation of migration rate in Iraqi population

Migration rates between other populations and Iraqi were inferred with the MIGRATE program version 4.2.1454 using coalescence theory.

The Bayesian inference procedure was chosen for the estimation of population genetic parameters. One long chain was run, with a long sampling increment of 1,000. The sampling increment allows a wider search of genealogy space since not every genealogy will be sampled. The number of discarded trees per chain (burn-in) was set to 5,000. According to the increment value and the number of discarded trees, each sample was visited 5,000,000 times (P. Beerli, personal communication).

Metropolis-Coupled MCMC (“MCMCMC”) or “heating” was applied for auxiliary searches with more permissive acceptance criteria55,56,57. The search was run with four chains at different temperatures (1.0, 1.5, 3.0, and 10,000) with an adaptive heating scheme that manipulated the temperatures according to their swapping success (P. Beerli, personal communication). The hotter chains move more freely and explore more genealogy space than the cold chains.

Input data files were prepared using the PGD Spider data converting tool58. Gene flow was investigated at three levels: level one is the out-of-Africa migration to the Arabian Peninsula; level two investigated the movement of Arabs inside the Arabian Peninsula; and level three investigated the migration rate between the three neighbouring countries Iraq, Saudi Arabia and Kuwait.

Four gene flow models were designed. The first model represents direct migration from one population to the other, the second divergence from an ancestral population and the third divergence from the ancestral population with ongoing immigration. The fourth model assumes that two populations belong to the same panmictic population, and is only used in level three. The log marginal likelihood of the different runs was used to generate the Bayes factors. The Bayes factors were used for model comparison, where their magnitudes give evidence of how different the models are. Supplementary Figure S10 shows the migration models that were used in this study.

Data availability

The materials, data and associated protocols are available to readers without undue qualification in material transfer agreements.

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Download references

Acknowledgements

The Medico-Legal Institute in Iraq and all DNA donors are acknowledged as without their donation, this research would not have been possible. We are indebted to Professor Peter Beerli and Professor Whit Athey for their valuable advice and directions.

Funding

The funding was provide by Iraqi Cultural Attaché in London (S1126).

Author information

Affiliations

  1. Department of Biomedical and Forensic Sciences, College of Life and Natural Sciences, University of Derby, Derby, DE22 1GB, UK

    Hayder Lazim

  2. Ministry of Interior of Qatar, Doha, Qatar

    Eida Khalaf Almohammed

  3. School of Forensic and Applied Sciences, University of Central Lancashire, Preston, PR1 2HE, UK

    Sibte Hadi & Judith Smith

Contributions

H.L.: Substantial contributions to the conception, design of the work, the acquisition, analysis and interpretation of data, drafting the paper and substantially revising it. E.K.A.: Substantial contributions to the conception, design of the work, drafting the paper and substantially revising it. S.H.: Substantial contributions to the conception, design of the work, analysis and interpretation of data, drafting the paper and substantially revising it. J.S.: Substantial contributions to the conception, design of the work, analysis and interpretation of data, drafting the paper and substantially revising it.

Corresponding author

Correspondence to Hayder Lazim.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Sours: https://www.nature.com/articles/s41598-020-72283-1
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In Human Genetics, J2 haplogroup (AKA J-M172) is among the most frequent Y DNA haplogroups in the Middle East and in the Arab World. The geographic origin is believed to be in the cressant fertile (Iraq,Turkey and Syria) The age is estimated to be 18,500 +/- 3,500 thousands years ago See more details about J2 haplogroup in this page:Haplogroup_J2_(Y-DNA)
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The Y-DNA Haplogroup J story

Early origins
The origin of Y-DNA Haplogroup J maps to the Middle East around the ‘Fertile Crescent’, an area also known as the ‘Cradle of Civilization’ since this area saw the birth of many technological advancements that helped humans move from nomadic hunter-gatherers to an agriculture-based society living in one place.  The sprouting of some the first cities and empires in human history were contingent on these developments and featured the proliferation of Haplogroup J.   

Y-DNA Haplogroup J is a descendent of suprahaplogroup F, which encompasses a large group Y-DNA lineages (haplogroups F-T, see Figure 3). Suprahaplogroup F is believed to have migrated from Africa approximately 50kya.  Haplogroup J arose approximately 30kya (see Figure 4) and has been defined by a number of unique Y-chromosome polymorphisms; the 12f2a deletion and the M304 and P209 SNPs.

