Post by seekeroftruth on Feb 21, 2014 18:07:04 GMT -5
Differential Greek and northern African migrations to Sicily are supported by genetic evidence from the Y chromosome
By:Di Gaetano, C (Di Gaetano, Cornelia)[ 1 ] ; Cerutti, N (Cerutti, Nicoletta)[ 1 ] ; Crobu, F (Crobu, Francesca)[ 1 ] ; Robino, C (Robino, Carlo)[ 2 ] ; Inturri, S (Inturri, Serena)[ 2 ] ; Gino, S (Gino, Sarah)[ 2 ] ; Guarrera, S (Guarrera, Simonetta)[ 3 ] ; Underhill, PA (Underhill, Peter A.)[ 4 ] ; King, RJ (King, Roy J.)[ 5 ] ; Romano, V (Romano, Valentino)[ 6 ] ...More
EUROPEAN JOURNAL OF HUMAN GENETICS
Volume: 17
Issue: 1
Pages: 91-99
DOI: 10.1038/ejhg.2008.120
Published: JAN 2009
View Journal Information
Abstract
The presence or absence of genetic heterogeneity in Sicily has long been debated. Through the analysis of the variation of Y-chromosome lineages, using the combination of haplogroups and short tandem repeats from several areas of Sicily, we show that traces of genetic flows occurred in the island, due to ancient Greek colonization and to northern African contributions, are still visible on the basis of the distribution of some lineages. The genetic contribution of Greek chromosomes to the Sicilian gene pool is estimated to be about 37% whereas the contribution of North African populations is estimated to be around 6%. In particular, the presence of a modal haplotype coming from the southern Balkan Peninsula and of its one-step derivates associated to E3b1a2-V13, supports a common genetic heritage between Sicilians and Greeks. The estimate of Time to Most Recent Common Ancestor is about 2380 years before present, which broadly agrees with the archaeological traces of the Greek classic era. The Eastern and Western part of Sicily appear to be significantly different by the chi(2)-analysis, although the extent of such differentiation is not very high according to an analysis of molecular variance. The presence of a high number of different haplogroups in the island makes its gene diversity to reach about 0.9. The general heterogeneous composition of haplogroups in our Sicilian data is similar to the patterns observed in other major islands of the Mediterranean, reflecting the complex histories of settlements in Sicily.
Introduction
Sicily is the largest island in the Mediterranean basin and has served as a meeting place for different populations. Archaeological data indicate that this largest Mediterranean island was initially peopled by hunter-gathers approximately 10 000 years BP.1 Subsequent settlements may also have occurred prior to the transition to agriculture that began around 7000 years BP. During historical times, various ethnic groups that include Greeks, Phoenicians, Romans, Arabs and the Normans, left their legacy in Sicily.
Both the presence of genetic subdivision2, 3 and its absence4 have been reported in some analyses of classical polymorphism data. A more recent study using data from 9 autosomal microsatellite loci and 10 mitochondrial DNA (mtDNA) haplogroups (Hgs) reported a genetic differentiation consistent with that of other Mediterranean regions and correlated with longitude, although the causal underlying demography remained unclear.5
Several hypotheses have been proposed to explain this heterogeneity. It could be traced back to pre-Greek times when the Sicani, the first inhabitants of the island, were pushed westwards by the arrival of Siculi from Italy (about 1200 BP). Alternatively, the origin of such differentiation could be attributed to the Greek colonization between 2750 and 2200 BP in the southeastern region versus the west that was settled by Phoenicians (Figure 1a). Preliminary studies of the Y-chromosome Hg composition showed that approximately 60% of the Sicilian Y-chromosome Hgs are also prevalent in southern Italy and Greece.6 The presence of the lineage E3b1b-M81 in Sicily and Iberia reflects gene flows also from North Africa.7 But while Greek surnames display east–west differentiation,8, 9 the correlation of genetic diversification with longitude and the extent to which Greek colonization mediated gene-flow episodes remain still uncertain.
