The tree is annotated for synonymous (in red followed by the letter s), non-synonymous (in blue f... more The tree is annotated for synonymous (in red followed by the letter s), non-synonymous (in blue followed by ns), tRNA (coloured in orange), rRNA (in yellow) and control region (in black) nucleotides changes. All the nucleotide substitutions that are recurrent in the tree are underlined and reversions are marked with an exclamation mark (!).
We built a genetic risk score (GRS) from the most complete landscape of the Alzheimer disease (AD... more We built a genetic risk score (GRS) from the most complete landscape of the Alzheimer disease (AD) genetics. We extended its analysis in 16 European countries and observed a consistent association of this GRS with AD risk, age at onset and cerebrospinal fluid (CSF) AD biomarker levels regardless of theApolipoprotein E (APOE)genotype. This GRS was also associated with AD risk (independently ofAPOE) with a decreasing order of magnitude in those with an European-American, North-African, East-Asian, Latin-American, African-American background respectively. No association of the GRS to AD was seen in sub-Saharan African and Indian populations. This GRS captures information specific to AD as its association decreases as the diagnosis broadens. In conclusion, a simple GRS captures shared genetic information specific to AD between multi-ancestry populations. However, more population diversity is needed to better understand the AD genetic complexity across populations.
Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex ... more Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show ...
For time estimates, we used rho (ρ) and maximum likelihood (ML), with a mutation rate of one subs... more For time estimates, we used rho (ρ) and maximum likelihood (ML), with a mutation rate of one substitution every 3,624 years, corrected for purifying selection, and a synonymous rate of one substitution every 7,884 years. The full set of dated founders is shown for each model tested.
The single nucleotide polymorphisms (SNPs) of the dopamine D3 receptor (DRD3), the CUB and sushi ... more The single nucleotide polymorphisms (SNPs) of the dopamine D3 receptor (DRD3), the CUB and sushi multiple domains 1 (CSMD1) and the neuregulin 1 (NRG1) genes were used to study the genetic diversity and affinity among North African populations and to examine their genetic relationships in worldwide populations.
The dopamine - related genes, like dopamine D2 receptor (DRD2) gene and ankyrin repeat and kinase... more The dopamine - related genes, like dopamine D2 receptor (DRD2) gene and ankyrin repeat and kinase domain containing 1 (ANKK1) gene are implicated in neurological functions. Some polymorphisms of the DRD2/ANKK1 locus (TaqIA, TaqIB, TaqID) have been used to study genetic diversity and the evolution of human populations. The present investigation aims to assess the genetic diversity in seven North African populations in order to explore their genetic structure and to compare them to others worldwide populations studied for the same locus. Nine single nucleotide polymorphisms (SNPs) from the DRD2/ANKK1 locus (rs1800497 TaqIA, rs2242592, rs1124492, rs6277, rs6275, rs1079727, rs2002453, rs2234690 and rs1079597 TaqIB) were typed in 366 individuals from seven North African populations: six from Tunisia (Sousse, Smar, Kesra, Kairouan, Mehdia and Kerkennah) and one from Libya. The allelic frequencies of rs2002453 and rs2234690 were higher in the Smar population than in the other North African populations. More, the Smar population showed the lowest average heterozygosity (0.313). The principal component analysis (PCA) showed that the Smar population was clearly separated from others. Furthermore, linkage disequilibrium analysis shown a high linkage disequilibrium in the North African population and essentially in Smar population. Comparison with other world populations has shown that the heterozygosity of North African population was very close to that of the African and European populations. The PCA and the haplotypic analysis suggested the presence of an important Eurasian genetic component for the North African population. These results suggested that the Smar population was isolated from the others North Africans ones by its peculiar genetic structure because of isolation, endogamy and genetic drift. On the other hand, the North African population is characterized by a multi ancestral gene pool from Eurasia and sub-Saharan Africa due to human migration since prehistoric times.
