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Study of the genetic relationship and diversity patterns in the Azores based on 15 STR markers
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Forensic Science International: Genetics Supplement Series 1 (2008) 312–314 www.elsevier.com/locate/FSIGSS
Research article
Study of the genetic relationship and diversity patterns in the Azores based on 15 STR markers C.C. Branco a,b,*, M. Sa˜o Bento a, C.T. Gomes a, R. Cabral a,b, A.M. Vicente c, P.R. Pacheco a,b, L. Mota-Vieira a,b a
Molecular Genetics and Pathology Unit, Hospital of Divino Espı´rito Santo, Sa˜o Miguel, Azores, Portugal b Instituto Gulbenkian de Cieˆncia, Oeiras, Portugal c Centro de Biopatologia, Instituto Nacional de Sau´de Dr Ricardo Jorge, Lisboa, Portugal Received 16 August 2007; accepted 7 October 2007
Abstract The Azores, the largest Portuguese archipelago, is composed of nine islands unevenly distributed by three groups: the Eastern group (Sa˜o Miguel and Santa Maria), the Central (Terceira, Pico, Faial, Sa˜o Jorge and Graciosa) and the Western group (Flores and Corvo). Here, we describe the genetic diversity patterns for each Azorean island and their genetic relationship based on a total of 554 samples. Genotyping was carried out by the multiplex STR system PowerPlex1 16 (Promega). The results demonstrate that the average gene diversity values vary between 0.768 and 0.797 for Corvo and Terceira, respectively. The comparison of these data with mainland Portugal (0.765) reveals higher values for the Azorean islands. The dendrogram shows that the most distantly apart are Flores and Corvo; however, there is no genetic differentiation between all islands. Moreover, we observe a clustering of the island’s populations by their geographical and socio-cultural proximity. On the other hand, historical records mention a differential settlement between islands. The results show that, nowadays, there are no regional genetic differences in the archipelago due to internal migration. Taken together, the knowledge here obtained will provide insights about the allelic structure of health-related genetic variation in the Azorean population. # 2008 Elsevier Ireland Ltd. All rights reserved. Keywords: The Azores; STRs; Genetic diversity; Population genetics
1. Introduction The Azores, the largest Portuguese archipelago, are composed of nine islands unevenly distributed by three groups: the Eastern group with two islands – Sa˜o Miguel and Santa Maria, the Central which includes five islands – Terceira, Pico, Faial, Sa˜o Jorge and Graciosa and the Western group with Flores and Corvo. At the time of its discovery, in the 15th century, the archipelago was not inhabited. The settlement of the Azores began in 1439 with Portuguese individuals, but the peopling was a slow and difficult process. Historical data report that the Portuguese crown was compelled to give out land and privileges, not only to mainland Portuguese but also to
* Corresponding author at: Molecular Genetics and Pathology Unit, Hospital of Divino Espirito Santo of Ponta Delgada, EPE, Av. D. Manuel I, 9500-370, Ponta Delgada, Sa˜o Miguel, Azores, Portugal. Tel.: +351 296 203 631; fax: +351 296 203 090. E-mail address: [email protected] (C.C. Branco). 1875-1768/$ – see front matter # 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigss.2007.10.041
foreigners, in order to attract people to the islands. These foreigners included Jews, Moorish prisoners, black slaves (Guinea, Cabo Verde and Sa˜o Tome´), Flemish, French, Scottish, English and Spanish [1]. Here, we characterize the overall diversity of each Azorean island based on the analysis of 15 autosomal STRs.
2. Material and methods The study of the genetic diversity was based on a sample composed of 592 healthy Azoreans, obtained from the anonymous DNA bank located at the Hospital of Divino Espirito Santo (Ponta Delgada, Sa˜o Miguel island), the central hospital of the Azores. This bank was built according to the international ethical guidelines for sample collection, processing and storage [2]. The sample distribution per geographic group and island was the following: Eastern group, 166 (Sa˜o Miguel, 114 and Santa Maria, 52); Central group, 320 (Terceira,
C.C. Branco et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 312–314
313
Table 1 Average gene diversity for each Azorean island
Average GD
Sa˜o Miguel (N = 114)
Santa Maria (N = 52)
Terceira (N = 103)
Faial (N = 53)
Pico (N = 66)
Sa˜o Jorge (N = 51)
Graciosa (N = 47)
Flores (N = 76)
Corvo (N = 30)
0.7929
0.7872
0.7979
0.7880
0.7897
0.7879
0.7865
0.7908
0.7717
Fig. 1. Neighbor-Joinning tree and Principal Component analysis based on allele frequencies.