The precise location for the origin of Haplogroup J is not known, but its prominence in the Near East/West Asia and the Middle East/Central Asia indicates that it likely arose in one of these regions.  It is closely associated with the Fertile Crescent; an area spanning the Nile and Tigris/Euphrates River systems, with the Levant (present day Lebanon) in between.  This region has encompassed many early cultures and empires from the Stone Age (Neolithic) to the Iron Age and has also been dubbed the ‘Cradle of Civilization’.  Societies, dynasties and empires in this broad region include the Sumerian, Assyrian, Babylonian, Egyptian, Phoenician and Persian.  Haplogroup J is also particularly abundant in Anatolia (present day Turkey) and the Y-chromosome diversity observed here suggests that this area is a possible source of this clade.  Owing to these strategic locations, Y-DNA Haplogroup J is common on three continents: Asia, Europe and Africa.

SNPy trails and the spread of Haplogroup J
Middle East populations belonging to Y-DNA Haplogroup J migrated during or after the Neolithic era to Mediterranean regions and back to Africa; although this did not reach sub-Saharan regions .  This spread contributes significantly to populations in European and African countries around the Mediterranean Sea.  Moreover, this migration, also termed a "demic diffusion", is believed to be the source of new agriculture practices, which included domestication of animals or pastoralism.  It is also associated with sedentism or the custom of living in one place as opposed to the more mobile hunter-gatherer and nomadic lifestyle.  Thus, the movement is tied to the rise of cities and city-states.   While Y-DNA Haplogroup J is linked with this important Neolithic demic diffusion, additional migrations subsequent to this provided other diasporic episodes of this haplogroup and its subclades.

J2. M172.

The J2 subclade is similar in distribution to J1, but it is typically present at a higher frequency.  J2 is distinguished from J1 by a lower frequency in Arab populations and the near absence in Africa.  The J2 subclade is highest in Anatolia and prominent in Mesopotamia and the Levant – all areas that served as centers of agricultural revolution.  J2 is common among Turkish, Kurdish and Jewish populations and significant frequencies are found in the Caucasus, Iran, and Southcentral Asia.  TMRCA estimates for this haplogroup range from 4-15kya.   

J2 may be an important Y-chromosome lineage that was part of the demic diffusion and introduction of new agricultural practices into Europe from the Middle East and Anatolia during the Neolithic period.  Anatolia could represent a Mesolithic pocket of the J2 subclade, which spread later to Europe in the Neolithic-Holocene periods (10kya) and subsequently featured in the emergence and progress of the Bronze Age (5kya).    

Prominent European areas of J2 abundance include the Iberian Peninsula, Italy, the Balkans and Greece.  An interesting general feature is that J2 frequencies drop off considerably in the Northward direction.  From the Balkan Peninsula, there is a drop in abundance moving into and beyond the Carpathian Mountain countries of Ukraine, Romania, and Hungary.  A similar sharp drop-off between Nepal and Tibet is attributed to the geographic barrier of the Himalayan Mountains.  In Russia, the J2 subclade is more frequent than J1, but because it is much lower than the neighboring Caucasus region (e.g. Georgia, Azerbaijan) to the South, there appears to be infrequent patrilineal gene flow from the Caucasus to Russia.  The Caucasus Mountain Range may have been an effective barrier separating Russia to the North and the Caucasus to the South.  See Figure 6 for the sites of these mountains.  

Tthe diffusion of the J2 subclade into Europe may have been by mediated by the Mediterranean Sea.  The J2 subclade is abundant on several Mediterranean Islands: Crete, Cyprus, Malta, Sicily, Sardinia and Korčula (Croatia).  The frequency of J haplogroups can distinguish Mediterranean groups (North Africa) (Near East/Arabs) (Central/East/Lebanon) (West).  Similarly, using STR data, three groups can be revealed (North African)(Arab/Palestinians)(Mediterranean/Italy/Sardinia).  The J2 chromosomes in Crete are more similar to those found in Anatolia than those found in Greece when the DYS413 and other STR data are taken into account.  This shows that there are sufficient genetic differences to differentiate the populations and it may represent multiple episodes of J subclade expansion and dispersal. 