The TAS2R38 gene is involved in bitter taste perception. This study documents the distinctive div... more The TAS2R38 gene is involved in bitter taste perception. This study documents the distinctive diversity patterns in Northern Africa of functional SNPs rs713598 and rs1726866 at the TAS2R38 locus and places those patterns in the context of global TAS2R38 diversity. We analyzed data previously genotyped with Taqman Applied Biosystem for rs713598 and rs1726866 for 375 unrelated subjects (305 Tunisians from seven locations: Mahdia, Sousse, Kesra, Nebeur, Kairouan, Smar and Kerkennah plus 70 Libyans). Data were analyzed to present haplotypes and genotypes and were compared to the data from worldwide populations. We provide information about TAS2R38 diversity in a part of the world that is relatively under-studied. Considering respectively the two SNPs rs713598 and rs1726866, the (C-A) nucleotide haplotype leading to PV amino acid haplotype is extremely rare almost everywhere, but it is relatively frequent (between 6% and 10%) in Northern Africa where it does coexist with the globally common haplotypes (PA, AA and AV). Given its higher frequency in Northern Africa, we propose the (C-A) haplotype as a biogeographic marker for forensic purposes.
To obtain refreshed insights into the paternal lineages of Tunisian populations, Y-chromosome div... more To obtain refreshed insights into the paternal lineages of Tunisian populations, Y-chromosome diversity was assessed in two populations belonging to an Arab genealogical lineage, Kairouan and Wesletia, as well as in four Tunisian Andalusian populations, Testour, Slouguia, Qalaat-El-Andalous and El Alia. The Arabs from Kairouan revealed 73.47% of E-M81 and close affinities with Berber groups, indicating they are likely arabized Berbers, clearly differentiated from the Arabs from Wesletia, who harbored the highest frequency (71.8%) of the Middle Eastern component ever observed in North Africa. In the Tunisian Andalusians, the North African component largely prevailed, followed by the Middle Eastern contribution. Global comparative analysis highlighted the heterogeneity of Tunisian populations, among which, as a whole, dominated a set of lineages ascribed to be of autochthonous Berber origin (71.67%), beside a component of essentially Middle Eastern extraction (18.35%), and signatures ...
Objectives: Through previous mitochondrial DNA studies, the Middle Eastern maternal genetic contr... more Objectives: Through previous mitochondrial DNA studies, the Middle Eastern maternal genetic contribution to Tunisian populations appears limited. In fact, most of the studied communities were cosmopolitan, or of Berber or Andalusian origin. To provide genetic evidence for the actual contribution of Middle Eastern mtDNA lineages to Tunisia, we focused on two Arab speaking populations from Kairouan and Wesletia known to belong to an Arab genealogical lineage. Materials and Methods: A total of 114 samples were sequenced for the mtDNA HVS-I and HVS-II regions. Using these data, we evaluated the distribution of Middle Eastern haplogroups in the study populations, constructed interpolation maps, and established phylogenetic networks allowing estimation of the coalescence time for three specific Middle Eastern subclades (R0a, J1b, and T1). Results: Both studied populations displayed North African genetic structure and Middle Eastern lineages with a frequency of 12% and 28.12% in Kairouan and Wesletia, respectively. TMRCA estimates for haplogroups T1a, R0a, and J1b in Tunisian Arabian samples were around 15 000 YBP, 9000 to 5000 YBP, and 960 to 600 YBP, respectively. Conclusions: The Middle Eastern maternal genetic contribution to Tunisian populations, as to other North African populations, occurred mostly in deep prehistory. They were brought in different migration waves during the Upper Paleolithic, probably with the expansion of Iberomaurusian culture, and during Epipaleolithic and Early Neolithic periods, which are concomitant with the Capsian civilization. Middle Eastern lineages also came to Tunisia during the recent Islamic expansion of the 7th CE and the subsequent massive Bedouin migration during the 11th CE. 1 | I NT ROD UCTI ON Extending across the southern part of the Mediterranean Sea, North Africa is known for its complex population history and its periodic gene flow with neighboring Middle Eastern populations, across the Suez Isthmus toward the Levant, and with European populations across the Straits of Gibraltar toward the Iberian Peninsula. Sub-Saharan gene flow might also have occurred during several episodes of climatic warming, the most recent being the Early Holocene (Castañeda et al., 2009; Larrasoaña, Roberts, & Rohling, 2013; Sereno et al., 2008). North Africa was inhabited by different human groups such as Mousterians, Aterians and Iberomaurusians during the Paleolithic period, followed by the Capsians extending from the Epipaleolithic to the Early Neolithic times (Barton,