103; Pico, 66; Sa˜o Jorge, 51 and Faial, 53; Graciosa, 47) and Western group, 106 (Flores 76 and Corvo, 30). The PCR co-amplification of the 15 STR loci (Penta-E, D18S51, D21S11, TH01, D3S1358, FGA, TPOX, D8S1179, vWA, Penta-D, CSF1PO, D16S539, D7S820, D13S317 and D5S818) and Amelogenin was performed using the multiplex STR system PowerPlex1 16 (Promega), according to the manufacturer’s instructions. Allele frequencies were calculated by direct counting; the Hardy–Weinberg equilibrium and gene diversity were assessed by the Arlequin. Slatkins FST genetic distance matrix was computed between pairs of populations by Arlequin and used to construct a Neighbor-Joining (NJ) tree by PHYLIP 3.63. We used TreeView 1.6.6 to display tree phylogenies obtained from NJ. 3. Results and discussion The assessment of genetic diversity of all the Azorean islands’ populations was based on the allele distribution of 15 STR markers. All markers are in HWE, considering a 99% confidence ( p < 0.01), and are relatively polymorphic. Comparing the allele composition of our sample and published data, we observe the presence of rare alleles in the Azores, namely D18S51*24 and FGA*25.2. The most interesting is FGA*25.2, which was found in Sa˜o Miguel and Faial islands, and is particularly frequent in India. Table 1 shows the gene diversity (GD) for each marker. The gene diversity values reveal that Terceira shows the highest value (0.7979) and Corvo presents the lowest (0.7717). However, all values are similar between islands and do not show a statistically significant
difference (x2, p = 0.999). The average gene diversity for the whole Azorean population is 0.788. The relationship between all islands was assessed by FST genetic distances and displayed by NJ and Principal Component (PC). The NJ tree (Fig. 1) demonstrates that Corvo is the most genetically different island when compared with the other islands. Moreover, the data shows a closer proximity between the Azorean Central (Terceira, Pico, Faial, Sa˜o Jorge and Graciosa) and Eastern (Sa˜o Miguel and Santa Maria) groups. These results are supported by the AMOVA analysis where the Western group is the most different when compared with the other two groups. Nevertheless, these differences are not significant, only 1% of variance is observed between all groups of islands. To complement the NJ analysis and to obtain the graphical view of the islands genetic similarity distribution we performed the PC analysis (Fig. 1). The first and second PC accounts for 82.6 and 9.6% of the genetic variance observed, respectively, and their plot shows a similar pattern to that displayed in the NJ tree. The data described here show that the Azorean population is an out-bred population with no genetic structure and are consistent with our previous results on Y-chromosome [3] and Alu insertion polymorphisms [4]. This suggests that despite living in different islands, this population can be treated as a homogeneous genetic group, which consequently, could possibly present the same drug-response pattern. Funding source We would like to express our gratitude to all blood donors, all health professionals of Azorean Health Centres,
314
C.C. Branco et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 312–314
of the Servic¸o de Patologia Clinica do Hospital da Horta, EPE, and of the Servic¸o de Hematologia do Hospital do Divino Espirito Santo de Ponta Delgada, EPE, directly involved in the blood collection, as well as the Secretaria Regional dos Assuntos Sociais of Azores. This work was supported by grants from the Direcc¸a˜o Regional da Cieˆncia e Tecnologia, Azores (Ref. M1.2.1/l/003/2005) and Fundac¸a˜o para a Cieˆncia e a Tecnologia (POCI/SAL MMO/ 58413/2004) of Portugal. CCB and PRP are founded by grants (Ref. SFRH/BD/12254/2003 and SFRH/BD/27453/ 2006, respectively) from Fundac¸a˜o para a Cieˆncio e a Tecnologia – Operational Programs Science Technology and Innovation (POCTI), Portugal. The sponsors had no involvement in the development of the paper or decisions related to the paper.
Conflict of interest None. References [1] J.H. Guill, A History of the Azores Islands, Division of Golden Shield International Publications Cooperation, California, 1993. [2] L. Mota-Vieira, P.R. Pacheco, M.L. Almeida, et al., Human DNA bank in Sa˜o Miguel island (Azores): a resource for genetic diversity studies, in: A. Amorim, F. Coˆrte-Real, N. Morling (Eds.), Progress in Forensic Genetics, Proceedings of the 21st International Congress of Forensic Genetics: 13–17 September Ponta Delgada, vol. 1288, 2005, pp. 388–390. [3] P.R. Pacheco, C.C. Branco, R. Cabral, et al., The Y-chromosomal heritage of the Azores Islands population, Ann. Hum. Genet. 69 (2005) 145–156. [4] C.C. Branco, R. Palla, S. Lino, et al., Assessment of the Azorean ancestry by Alu insertion polymorphisms, Am. J. Hum. Biol. 18 (2006) 223–226.