The J2 subclade is abundant in Iran (30%), known throughout much of history as Persia.  Studies support the introduction of this subclade here from Anatolia, with less contribution from the East in the direction of Pakistan.  The barriers presented by the Hindu Kush mountains in Pakistan and deserts in Iran, may have limited gene flow from the East.  The attraction of the fertile Mesopotamian valley may have favored the migration from Anatolia in the West, thus producing a general West to East migration pattern and spread of J2 into Iran.  A genetic separation between the North and South of Iran may have also been aided by the deserts separating these regions.  Furthermore, cultural alliances between Anatolia and Persia have been strong as exemplified by Babylonian, Assyrian, Persian and Ottoman Empires, lending support to the idea that there was a strong connection from Turkey, through Iraq to South Iran.  It is quite possible that these empires aided the dissemination of Haplogroup J.       

The J2 subclade is abundant in India (2-20%), and its frequency peaks in the Northwest region.  Anatolia is most likely the source of this subclade in India, again consistent with the West to East flow of J2.  The date of this invasion points to a period during or after the Neolithic era.  J2 lineage is also found in SW India with an interesting frequency trend: a higher fraction of J2 in the higher castes and decreasing amounts in lower castes. 

The J2a subclade is present in the Middle East and Southcentral Asia (~4%), the latter of which includes India and Nepal.  In India, there is a general trend for increased J2a frequency in higher castes. It has also been found in Crete (1-2%).  

J2a4h(10).L24 L25

This sub group has a wide distribution in the world. It is found in the middle East, North Africa, Europe, India and the amercias.

J2a4a. M47

The J2a4a subclade is found at low levels in Anatolia (1-4%) and Georgia (2%).  In the Middle East, it has been detected at similar levels in Iran, Iraq, Qatar and the United Arab Emirates.  This appears to be a relatively low frequency J subclade.
We have 14 participants in J2-arab project who belong to J2a4a, 3 of them is confirmed by the SNP deep clade and the the other 11 particiapnts are predicted J2a4a

J2a4b. M67

The estimated TMRCA is 9kya for the J2a4b subclade . This subclade is abundant in the Caucasus (Georgia 13%, Azerbaijan 4%) and is ancient group – TMRCA estimates at 12kya.  It has also been found at appreciable levels (1-8%) in Anatolia, with preponderance in the Northwest as well as in Italy (~5%) and the Iberian Peninsula (2-3%).  This has led to proposals for migration over land from Anatolia via the Bosphorus Isthmus or over the Mediterranean Sea.  Notably, 10% of the Y-chromosomes on Crete are of this variety.  J2a4b is also found in the Arabian Peninsula, Iraq, Lebanon, Pakistan and India.  Significant frequencies (10-20%) are also found in Jewish populations. 

J2a4b1. M92

Its distribution has been recorded in Italy (5%), Anatolia (~4%) and the Balkan Peninsula (~3%).  Notable levels have also been located in South Iran, Iraq, Pakistan and Northwest India.  Its presence in Europe, may indicate that the Bosphorus Isthmus was a migratory route.  Alternatively, the Mediterranean Sea could have been used for the spread of this subclade.  It has been found in Ashkenazi Jews, but not Sephardic Jews. 

J2a4b1a.  M327

Little information is currently known for the J2a4b1a subclade, but it appears to a minor and infrequent subclade.  It has been found in Konya in Turkey (<1%).

J2a4b2. M163

A minor J subclade, currently it has only been found at very low levels (0.2%) in Spain (non-Basques). 

J2a4c.  M68

J2a4c appears to be a minor subclade with low levels (1%) detected in Iraq and India. 

J2a4h1a1a. M137

A limited set of studies have failed to detect this subclade and it appears to be a very minor subclade. 

J2a4h2. M158

Modest levels (1-2%) of the J2a4h2 subclade have been uncovered in Anatolia, Pakistan and India. 

J2a4h1a1b. M289

J2a4h1a1b appears to be a minor subclade.  Currently it has only been detected in the Druze in Israel (5%). 

J2a4h3.  M318

J2a4h3 appears to be a minor subclade.  Currently it has been detected in Israel for those of Libyan Jewish ancestry (5%) and among jewish population of Jerba island in Tunisia. 