Tunisia is a country of great interest for human population genetics due to its strategic geograp... more Tunisia is a country of great interest for human population genetics due to its strategic geographic position and rich human settlement history. These factors significantly contributed to the genetic makeup of present-day Tunisians harbouring components of diverse geographic origins. Here, we investigated the genetic structure of Tunisians by performing a mitochondrial DNA (mtDNA) comparison of 15 Tunisian population groups, in order to explore their complex genetic landscape. All Tunisian data were also analysed against 40 worldwide populations. Statistical results (Tajima's D and Fu's F S tests) suggested recent population expansion for the majority of studied populations, as well as showed (AMOVA test) that all populations were significantly different from each other, which is evidence of population structure even if it is not guided by geographic and ethnic effects. Gene flow analysis revealed the assignment of Tunisians to multiple ancestries, which agrees with their genetic heterogeneity. The resulting picture for the mtDNA pool confirms the evidence of a recent expansion of the Tunisian population and is in accordance with a mosaic structure, composed by North African, Middle Easterner, European and Sub-Saharan lineages, resulting from a complex settlement history.
American journal of physical anthropology, Sep 18, 2016
North Africa has a complex demographic history of migrations from within Africa, Europe, and the ... more North Africa has a complex demographic history of migrations from within Africa, Europe, and the Middle East. However, population genetic studies, especially for autosomal genetic markers, are few relative to other world regions. We examined autosomal markers for eight Tunisian and Libyan populations in order to place them in a global context. Data were collected by TaqMan on 399 autosomal single nucleotide polymorphisms on 331 individuals from Tunisia and Libya. These data were combined with data on the same SNPs previously typed on 2585 individuals from 57 populations from around the world. Where meaningful, close by SNPs were combined into multiallelic haplotypes. Data were evaluated by clustering, principal components, and population tree analyses. For a subset of 102 SNPs, data from the literature on seven additional North African populations were included in analyses. Average heterozygosity of the North African populations is high relative to our global samples, consistent wit...
Ancestry inference for a person using a panel of SNPs depends on the variation of frequencies of ... more Ancestry inference for a person using a panel of SNPs depends on the variation of frequencies of those SNPs around the world and the amount of reference data available for calculation/comparison. The Kidd Lab panel of 55 AISNPs has been incorporated in commercial kits by both Life Technologies and Illumina for massively parallel sequencing. Therefore, a larger set of reference populations will be useful for researchers using those kits. We have added reference population allele frequencies for 52 population samples to the 73 previously entered so that there are now allele frequencies publicly available in ALFRED and FROG-kb for a total of 125 population samples.
ABSTRACT The estimate of the neutrality of a population is often made from a single measurement b... more ABSTRACT The estimate of the neutrality of a population is often made from a single measurement based on simulations of random patterns. Disputed cases pose a problem regarding the decision-making about the neutrality of the study population. We propose in this paper to provide assistance to the decision of this problem by coupling a genetically neutral populations simulator to a fast adjusted non-parametric estimator of simulated distributions. The choice of the Epanechnikov kernel for the non-parametric method of estimating the kernel allows an analytical approach of the optimal bandwidth, which leads to an improvement in the complexity and therefore a gain in computing time. The fast and reliable estimation of simulated distributions allows to assess the credibility of the decisions about the neutrality of these populations. These results are illustrated by two Tunisian populations whose neutrality is not genetically determined.
We show that the very patchy genetic landscape that is emerging for North African mtDNA diversity... more We show that the very patchy genetic landscape that is emerging for North African mtDNA diversity is mainly due to the sampling strategy being conducted in small villages, where individual ethnic affiliation to one of the main groups (Berber or Arab) is considered to be safer. The standard diversity measures and haplogroup distribution were significantly higher in a sample from a town than one from a village. Thus, the sampling strategy is a main factor to be taken into account before the construction of a forensic database in North African highly structured countries. D 2005 Published by Elsevier B.V.