(a) Geographical map showing the main colonies by Greeks (triangles) and Phoenicians (circles) in the Mediterranean (seventh to sixth centuries BC). (b) Frequency distribution of the most representative haplotype 13-13-30-24-10-11-13 associated to the E3b1a2-V13 chromosomes in Sicily, in other populations taken from literature15, 23, 29, 30 and in samples from YHRD. The allelic combinations refer to the following order of loci: DYS19-DYS389I-DYS389II-DYS390-DYS391-DYS392-DYS393. (c) Frequency distribution of the haplotype 13-14-30-24-9-11-13 associated to the E3b1b-M81 chromosomes in Sicily (data from this study), in other populations taken from literature29 and in samples from YHRD.
Thanks to its haploid nature, Y-chromosome diversification is often highly correlated with geography.10 Recently, many authors showed that Y-chromosome combination of Hgs and short tandem repeats (STRs) are highly informative about the origin of male specific lineages, because of the detailed haplotypes that can be obtained and their geographical specificity.10, 11, 12, 13
In this paper, we evaluate the composition of Y-chromosome lineages using the combination of 33 biallelic markers and 12 STRs in samples coming from different areas of the island. We show diachronic genetic strata potentially linked to distinct historical colonization episodes within the Mediterranean basin. In addition, we estimate the extent of gene flow from both Greece and North Africa.
Materials and methods
A total of 236 samples from 9 different areas of Sicily were studied. Latitudes (N) and longitudes (E) of each area are summarized in Figure 2.
(Top) The geographical map of the nine Sicilian samples is shown. Their latitude (N), longitude (E) and sample size are: (1) Trapani (TP) 38°07', 12°07', 33; (2) Mazara del Vallo (MZ) 37°65', 12°58', 18; (3) Santa Ninfa (SN) 37°77', 12°88', 31; (4) Alcamo (AL) 37°97', 12°97', 24; (5) Caccamo (CA) 37°93', 13°07', 16; (6) Sciacca (SC) 37°05', 13°07', 28; (7) Piazza Armerina (PZ) 37°38', 14°37', 28; (8) Troina (TR) 37°78', 14°60', 30; (9) Ragusa (RG) 36°93', 14°75', 28. The histogram plots the frequencies of the main haplogroups in the eastern and the western sides of the island.
Samples have further been grouped on the basis of historical and geographical criteria: western Sicily (WSI) includes 122 men from Trapani, Alcamo, Mazara del Vallo, Santa Ninfa and Caccamo; eastern Sicily (ESI) includes 114 men from Sciacca, Ragusa, Piazza Armerina and Troina. The partition reflects the history of the colonization occurred in the middle of the last millennium BC by the Greeks and the Phoenicians, who established their outposts in opposite parts of the island. We included Sciacca in the eastern part because of its ties to the important nearby Greek colony of Selinunte.
DNA extraction was carried out according to the phenol–chloroform protocol method. A set of 32 binary markers was tested, allowing us to assign the analysed Y chromosomes to Hgs. All polymorphisms have been previously reported.13, 14, 15, 16 The presence of the Y Alu polymorphic insertion was tested as described elsewhere.17 Genotyping was done by using the denaturing high performance liquid chromatography method proposed by Oefner and Underhill,18 with a phylogenetic hierarchical approach. The V12, V13, V22 polymorphisms, defining Hgs E3b1a1, E3b1a2 and E3b1a3, have been analysed as described in Cruciani et al.16 Data are referred to terminal mutation and according to the International Society of Genetic Genealogy nomenclature. The microsatellites DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393 and DYS385 A/B were analysed on all the samples. The E3b1a-M78 and the J2-M172 chromosomes were also typed for DYS439 plus DYS460 and DYS445 respectively. 5′-Fluorescently labelled PCR products were electrophoresed on an ABI PRISM 310 Genetic Analyzer. Genotypes were assigned by using control DNA samples provided by L Roewer (Institute of Legal Medicine, Charité, Berlin) and self-made allelic ladders provided by GeneScan software (Applied Biosystems). The DYS389II (AB fragment) allele number was determined by subtracting the DYS389I (CD fragment) repeat number.
Nomenclature is according to Kayser et al,19 with the exception of locus DYS389 where a monomorphic (TCTG)3 motif is included in the repeat count thus uniformly increasing the repeat size by three.