J2a4d. M319

The J2a4d subclade, defined by SNP M319, has been found in Crete (6-9%), which may be source of M319 subclade, as this subclade is infrequent and not found in many other areas.  Presently, Israel is the only other location where this subclade has been found. 

J2a4e. M339

The J2a4e subclade has not been studied extensively. It appears with a very low frequency in parts of Anatolia (1%). 

J2a2. M340

The J2a2 subclade has not been studied extensively. It appears with a very low frequency in parts of Anatolia (1%). 

J2a4f. M419

The M419 defines the J2a4f subclade.  It has not been widely studied, and has been found at <1% in Northern Iran.  Likely to be a minor subclade.

J2a4g. P81

Currently, no information is available for the distribution and frequency of this haplogroup J subclade. 

J2a3. P279

Currently, no information is available for the distribution and frequency of this haplogroup J subclade.

J2b. M12, M102, M221, M314

The J2b subclade has a similar European distribution to Y-chromosome subclade E-V13 and TMRCA estimate (~4.4kya), which is consistent with a common route of dispersal.  It is most prominent in Balkans, Greece and Italy (North and Central regions), reaching frequencies around 5-10%.  Present day countries with the highest frequencies include Albania, Hungary, Greece and Macedonia.  This haplogroup population may have moved through the Balkans and north into Europe via rivers, such as the Danube.  It is present in Crete and the Iberian Peninsula, which could also indicate a spread by sea-faring routes in the Mediterranean.  

The J2b subclade is also present in Pakistan, India and Iran (3-4%).  It displays a modest frequency in Egypt, Oman, Qatar and the United Arab Emirates (1-4%) and Africa.  These trends in Arab populations and Africa are reminiscent of the distribution of the J1 subclade and provides evidence that the several of the J subclades share some history in dispersal and expansion.    

Currently, no information is available for the distribution and frequency of this haplogroup J subclade.

The J2b2 subclade is present in India, where it appears to have the highest frequency among the middle castes (Dravidian and Indo-European).  Its overall level in India is ~5% and this frequency drops in half in neighboring Pakistan.  J2b2 is also found in Nepal, but no J2b2 has been found in Tibet, providing strong evidence that the Northern spread of this subclade was prevented by the Himalaya Mountains.

The J2b2 subclade is also present in Anatolia, specifically in the southern and eastern regions, which have been proposed as a source of J haplogroups for many regions.  An interesting peak of the J2b2 subclade has been detected in Kosovar Albanians (~17%), whereas the J2b2 levels range from 1 to 4% in the Balkans overall. 

Within the J2b2 subclade defined by SNP241, there is a DYS455 deletion allele (8 repeats or DYS455=8) that is not found in the J2b1 (SNP M205) subclade.  

J2b2a. M99

Currently, no information is available for the distribution and frequency of this haplogroup J subclade.

J2b2b. M280

The J2b2b subclade has so far only been detected in Greece (2%).  It appears to be absent from surrounding areas and it is likely to represent a minor J subclade. 

J2b2c. M321

Limited information is available for the J2b2c subclade and the information available so far has only shown it to be present in Libyan Jewish population in Israel (5%). 

J2b2d.  P84

Currently, no information is available for the distribution and frequency of this haplogroup J subclade.


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Sours: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355514/

Dna map arab

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

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Arabs get a DNA test

DNA analysis proves Arabs aren't entirely Arab

The National Geographic's Genographic project gives us surprising information about Arab genetic makeup.

National Geographic's Genographic Project, launched in 2005, uses science to bring people together where politics have failed.  

Through DNA analysis, the project is answering people's questions regarding ethnicity, race, and the overall origins of the human population and how we came to populate the Earth. 

The Genographic Project lists a group of reference populations, where the typical national of each country is described according to genetic makeup. These are based on hundreds of DNA samples and advanced DNA analysis. Four Arab countries were part of the reference population list. 

Here are some surprising discoveries on the genetic makeup of these four Arab nationalities. 

Note that the Genographic Project only listed four Arab nationalities in their reference populations, which is the basis of this article. 

Did you know that native Egyptians' genetic makeup is 4 percent Jewish diaspora? 