Forensic Science International: Genetics Supplement Series 1 (2008) 312–314 www.elsevier.com/locate/FSIGSS
Research article
Study of the genetic relationship and diversity patterns in the Azores based on 15 STR markers C.C. Branco a,b,*, M. Sa˜o Bento a, C.T. Gomes a, R. Cabral a,b, A.M. Vicente c, P.R. Pacheco a,b, L. Mota-Vieira a,b a
Molecular Genetics and Pathology Unit, Hospital of Divino Espı´rito Santo, Sa˜o Miguel, Azores, Portugal b Instituto Gulbenkian de Cieˆncia, Oeiras, Portugal c Centro de Biopatologia, Instituto Nacional de Sau´de Dr Ricardo Jorge, Lisboa, Portugal Received 16 August 2007; accepted 7 October 2007
Abstract The Azores, the largest Portuguese archipelago, is composed of nine islands unevenly distributed by three groups: the Eastern group (Sa˜o Miguel and Santa Maria), the Central (Terceira, Pico, Faial, Sa˜o Jorge and Graciosa) and the Western group (Flores and Corvo). Here, we describe the genetic diversity patterns for each Azorean island and their genetic relationship based on a total of 554 samples. Genotyping was carried out by the multiplex STR system PowerPlex1 16 (Promega). The results demonstrate that the average gene diversity values vary between 0.768 and 0.797 for Corvo and Terceira, respectively. The comparison of these data with mainland Portugal (0.765) reveals higher values for the Azorean islands. The dendrogram shows that the most distantly apart are Flores and Corvo; however, there is no genetic differentiation between all islands. Moreover, we observe a clustering of the island’s populations by their geographical and socio-cultural proximity. On the other hand, historical records mention a differential settlement between islands. The results show that, nowadays, there are no regional genetic differences in the archipelago due to internal migration. Taken together, the knowledge here obtained will provide insights about the allelic structure of health-related genetic variation in the Azorean population. # 2008 Elsevier Ireland Ltd. All rights reserved. Keywords: The Azores; STRs; Genetic diversity; Population genetics
1. Introduction The Azores, the largest Portuguese archipelago, are composed of nine islands unevenly distributed by three groups: the Eastern group with two islands – Sa˜o Miguel and Santa Maria, the Central which includes five islands – Terceira, Pico, Faial, Sa˜o Jorge and Graciosa and the Western group with Flores and Corvo. At the time of its discovery, in the 15th century, the archipelago was not inhabited. The settlement of the Azores began in 1439 with Portuguese individuals, but the peopling was a slow and difficult process. Historical data report that the Portuguese crown was compelled to give out land and privileges, not only to mainland Portuguese but also to
* Corresponding author at: Molecular Genetics and Pathology Unit, Hospital of Divino Espirito Santo of Ponta Delgada, EPE, Av. D. Manuel I, 9500-370, Ponta Delgada, Sa˜o Miguel, Azores, Portugal. Tel.: +351 296 203 631; fax: +351 296 203 090. E-mail address: [email protected] (C.C. Branco). 1875-1768/$ – see front matter # 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigss.2007.10.041
foreigners, in order to attract people to the islands. These foreigners included Jews, Moorish prisoners, black slaves (Guinea, Cabo Verde and Sa˜o Tome´), Flemish, French, Scottish, English and Spanish [1]. Here, we characterize the overall diversity of each Azorean island based on the analysis of 15 autosomal STRs.
2. Material and methods The study of the genetic diversity was based on a sample composed of 592 healthy Azoreans, obtained from the anonymous DNA bank located at the Hospital of Divino Espirito Santo (Ponta Delgada, Sa˜o Miguel island), the central hospital of the Azores. This bank was built according to the international ethical guidelines for sample collection, processing and storage [2]. The sample distribution per geographic group and island was the following: Eastern group, 166 (Sa˜o Miguel, 114 and Santa Maria, 52); Central group, 320 (Terceira,
C.C. Branco et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 312–314
313
Table 1 Average gene diversity for each Azorean island
Average GD
Sa˜o Miguel (N = 114)
Santa Maria (N = 52)
Terceira (N = 103)
Faial (N = 53)
Pico (N = 66)
Sa˜o Jorge (N = 51)
Graciosa (N = 47)
Flores (N = 76)
Corvo (N = 30)
0.7929
0.7872
0.7979
0.7880
0.7897
0.7879
0.7865
0.7908
0.7717
Fig. 1. Neighbor-Joinning tree and Principal Component analysis based on allele frequencies.