Gene diversity was calculated as described by Nei20 using the Arlequin software (http://cmpg.unibe.ch/software/
arlequin3).
The proportion of genetic variance due to differences within or between populations was hierarchically apportioned through the analysis of molecular variance (AMOVA)21 included in the Arlequin software.
The admixture analysis code Admix2_0 was used to compute the estimators mY initially described in Bertorelle and Excoffier.22 The analysis was performed on E3b1b-M81 using as parental populations: Algerians and Tunisians (63 of 202 individuals), Egyptians (7 of 53 individuals) provided by Arredi et al23 and Continental Greeks (0 of 222 individuals; AP, unpublished data). A similar admixture analysis was performed for marker E3b1a2-V13 by using as parental populations: Greece (by pooling samples 30, 31 and 32, for a total of 35 out of 286 individuals) and northwestern Africa (by pooling samples from 35 up to 41, for a total of 2 out of 344 individuals) and northeastern Africa populations (by pooling samples from 43 up to 48, for a total of 3 out of 329 individuals) provided by Cruciani et al.12
The phylogenetic relationships were represented by the method of reduced median networks using the reduced median algorithm (r=2),24 followed by the median-joining algorithm (ε=0).25 The Network 4.1.1.2 software was used (www.fluxus-engineering.com).
The Time to Most Recent Common Ancestor (TMRCA) estimate and confidence interval (CI) were calculated using five STRs (DYS19, DYS391, DYS393, DYS439, DYS460) with the software Ytime v2.07 under the Simple Stepwise Mutation Model.26 The mutation rate used is the average of rates taken from Gusmão et al27 for DYS460 and from the Y Chromosome Haplotype Reference Database (YHRD, http://www.yhrd.org) for the other microsatellites.
Geographic maps built according to the Kriging procedure28 and implemented by the Surfer System (Golden Software) display STRs haplotype distributions under a particular Hg in Sicily and in other populations of the Mediterranean basin. Data were taken from the literature15, 23, 29, 30 and from YHRD. Principal component analysis was performed by using the R-package software v2.0.1 (http://www.r-project.org/).
By:Di Gaetano, C (Di Gaetano, Cornelia)[ 1 ] ; Cerutti, N (Cerutti, Nicoletta)[ 1 ] ; Crobu, F (Crobu, Francesca)[ 1 ] ; Robino, C (Robino, Carlo)[ 2 ] ; Inturri, S (Inturri, Serena)[ 2 ] ; Gino, S (Gino, Sarah)[ 2 ] ; Guarrera, S (Guarrera, Simonetta)[ 3 ] ; Underhill, PA (Underhill, Peter A.)[ 4 ] ; King, RJ (King, Roy J.)[ 5 ] ; Romano, V (Romano, Valentino)[ 6 ] ...More
EUROPEAN JOURNAL OF HUMAN GENETICS
Volume: 17
Issue: 1
Pages: 91-99
DOI: 10.1038/ejhg.2008.120
Published: JAN 2009
View Journal Information
Abstract
The presence or absence of genetic heterogeneity in Sicily has long been debated. Through the analysis of the variation of Y-chromosome lineages, using the combination of haplogroups and short tandem repeats from several areas of Sicily, we show that traces of genetic flows occurred in the island, due to ancient Greek colonization and to northern African contributions, are still visible on the basis of the distribution of some lineages. The genetic contribution of Greek chromosomes to the Sicilian gene pool is estimated to be about 37% whereas the contribution of North African populations is estimated to be around 6%. In particular, the presence of a modal haplotype coming from the southern Balkan Peninsula and of its one-step derivates associated to E3b1a2-V13, supports a common genetic heritage between Sicilians and Greeks. The estimate of Time to Most Recent Common Ancestor is about 2380 years before present, which broadly agrees with the archaeological traces of the Greek classic era. The Eastern and Western part of Sicily appear to be significantly different by the chi(2)-analysis, although the extent of such differentiation is not very high according to an analysis of molecular variance. The presence of a high number of different haplogroups in the island makes its gene diversity to reach about 0.9. The general heterogeneous composition of haplogroups in our Sicilian data is similar to the patterns observed in other major islands of the Mediterranean, reflecting the complex histories of settlements in Sicily.