Typically, an Egyptian native's genetic composition is 68 percent North African, 17 percent Arabian, 4 percent Jewish diaspora, and 3 percent from Eastern Africa, Asia Minor and Southern Europe each.

The link to North Africa dates back to when ancient populations first migrated from the continent, which they did through the northeastern route on their way to southwest Asia. 

The spread of agriculture led to further migrations from the Fertile Crescent back into Africa as did the spread of Islam from the Arabian peninsula in the 7th century.

Native Kuwaitis' genetic makeup is: 84 percent Arabian, 7 percent from Asia minor, 4 percent North African and 3 percent from East Africa. 

Ancient migrants passed through the Middle East when journeying from Africa to Eurasia. Some migrants loved the region so much they decided to stay, developing genetic patterns that were passed down to other generations.

The smaller components from Northern Africa and Eastern Africa may be due to the Arab slave trade, from the 8th to the 19th century. 

Lebanese natives' genetic makeup is the most diverse of all four Arab nationalities.

Typically, a Lebanese natives is 44 percent Arabian, 14 percent Jewish diaspora, 11 percent North African, 10% from Asia minor, 5percent Southern European and 2 percent Eastern African. 

Ancient migrants passed through the Middle East when journeying from Africa to Eurasia. Some of these migrants settled in Lebanon, developing genetic patterns that transcended generations over time.

The Silk Road added genetic patterns from the farther north and east. 

Natives of Tunisia have a pretty interesting genetic composition. They are 88 percent North African, 5 percent Western European, 4 percent Arabian and 2 percent from Western and Central Africa combined.  

Historically, Tunisia's location on the Mediterranean Sea contributed greatly to its broad genetic diversity. 

The Arabian component came about with the arrival of agriculture from the Middle East as well as the spread of Islam in the 7th century. 

1. Georgia: 5 percent 

2. Iran: 56 percent  

3. The Luhya people of Kenya: 2 percent

4. Natives of Madagascar: 2 percent  

5. The Northern Caucasus (including Dagestanis and Abkhazians): 9 percent

6. Tajikistan (Pamiri mountains): 6 percent 

7. Sardinia: 3 percent

8. Southern India: 2 percent 

9. Western India: 6 percent 

10. Indonesia: 6 percent  

11. Ethiopia: 11 percent  

12. Ashkenazi Jews (Jews who originated in Eastern Europe): 10 percent 

Earlier in 2016, a video produced by Momondo -a travel agency- was made to show the impact genographic tests can have on people's perceptions.  

67 people from all around the world took a DNA test and were then put in a room where the results were revealed to them out loud. 

Watch it to see how perceptions can be changed using science and technology. 

Sours: https://stepfeed.com/dna-analysis-proves-arabs-aren-t-entirely-arab-4864

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DNA from the Bible's Canaanites lives on in modern Arabs and Jews

They are best known as the people who lived “in a land flowing with milk and honey” until they were vanquished by the ancient Israelites and disappeared from history. But a scientific report published today reveals that the genetic heritage of the Canaanites survives in many modern-day Jews and Arabs.

The study in Cellalso shows that migrants from the distant Caucasus Mountains combined with the indigenous population to forge the unique Canaanite culture that dominated the area between Egypt and Mesopotamia during the Bronze Age, lasting from approximately 3500 B.C. until 1200 B.C.

The team extracted ancient DNA from the bones of 73 individuals buried over the course of 1,500 years at five Canaanite sites scattered across Israel and Jordan. They also factored in data from an additional 20 individuals from four sites previously reported.

“Individuals from all sites are highly genetically similar,” says co-author and molecular evolutionist Liran Carmel of Jerusalem’s Hebrew University. So while the Canaanites lived in far-flung city states, and never coalesced into an empire, they shared genes as well as a common culture.

The researchers also compared the ancient DNA with that of modern populations and found that most Arab and Jewish groups in the region owe more than half of their DNA to Canaanites and other peoples who inhabited the ancient Near East—an area encompassing much of the modern Levant, Caucasus, and Iran.

an archaeologist excavating a skull

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The study—a collaborative effort between Carmel’s lab, the ancient DNA lab at Harvard University headed by geneticist David Reich, and other groups—was by far the largest of its type in the region. Its findings are the latest in a series of recent breakthroughs in our understanding of this mysterious people who left behind few written records.