Archaeological studies have revealed cultural connections between the two sides of the Red Sea da... more Archaeological studies have revealed cultural connections between the two sides of the Red Sea dating to prehistory. The issue has still not been properly addressed, however, by archaeogenetics. We focus our attention here on the mitochondrial haplogroup HV1 that is present in both the Arabian Peninsula and East Africa. The internal variation of 38 complete mitochondrial DNA sequences (20 of them presented here for the first time) affiliated into this haplogroup testify to its emergence during the late glacial maximum, most probably in the Near East, with subsequent dispersion via Additional Supporting Information may be found in the online version of this article.
The tree is annotated for synonymous (in red followed by the letter s), non-synonymous (in blue f... more The tree is annotated for synonymous (in red followed by the letter s), non-synonymous (in blue followed by ns), tRNA (coloured in orange), rRNA (in yellow) and control region (in black) nucleotides changes. All the nucleotide substitutions that are recurrent in the tree are underlined and reversions are marked with an exclamation mark (!).
We built a genetic risk score (GRS) from the most complete landscape of the Alzheimer disease (AD... more We built a genetic risk score (GRS) from the most complete landscape of the Alzheimer disease (AD) genetics. We extended its analysis in 16 European countries and observed a consistent association of this GRS with AD risk, age at onset and cerebrospinal fluid (CSF) AD biomarker levels regardless of theApolipoprotein E (APOE)genotype. This GRS was also associated with AD risk (independently ofAPOE) with a decreasing order of magnitude in those with an European-American, North-African, East-Asian, Latin-American, African-American background respectively. No association of the GRS to AD was seen in sub-Saharan African and Indian populations. This GRS captures information specific to AD as its association decreases as the diagnosis broadens. In conclusion, a simple GRS captures shared genetic information specific to AD between multi-ancestry populations. However, more population diversity is needed to better understand the AD genetic complexity across populations.
Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex ... more Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show ...
For time estimates, we used rho (ρ) and maximum likelihood (ML), with a mutation rate of one subs... more For time estimates, we used rho (ρ) and maximum likelihood (ML), with a mutation rate of one substitution every 3,624 years, corrected for purifying selection, and a synonymous rate of one substitution every 7,884 years. The full set of dated founders is shown for each model tested.
The single nucleotide polymorphisms (SNPs) of the dopamine D3 receptor (DRD3), the CUB and sushi ... more The single nucleotide polymorphisms (SNPs) of the dopamine D3 receptor (DRD3), the CUB and sushi multiple domains 1 (CSMD1) and the neuregulin 1 (NRG1) genes were used to study the genetic diversity and affinity among North African populations and to examine their genetic relationships in worldwide populations.
The dopamine - related genes, like dopamine D2 receptor (DRD2) gene and ankyrin repeat and kinase... more The dopamine - related genes, like dopamine D2 receptor (DRD2) gene and ankyrin repeat and kinase domain containing 1 (ANKK1) gene are implicated in neurological functions. Some polymorphisms of the DRD2/ANKK1 locus (TaqIA, TaqIB, TaqID) have been used to study genetic diversity and the evolution of human populations. The present investigation aims to assess the genetic diversity in seven North African populations in order to explore their genetic structure and to compare them to others worldwide populations studied for the same locus. Nine single nucleotide polymorphisms (SNPs) from the DRD2/ANKK1 locus (rs1800497 TaqIA, rs2242592, rs1124492, rs6277, rs6275, rs1079727, rs2002453, rs2234690 and rs1079597 TaqIB) were typed in 366 individuals from seven North African populations: six from Tunisia (Sousse, Smar, Kesra, Kairouan, Mehdia and Kerkennah) and one from Libya. The allelic frequencies of rs2002453 and rs2234690 were higher in the Smar population than in the other North African populations. More, the Smar population showed the lowest average heterozygosity (0.313). The principal component analysis (PCA) showed that the Smar population was clearly separated from others. Furthermore, linkage disequilibrium analysis shown a high linkage disequilibrium in the North African population and essentially in Smar population. Comparison with other world populations has shown that the heterozygosity of North African population was very close to that of the African and European populations. The PCA and the haplotypic analysis suggested the presence of an important Eurasian genetic component for the North African population. These results suggested that the Smar population was isolated from the others North Africans ones by its peculiar genetic structure because of isolation, endogamy and genetic drift. On the other hand, the North African population is characterized by a multi ancestral gene pool from Eurasia and sub-Saharan Africa due to human migration since prehistoric times.