Introduction
Sicily is the largest island in the Mediterranean basin and has served as a meeting place for different populations. Archaeological data indicate that this largest Mediterranean island was initially peopled by hunter-gathers approximately 10 000 years BP.1 Subsequent settlements may also have occurred prior to the transition to agriculture that began around 7000 years BP. During historical times, various ethnic groups that include Greeks, Phoenicians, Romans, Arabs and the Normans, left their legacy in Sicily.
Both the presence of genetic subdivision2, 3 and its absence4 have been reported in some analyses of classical polymorphism data. A more recent study using data from 9 autosomal microsatellite loci and 10 mitochondrial DNA (mtDNA) haplogroups (Hgs) reported a genetic differentiation consistent with that of other Mediterranean regions and correlated with longitude, although the causal underlying demography remained unclear.5
Several hypotheses have been proposed to explain this heterogeneity. It could be traced back to pre-Greek times when the Sicani, the first inhabitants of the island, were pushed westwards by the arrival of Siculi from Italy (about 1200 BP). Alternatively, the origin of such differentiation could be attributed to the Greek colonization between 2750 and 2200 BP in the southeastern region versus the west that was settled by Phoenicians (Figure 1a). Preliminary studies of the Y-chromosome Hg composition showed that approximately 60% of the Sicilian Y-chromosome Hgs are also prevalent in southern Italy and Greece.6 The presence of the lineage E3b1b-M81 in Sicily and Iberia reflects gene flows also from North Africa.7 But while Greek surnames display east–west differentiation,8, 9 the correlation of genetic diversification with longitude and the extent to which Greek colonization mediated gene-flow episodes remain still uncertain.
(a) Geographical map showing the main colonies by Greeks (triangles) and Phoenicians (circles) in the Mediterranean (seventh to sixth centuries BC). (b) Frequency distribution of the most representative haplotype 13-13-30-24-10-11-13 associated to the E3b1a2-V13 chromosomes in Sicily, in other populations taken from literature15, 23, 29, 30 and in samples from YHRD. The allelic combinations refer to the following order of loci: DYS19-DYS389I-DYS389II-DYS390-DYS391-DYS392-DYS393. (c) Frequency distribution of the haplotype 13-14-30-24-9-11-13 associated to the E3b1b-M81 chromosomes in Sicily (data from this study), in other populations taken from literature29 and in samples from YHRD.
Thanks to its haploid nature, Y-chromosome diversification is often highly correlated with geography.10 Recently, many authors showed that Y-chromosome combination of Hgs and short tandem repeats (STRs) are highly informative about the origin of male specific lineages, because of the detailed haplotypes that can be obtained and their geographical specificity.10, 11, 12, 13
In this paper, we evaluate the composition of Y-chromosome lineages using the combination of 33 biallelic markers and 12 STRs in samples coming from different areas of the island. We show diachronic genetic strata potentially linked to distinct historical colonization episodes within the Mediterranean basin. In addition, we estimate the extent of gene flow from both Greece and North Africa.
Materials and methods
A total of 236 samples from 9 different areas of Sicily were studied. Latitudes (N) and longitudes (E) of each area are summarized in Figure 2.
(Top) The geographical map of the nine Sicilian samples is shown. Their latitude (N), longitude (E) and sample size are: (1) Trapani (TP) 38°07', 12°07', 33; (2) Mazara del Vallo (MZ) 37°65', 12°58', 18; (3) Santa Ninfa (SN) 37°77', 12°88', 31; (4) Alcamo (AL) 37°97', 12°97', 24; (5) Caccamo (CA) 37°93', 13°07', 16; (6) Sciacca (SC) 37°05', 13°07', 28; (7) Piazza Armerina (PZ) 37°38', 14°37', 28; (8) Troina (TR) 37°78', 14°60', 30; (9) Ragusa (RG) 36°93', 14°75', 28. The histogram plots the frequencies of the main haplogroups in the eastern and the western sides of the island.
