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vol.32 issue1Analysis of the CCR5 gene coding region diversity in five South American populations reveals two new non-synonymous alleles in Amerindians and high CCR5*D32 frequency in Euro-Brazilians author indexsubject indexarticles search
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Genetics and Molecular Biology

Print version ISSN 1415-4757

Genet. Mol. Biol. vol.32 no.1 São Paulo  2009 Epub Jan 10, 2009

http://dx.doi.org/10.1590/S1415-47572009005000001 

Genet Mol BiolGMBGenetics and Molecular BiologyGenet Mol Biol1415-47571678-4685Sociedade Brasileira de GenéticaRibeirão Preto, SP, BrazilGENETICSGenetic signatures of parental contribution in black and white populations in BrazilHistorical genetics in BrazilGuerreiro-JuniorVanderleiBisso-MachadoRafaelMarreroAndreaHünemeierTábitaSalzanoFrancisco M.BortoliniMaria CátiraDepartamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul Porto AlegreRSBrazil Maria Cátira Bortolini. Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970 Porto Alegre, RS, Brazil. E-mail: maria.bortolini@ufrgs.br. 042006321xxxxxx3101200814052008Copyright by the Brazilian Society of Genetics.2009This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Two hundred and three individuals classified as white were tested for 11 single nucleotide polymorphisms plus two insertion/deletions in their Y-chromosomes. A subset of these individuals (n = 172) was also screened for sequences in the first hypervariable segment of their mitochondrial DNA (mtDNA). In addition, complementary studies were done for 11 of the 13 markers indicated above in 54 of 107 black subjects previously investigated in this southern Brazilian population. The prevalence of Y-chromosome haplogroups among whites was similar to that found in the Azores (Portugal) or Spain, but not to that of other European countries. About half of the European or African mtDNA haplogroups of these individuals were related to their places of origin, but not their Amerindian counterparts. Persons classified in these two categories of skin color and related morphological traits showed distinct genomic ancestries through the country. These findings emphasize the need to consider in Brazil, despite some general trends, a notable heterogeneity in the pattern of admixture dynamics within and between populations/groups. admixture dynamicsmtDNAY-chromosome markersIntroductionThe great maritime expeditions and colonial expansion by Europeans during the 15th and 16th centuries considerably changed their history and those of the colonized peoples. The cultural impact of colonization has been known for a long time, but only more recently have its genetic aspects have been investigated. Genetic studies of Brazilian populations have shown, for example, that the extent of admixture among Europeans, Africans and Native Americans is higher than perceived by phenotypic characteristics, and that marriages during the Colonial Era were mainly asymmetric, with most of the Y-chromosomes present in contemporary white Brazilian populations being of European origin, but a significant portion of the mtDNA lineages being of Amerindian or African origin (Alves-Silva et al., 2000; Carvalho-Silva et al., 2001). However, marked regional differences have been reported for white Brazilian populations, indicating that there can be considerable variation in the general trends (Callegari-Jacques et al., 2003; Marrero et al., 2005, 2007a; Zembrzuski et al., 2006). DNA studies with urban black populations have been less common but have also identified important regional differences (Bortolini et al., 1999; Hünemeier et al., 2007; Gonçalves et al., 2008).In this work, we investigated the genetic background of people classified as white or black living in the same city (Porto Alegre, the capital of the southernmost state of Brazil). Our results reveal details about the history of Porto Alegres human population and indicate the extent of genetic admixture, as well as the nature of this process within and between these two major color groups in Brazils four distinct geographical regions. These findings also show how it is possible to discover details of the ancestral history of a contemporary population based on its current genetic characteristics.Subjects and Methods Population samples and DNA extractionThe history of Porto Alegre (30°5' S, 5°10' W), the capital of the Brazilian state of Rio Grande do Sul, dates from 1730 when Jerônimo de Ornellas, an immigrant from Madeira Island, received a large plot of land (sesmaria) in this area from the Portuguese crown. The little village that was subsequently formed showed significant population growth only after the arrival of ~500 couples from the Azores archipelago (another Portuguese colony), from 1752 to 1754 (Flores, 1996). The importance of the Azorian migration to Rio Grande do Sul, especially Porto Alegre, is illustrated by Laytano (1974), who stated that in 1780 about 55% of the 18,000 inhabitants of the town were Azorian or of Azorian-descendent. The pre-Columbian inhabitants, the Guarani Indians, were displaced, although in other regions of the state they, as well as other natives, were still present (Noelli et al., 1997). Subsequent waves of European migration, especially from Portugal, Spain, Italy and Germany, contributed to the growth of Porto Alegre and nearby cities. The presence of African slaves is also mentioned in historical records (Nogueról, 2005), although their proportion relative to the total population is unknown. Currently, the urban complex formed by the capital and neighboring cities has 3,152,596 inhabitants, 7% and 88% of whom are classified as blacks (pretos, in Portuguese) and whites (brancos), respectively (Brazilian Institute of Geography and Statistics-IBGE, 2000). In Brazil, skin color rather than ancestry is used to define an equivalent to “race”, and in the present study the word “black” will be used to refer to pretos and any person identified and/or self-identified with some other term that suggests African ancestry, such as mulato or pardo. “White” will be used to define those who, based on their physical traits and information, show no admixture with non-Europeans.Two hundred and three unrelated individuals living in Porto Alegre and its metropolitan region, phenotypically classified as white by the interviewer of the research group, were studied. DNA