The TAS2R38 gene is involved in bitter taste perception. This study documents the distinctive div... more The TAS2R38 gene is involved in bitter taste perception. This study documents the distinctive diversity patterns in Northern Africa of functional SNPs rs713598 and rs1726866 at the TAS2R38 locus and places those patterns in the context of global TAS2R38 diversity. We analyzed data previously genotyped with Taqman Applied Biosystem for rs713598 and rs1726866 for 375 unrelated subjects (305 Tunisians from seven locations: Mahdia, Sousse, Kesra, Nebeur, Kairouan, Smar and Kerkennah plus 70 Libyans). Data were analyzed to present haplotypes and genotypes and were compared to the data from worldwide populations. We provide information about TAS2R38 diversity in a part of the world that is relatively under-studied. Considering respectively the two SNPs rs713598 and rs1726866, the (C-A) nucleotide haplotype leading to PV amino acid haplotype is extremely rare almost everywhere, but it is relatively frequent (between 6% and 10%) in Northern Africa where it does coexist with the globally common haplotypes (PA, AA and AV). Given its higher frequency in Northern Africa, we propose the (C-A) haplotype as a biogeographic marker for forensic purposes.
To obtain refreshed insights into the paternal lineages of Tunisian populations, Y-chromosome div... more To obtain refreshed insights into the paternal lineages of Tunisian populations, Y-chromosome diversity was assessed in two populations belonging to an Arab genealogical lineage, Kairouan and Wesletia, as well as in four Tunisian Andalusian populations, Testour, Slouguia, Qalaat-El-Andalous and El Alia. The Arabs from Kairouan revealed 73.47% of E-M81 and close affinities with Berber groups, indicating they are likely arabized Berbers, clearly differentiated from the Arabs from Wesletia, who harbored the highest frequency (71.8%) of the Middle Eastern component ever observed in North Africa. In the Tunisian Andalusians, the North African component largely prevailed, followed by the Middle Eastern contribution. Global comparative analysis highlighted the heterogeneity of Tunisian populations, among which, as a whole, dominated a set of lineages ascribed to be of autochthonous Berber origin (71.67%), beside a component of essentially Middle Eastern extraction (18.35%), and signatures ...
Objectives: Through previous mitochondrial DNA studies, the Middle Eastern maternal genetic contr... more Objectives: Through previous mitochondrial DNA studies, the Middle Eastern maternal genetic contribution to Tunisian populations appears limited. In fact, most of the studied communities were cosmopolitan, or of Berber or Andalusian origin. To provide genetic evidence for the actual contribution of Middle Eastern mtDNA lineages to Tunisia, we focused on two Arab speaking populations from Kairouan and Wesletia known to belong to an Arab genealogical lineage. Materials and Methods: A total of 114 samples were sequenced for the mtDNA HVS-I and HVS-II regions. Using these data, we evaluated the distribution of Middle Eastern haplogroups in the study populations, constructed interpolation maps, and established phylogenetic networks allowing estimation of the coalescence time for three specific Middle Eastern subclades (R0a, J1b, and T1). Results: Both studied populations displayed North African genetic structure and Middle Eastern lineages with a frequency of 12% and 28.12% in Kairouan and Wesletia, respectively. TMRCA estimates for haplogroups T1a, R0a, and J1b in Tunisian Arabian samples were around 15 000 YBP, 9000 to 5000 YBP, and 960 to 600 YBP, respectively. Conclusions: The Middle Eastern maternal genetic contribution to Tunisian populations, as to other North African populations, occurred mostly in deep prehistory. They were brought in different migration waves during the Upper Paleolithic, probably with the expansion of Iberomaurusian culture, and during Epipaleolithic and Early Neolithic periods, which are concomitant with the Capsian civilization. Middle Eastern lineages also came to Tunisia during the recent Islamic expansion of the 7th CE and the subsequent massive Bedouin migration during the 11th CE. 1 | I NT ROD UCTI ON Extending across the southern part of the Mediterranean Sea, North Africa is known for its complex population history and its periodic gene flow with neighboring Middle Eastern populations, across the Suez Isthmus toward the Levant, and with European populations across the Straits of Gibraltar toward the Iberian Peninsula. Sub-Saharan gene flow might also have occurred during several episodes of climatic warming, the most recent being the Early Holocene (Castañeda et al., 2009; Larrasoaña, Roberts, & Rohling, 2013; Sereno et al., 2008). North Africa was inhabited by different human groups such as Mousterians, Aterians and Iberomaurusians during the Paleolithic period, followed by the Capsians extending from the Epipaleolithic to the Early Neolithic times (Barton,