Samples have further been grouped on the basis of historical and geographical criteria: western Sicily (WSI) includes 122 men from Trapani, Alcamo, Mazara del Vallo, Santa Ninfa and Caccamo; eastern Sicily (ESI) includes 114 men from Sciacca, Ragusa, Piazza Armerina and Troina. The partition reflects the history of the colonization occurred in the middle of the last millennium BC by the Greeks and the Phoenicians, who established their outposts in opposite parts of the island. We included Sciacca in the eastern part because of its ties to the important nearby Greek colony of Selinunte.
DNA extraction was carried out according to the phenol–chloroform protocol method. A set of 32 binary markers was tested, allowing us to assign the analysed Y chromosomes to Hgs. All polymorphisms have been previously reported.13, 14, 15, 16 The presence of the Y Alu polymorphic insertion was tested as described elsewhere.17 Genotyping was done by using the denaturing high performance liquid chromatography method proposed by Oefner and Underhill,18 with a phylogenetic hierarchical approach. The V12, V13, V22 polymorphisms, defining Hgs E3b1a1, E3b1a2 and E3b1a3, have been analysed as described in Cruciani et al.16 Data are referred to terminal mutation and according to the International Society of Genetic Genealogy nomenclature. The microsatellites DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393 and DYS385 A/B were analysed on all the samples. The E3b1a-M78 and the J2-M172 chromosomes were also typed for DYS439 plus DYS460 and DYS445 respectively. 5′-Fluorescently labelled PCR products were electrophoresed on an ABI PRISM 310 Genetic Analyzer. Genotypes were assigned by using control DNA samples provided by L Roewer (Institute of Legal Medicine, Charité, Berlin) and self-made allelic ladders provided by GeneScan software (Applied Biosystems). The DYS389II (AB fragment) allele number was determined by subtracting the DYS389I (CD fragment) repeat number.
Nomenclature is according to Kayser et al,19 with the exception of locus DYS389 where a monomorphic (TCTG)3 motif is included in the repeat count thus uniformly increasing the repeat size by three.
Gene diversity was calculated as described by Nei20 using the Arlequin software (http://cmpg.unibe.ch/software/
arlequin3).
The proportion of genetic variance due to differences within or between populations was hierarchically apportioned through the analysis of molecular variance (AMOVA)21 included in the Arlequin software.
The admixture analysis code Admix2_0 was used to compute the estimators mY initially described in Bertorelle and Excoffier.22 The analysis was performed on E3b1b-M81 using as parental populations: Algerians and Tunisians (63 of 202 individuals), Egyptians (7 of 53 individuals) provided by Arredi et al23 and Continental Greeks (0 of 222 individuals; AP, unpublished data). A similar admixture analysis was performed for marker E3b1a2-V13 by using as parental populations: Greece (by pooling samples 30, 31 and 32, for a total of 35 out of 286 individuals) and northwestern Africa (by pooling samples from 35 up to 41, for a total of 2 out of 344 individuals) and northeastern Africa populations (by pooling samples from 43 up to 48, for a total of 3 out of 329 individuals) provided by Cruciani et al.12
The phylogenetic relationships were represented by the method of reduced median networks using the reduced median algorithm (r=2),24 followed by the median-joining algorithm (ε=0).25 The Network 4.1.1.2 software was used (www.fluxus-engineering.com).
The Time to Most Recent Common Ancestor (TMRCA) estimate and confidence interval (CI) were calculated using five STRs (DYS19, DYS391, DYS393, DYS439, DYS460) with the software Ytime v2.07 under the Simple Stepwise Mutation Model.26 The mutation rate used is the average of rates taken from Gusmão et al27 for DYS460 and from the Y Chromosome Haplotype Reference Database (YHRD, http://www.yhrd.org) for the other microsatellites.
Geographic maps built according to the Kriging procedure28 and implemented by the Surfer System (Golden Software) display STRs haplotype distributions under a particular Hg in Sicily and in other populations of the Mediterranean basin. Data were taken from the literature15, 23, 29, 30 and from YHRD. Principal component analysis was performed by using the R-package software v2.0.1 (http://www.r-project.org/).