Marc Haber, a geneticist at the Wellcome Trust’s Sanger Institute in Hinxton, United Kingdom, co-led a 2017 study of five Canaanite individuals from the coastal town of Sidon. The results showed that modern Lebanese can trace more than 90 percent of their genetic ancestry to Canaanites.

"Thieves and Canaanites"

As Egyptians built pyramids and Mesopotamians constructed ziggurats some 4,500 years ago, the Canaanites began to develop towns and cities between these great powers. They first appear in the historical record around 1800 B.C., when the king of the city-state of Mari in today’s eastern Syria complained about “thieves and Canaanites.”

Diplomatic correspondence written five centuries later mentions several Canaanite kings, who often struggled to maintain independence from Egypt. “The land of Canaan is your land and its kings are your servants,” acknowledged one Babylonian monarch in a letter to the Egyptian pharaoh Akhenaten.

Biblical texts, written many centuries later, insist that Yahweh promised the land of Canaan to the Israelites after their escape from Egypt. Jewish scripture says the newcomers eventually triumphed, but archaeological evidence doesn’t show widespread destruction of Canaanite populations. Instead, they appear to have been gradually overpowered by later invaders such as the Philistines, Greeks, and Romans.

a Khirbet Kerak Ware bowl

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The Canaanites spoke a Semitic language and were long thought to derive from earlier populations that settled in the region thousands of years before. But archaeologists have puzzled over red-and-black pottery discovered at Canaanite sites that closely resembles ceramics found in the Caucasus Mountains, some 750 miles to the northwest. Historians also have noted that many Canaanite names derive from Hurrian, a non-Semitic language originating in the Caucasus.

Whether this resulted from long-distance trade or migration was uncertain. The new study demonstrates that significant numbers of people, and not just goods, were moving around during humanity’s first era of cities and empires. The genes of Canaanite individuals proved to be a mix of local Neolithic people and the Caucasus migrants, who began showing up in the region around the start of the Bronze Age.

Carmel adds that the migration appears to have been more than a one-time event, and “could have involved multiple waves throughout the Bronze Age.”

One brother and sister who lived around 1500 B.C. in Megiddo, in what is now northern Israel, were from a family that had migrated relatively recently from the northeast. The team also noted that individuals at two coastal sites—Ashkelon in Israel and Sidon in Lebanon—show slightly more genetic diversity. That may be the result of broader trade links in Mediterranean port towns than inland settlements.

an excavation site in Israel

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Glenn Schwartz, an archaeologist at Johns Hopkins University who was not involved in the study, said that the biological data provides important insight into how Canaanites shared a notable number of genes as well as cultural traits. And Haber from the Wellcome Trust noted that the quantity of DNA results is particularly impressive, given the difficulty of extracting samples from old bones buried in such a warm climate that can quickly degrade genetic material.

Who came first?

Both Israeli and Palestinian politicians claim the region of Israel and the Palestinian territories is the ancestral home of their people, and maintain that the other group was a late arrival. “We are the Canaanites,” asserted Palestinian Authority President Mahmoud Abbas last year. “This land is for its people…who were here 5,000 years ago.” Israeli Prime Minister Benjamin Netanyahu, meanwhile, said recently that the ancestors of modern Palestinians “came from the Arabian peninsula to the Land of Israel thousands of years” after the Israelites.

The new study suggests that despite tumultuous changes in the area since the Bronze Age, “the present-day inhabitants of the region are, to a large extent, descended from its ancient residents,” concludes Schwartz—although Carmel adds that there are hints of later demographic shifts.

Carmel hopes to soon expand the findings by collecting DNA from the remains of those who can be identified as Judean, Moabite, Ammonite, and other groups mentioned in the Bible and other texts.

“One could analyze ‘Canaanite’ as opposed to ‘Israelite’ individuals,” adds archaeologist Mary Ellen Buck, who wrote a book on the Canaanites. “The Bible claims that these are distinct and mutually antagonistic groups, yet there's reason to believe that they were very closely related.”

Andrew Lawler is a journalist and author who has written about controversial excavations under Jerusalem and the search for the Lost Colony of Roanoke for National Geographic.

Sours: https://www.nationalgeographic.com/history/article/dna-from-biblical-canaanites-lives-modern-arabs-jews


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