103; Pico, 66; Sa˜o Jorge, 51 and Faial, 53; Graciosa, 47) and Western group, 106 (Flores 76 and Corvo, 30). The PCR co-amplification of the 15 STR loci (Penta-E, D18S51, D21S11, TH01, D3S1358, FGA, TPOX, D8S1179, vWA, Penta-D, CSF1PO, D16S539, D7S820, D13S317 and D5S818) and Amelogenin was performed using the multiplex STR system PowerPlex1 16 (Promega), according to the manufacturer’s instructions. Allele frequencies were calculated by direct counting; the Hardy–Weinberg equilibrium and gene diversity were assessed by the Arlequin. Slatkins FST genetic distance matrix was computed between pairs of populations by Arlequin and used to construct a Neighbor-Joining (NJ) tree by PHYLIP 3.63. We used TreeView 1.6.6 to display tree phylogenies obtained from NJ. 3. Results and discussion The assessment of genetic diversity of all the Azorean islands’ populations was based on the allele distribution of 15 STR markers. All markers are in HWE, considering a 99% confidence ( p < 0.01), and are relatively polymorphic. Comparing the allele composition of our sample and published data, we observe the presence of rare alleles in the Azores, namely D18S51*24 and FGA*25.2. The most interesting is FGA*25.2, which was found in Sa˜o Miguel and Faial islands, and is particularly frequent in India. Table 1 shows the gene diversity (GD) for each marker. The gene diversity values reveal that Terceira shows the highest value (0.7979) and Corvo presents the lowest (0.7717). However, all values are similar between islands and do not show a statistically significant
difference (x2, p = 0.999). The average gene diversity for the whole Azorean population is 0.788. The relationship between all islands was assessed by FST genetic distances and displayed by NJ and Principal Component (PC). The NJ tree (Fig. 1) demonstrates that Corvo is the most genetically different island when compared with the other islands. Moreover, the data shows a closer proximity between the Azorean Central (Terceira, Pico, Faial, Sa˜o Jorge and Graciosa) and Eastern (Sa˜o Miguel and Santa Maria) groups. These results are supported by the AMOVA analysis where the Western group is the most different when compared with the other two groups. Nevertheless, these differences are not significant, only 1% of variance is observed between all groups of islands. To complement the NJ analysis and to obtain the graphical view of the islands genetic similarity distribution we performed the PC analysis (Fig. 1). The first and second PC accounts for 82.6 and 9.6% of the genetic variance observed, respectively, and their plot shows a similar pattern to that displayed in the NJ tree. The data described here show that the Azorean population is an out-bred population with no genetic structure and are consistent with our previous results on Y-chromosome [3] and Alu insertion polymorphisms [4]. This suggests that despite living in different islands, this population can be treated as a homogeneous genetic group, which consequently, could possibly present the same drug-response pattern. Funding source We would like to express our gratitude to all blood donors, all health professionals of Azorean Health Centres,
314
C.C. Branco et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 312–314
of the Servic¸o de Patologia Clinica do Hospital da Horta, EPE, and of the Servic¸o de Hematologia do Hospital do Divino Espirito Santo de Ponta Delgada, EPE, directly involved in the blood collection, as well as the Secretaria Regional dos Assuntos Sociais of Azores. This work was supported by grants from the Direcc¸a˜o Regional da Cieˆncia e Tecnologia, Azores (Ref. M1.2.1/l/003/2005) and Fundac¸a˜o para a Cieˆncia e a Tecnologia (POCI/SAL MMO/ 58413/2004) of Portugal. CCB and PRP are founded by grants (Ref. SFRH/BD/12254/2003 and SFRH/BD/27453/ 2006, respectively) from Fundac¸a˜o para a Cieˆncio e a Tecnologia – Operational Programs Science Technology and Innovation (POCTI), Portugal. The sponsors had no involvement in the development of the paper or decisions related to the paper.
Conflict of interest None. References [1] J.H. Guill, A History of the Azores Islands, Division of Golden Shield International Publications Cooperation, California, 1993. [2] L. Mota-Vieira, P.R. Pacheco, M.L. Almeida, et al., Human DNA bank in Sa˜o Miguel island (Azores): a resource for genetic diversity studies, in: A. Amorim, F. Coˆrte-Real, N. Morling (Eds.), Progress in Forensic Genetics, Proceedings of the 21st International Congress of Forensic Genetics: 13–17 September Ponta Delgada, vol. 1288, 2005, pp. 388–390. [3] P.R. Pacheco, C.C. Branco, R. Cabral, et al., The Y-chromosomal heritage of the Azores Islands population, Ann. Hum. Genet. 69 (2005) 145–156. [4] C.C. Branco, R. Palla, S. Lino, et al., Assessment of the Azorean ancestry by Alu insertion polymorphisms, Am. J. Hum. Biol. 18 (2006) 223–226.