Tunisia is a country of great interest for human population genetics due to its strategic geograp... more Tunisia is a country of great interest for human population genetics due to its strategic geographic position and rich human settlement history. These factors significantly contributed to the genetic makeup of present-day Tunisians harbouring components of diverse geographic origins. Here, we investigated the genetic structure of Tunisians by performing a mitochondrial DNA (mtDNA) comparison of 15 Tunisian population groups, in order to explore their complex genetic landscape. All Tunisian data were also analysed against 40 worldwide populations. Statistical results (Tajima's D and Fu's F S tests) suggested recent population expansion for the majority of studied populations, as well as showed (AMOVA test) that all populations were significantly different from each other, which is evidence of population structure even if it is not guided by geographic and ethnic effects. Gene flow analysis revealed the assignment of Tunisians to multiple ancestries, which agrees with their genetic heterogeneity. The resulting picture for the mtDNA pool confirms the evidence of a recent expansion of the Tunisian population and is in accordance with a mosaic structure, composed by North African, Middle Easterner, European and Sub-Saharan lineages, resulting from a complex settlement history.
American journal of physical anthropology, Sep 18, 2016
North Africa has a complex demographic history of migrations from within Africa, Europe, and the ... more North Africa has a complex demographic history of migrations from within Africa, Europe, and the Middle East. However, population genetic studies, especially for autosomal genetic markers, are few relative to other world regions. We examined autosomal markers for eight Tunisian and Libyan populations in order to place them in a global context. Data were collected by TaqMan on 399 autosomal single nucleotide polymorphisms on 331 individuals from Tunisia and Libya. These data were combined with data on the same SNPs previously typed on 2585 individuals from 57 populations from around the world. Where meaningful, close by SNPs were combined into multiallelic haplotypes. Data were evaluated by clustering, principal components, and population tree analyses. For a subset of 102 SNPs, data from the literature on seven additional North African populations were included in analyses. Average heterozygosity of the North African populations is high relative to our global samples, consistent wit...
Ancestry inference for a person using a panel of SNPs depends on the variation of frequencies of ... more Ancestry inference for a person using a panel of SNPs depends on the variation of frequencies of those SNPs around the world and the amount of reference data available for calculation/comparison. The Kidd Lab panel of 55 AISNPs has been incorporated in commercial kits by both Life Technologies and Illumina for massively parallel sequencing. Therefore, a larger set of reference populations will be useful for researchers using those kits. We have added reference population allele frequencies for 52 population samples to the 73 previously entered so that there are now allele frequencies publicly available in ALFRED and FROG-kb for a total of 125 population samples.
ABSTRACT The estimate of the neutrality of a population is often made from a single measurement b... more ABSTRACT The estimate of the neutrality of a population is often made from a single measurement based on simulations of random patterns. Disputed cases pose a problem regarding the decision-making about the neutrality of the study population. We propose in this paper to provide assistance to the decision of this problem by coupling a genetically neutral populations simulator to a fast adjusted non-parametric estimator of simulated distributions. The choice of the Epanechnikov kernel for the non-parametric method of estimating the kernel allows an analytical approach of the optimal bandwidth, which leads to an improvement in the complexity and therefore a gain in computing time. The fast and reliable estimation of simulated distributions allows to assess the credibility of the decisions about the neutrality of these populations. These results are illustrated by two Tunisian populations whose neutrality is not genetically determined.
We show that the very patchy genetic landscape that is emerging for North African mtDNA diversity... more We show that the very patchy genetic landscape that is emerging for North African mtDNA diversity is mainly due to the sampling strategy being conducted in small villages, where individual ethnic affiliation to one of the main groups (Berber or Arab) is considered to be safer. The standard diversity measures and haplogroup distribution were significantly higher in a sample from a town than one from a village. Thus, the sampling strategy is a main factor to be taken into account before the construction of a forensic database in North African highly structured countries. D 2005 Published by Elsevier B.V.
Archaeological studies have revealed cultural connections between the two sides of the Red Sea da... more Archaeological studies have revealed cultural connections between the two sides of the Red Sea dating to prehistory. The issue has still not been properly addressed, however, by archaeogenetics. We focus our attention here on the mitochondrial haplogroup HV1 that is present in both the Arabian Peninsula and East Africa. The internal variation of 38 complete mitochondrial DNA sequences (20 of them presented here for the first time) affiliated into this haplogroup testify to its emergence during the late glacial maximum, most probably in the Near East, with subsequent dispersion via Additional Supporting Information may be found in the online version of this article.
Objectives: North Africa has a complex demographic history of migrations from within Africa, Euro... more Objectives: North Africa has a complex demographic history of migrations from within Africa, Europe, and the Middle East. However, population genetic studies, especially for autosomal genetic markers, are few relative to other world regions. We examined autosomal markers for eight Tunisian and Libyan populations in order to place them in a global context. Materials and Methods: Data were collected by TaqMan on 399 autosomal single nucleotide polymorphisms on 331 individuals from Tunisia and Libya. These data were combined with data on the same SNPs previously typed on 2585 individuals from 57 populations from around the world. Where meaningful, close by SNPs were combined into multiallelic haplotypes. Data were evaluated by clustering, principal components, and population tree analyses. For a subset of 102 SNPs, data from the literature on seven additional North African populations were included in analyses. Results: Average heterozygosity of the North African populations is high relative to our global samples, consistent with a complex demographic history. The Tunisian and Libyan samples form a discrete cluster in the global and regional views and can be separated from sub-Sahara, Middle East, and Europe. Within Tunisia the Nebeur and Smar are outlier groups. Across North Africa, pervasive East-West geographical patterns were not found. Discussion: Known historical migrations and invasions did not displace or homogenize the genetic variation in the region but rather enriched it. Even a small region like Tunisia contains considerable genetic diversity. Future studies across North Africa have the potential to increase our understanding of the historical demographic factors influencing the region. Am J Phys Anthropol 000:000–000, 2016. VC 2016 The Authors American Journal of Physical Anthropology
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Papers by Lotfi Cherni
Middle East. However, population genetic studies, especially for autosomal genetic markers, are few relative to other
world regions. We examined autosomal markers for eight Tunisian and Libyan populations in order to place them in
a global context.
Materials and Methods: Data were collected by TaqMan on 399 autosomal single nucleotide polymorphisms on
331 individuals from Tunisia and Libya. These data were combined with data on the same SNPs previously typed
on 2585 individuals from 57 populations from around the world. Where meaningful, close by SNPs were combined
into multiallelic haplotypes. Data were evaluated by clustering, principal components, and population tree analyses.
For a subset of 102 SNPs, data from the literature on seven additional North African populations were included in
analyses.
Results: Average heterozygosity of the North African populations is high relative to our global samples, consistent
with a complex demographic history. The Tunisian and Libyan samples form a discrete cluster in the global and
regional views and can be separated from sub-Sahara, Middle East, and Europe. Within Tunisia the Nebeur and
Smar are outlier groups. Across North Africa, pervasive East-West geographical patterns were not found.
Discussion: Known historical migrations and invasions did not displace or homogenize the genetic variation in
the region but rather enriched it. Even a small region like Tunisia contains considerable genetic diversity. Future
studies across North Africa have the potential to increase our understanding of the historical demographic factors
influencing the region. Am J Phys Anthropol 000:000–000, 2016. VC 2016 The Authors American Journal of Physical Anthropology