was extracted from whole blood according to Lahiri and Nurnberger (1991) or from saliva using QIAamp® kits (QIAGEN), according to the manufacturer's instructions. This investigation was approved by the Brazilian National Ethics Commission (CONEP Resolution no. 1333/2002).Y- chromosome markersHünemeier et al. (2007) recently presented and discussed the African portion of the Y-chromosomes and mtDNA lineages of a sample of 107 blacks from the same city. Here, we investigated additional Y-chromosome polymorphisms (see below) to characterize the non-African portion of the Y-chromosomes of this sample, and also considered the mtDNA lineages classified as Amerindian or European. This procedure standardized the set of uniparental markers investigated in the two samples, thereby allowing comparative analyses.Two hundred and three white men were genotyped for 13 binary loci (11 single nucleotide polymorphisms or SNPs: 92R7, M3, M242, M9, M17, M170, M173, M213, M269, SRY2627, M2, and two insertion/deletions, Yap ALU and 12f2) located in the non-recombinant region of the Y-chromosome (NRY). These markers define well the most common and widespread African, European and Native American Y-chromosomes. Genotyping was done according to the hierarchical order of markers presented by Jobling and Tyler-Smith (2003) using the primers and conditions described in Hammer and Horai (1995), Underhill et al. (1996, 2001), Hurles et al. (1999), Thomas et al. (1999), Rosser et al. (2000), Bortolini et al. (2003), Flores et al. (2003), Montiel et al. (2005), and Kayser et al. (2005). Haplogroups P*(xQ3,R1), Q3*, K(xP), Q*(xQ3), R1a1*(xDE), I*(xP,K,J), R1*(xR1a1,R1b3), F(xI,J,K,P), R1b3*(xR1b3f), R1b3f, E3a*, DE*(E3a) and J* were established using the markers indicated above in the order given. According to Jobling and Tyler-Smith (2003), designations such as P*(xQ3, R1) indicate partial typing of markers in a haplogroup and, in the present case, describes all chromosomes in clade P* except Q3* and R1*. We also investigated 11 of the biallelic loci indicated above (92R7, M3, M242, M9, M17, M170, M173, M213, M269, SRY2627 and 12f2) to characterize the non-African portion of the Y-chromosomes in the black sample previously studied by Hünemeier et al. (2007).Mitochondrial DNAThe first hypervariable segment (HVS-I) of the mtDNA control region was sequenced in a subset of 172 white individuals using primers and conditions previously described by Marrero et al. (2005). The sequence reactions were run in an automated ABI 310 sequencer. Both DNA strands were sequenced from positions 16050 to 16391, since this is the region for which most of the comparative information is available. Individuals with the “C-stretch” between positions 16183-16193, which is caused by the 16189C substitution, were re-sequenced in each direction so that each base was determined twice.The sequences were checked manually, and validated by using the CHROMAS LITE 2.0 program. Alignment relative to the revised Cambridge Reference Sequence (Andrews et al., 1999) was done using the BIOEDIT software (Hall, 1999). The filtering procedure described by Bandelt et al. (2002) was used to check the quality of the sequences and eliminate artifacts introduced during sequencing and editing. After filtering, the relationships between the lineages were examined with the NETWORK 4.2.0.0. program using the median-joining algorithm (Bandelt et al., 1999). Weight networks showing star tree patterns, together with other criteria such as those suggested by Yao et al. (2004), ensured that the data were essentially free of artifacts. The HVS-I sequences were classified into haplogroups according to recommended criteria (Bandelt et al., 2002; Salas et al., 2002, 2004; Kivisild et al., 2002; Torroni et al., 2006).Data analysisY-SNP and mtDNA haplogroup frequencies were obtained by counting. Estimates of parental continental contributions in the paternal and maternal data sets were obtained directly since the major haplogroups of mtDNA and Y-SNP are geographically specific. Population relationships were estimated through FST genetic distances using Arlequin version 3.01 (Schneider et al., 2000; Excoffier et al., 2005) and their statistical significance was assessed by permutation using 10,000 runs.Results and DiscussionsY-chromosome biallelic polymorphisms (SNPs)Based on the Y-chromosome distribution (Table 1), the most frequent haplogroup in Porto Alegre whites was R1b3* (51%), which was also the most common haplogroup found in another Brazilian city (Rio de Janeiro), as well as in the Azores and Portugal. The frequency of this haplogroup was lower (~13%) in Porto Alegre blacks.To test the hypothesis of random haplogroup distribution among populations we computed FST values based on the major hierarchical clustering for these analyses. There were no significant differences between Porto Alegre whites and those of the Azores, Portugal or Spain (FST = -0.00162, p = 0.6126; FST = 0.00235, p = 0.1622; FST = 0.00345, p = 0.1261, respectively), although the Porto Alegre white prevalences differ significantly from those of the other European countries considered. The difference between Porto Alegre and Rio de Janeiro was also significant (FST = 0.0120, p = 0.0090), but when the African (E3a, B*, and DE) and Amerindian (Q* and Q3*) haplogroups are excluded this significance disappeared (FST = 0.0056, p = 0.1441). Surprisingly, the haplogroups of European origin detected in Porto Alegre blacks were significantly different from those found in whites of the same city (FST = 0.1562, p = 0.000), and from those observed in Iberian populations. However, since the number of blacks studied was small (30), it is probable that these differences reflect sampling error rather than any phenomenon of the admixture process. The African portion of the Y-chromosomes of this black sample has been described in detail by Hünemeier et al. (2007).Mitochondrial DNAMultiple alignment with the reference sequence (Andrews et al., 1999) allowed the identification of 105 mtDNA lineages in white individuals (Table 2). This table also shows the non-African lineages identified in blacks, as well as those shared by the two samples.For 35 of the 69 European lineages (51%), identical matches were found for data in the literature from countries with an important history of migration to Rio Grande do Sul (Portugal/Azores, Spain, Italy, and Germany; data from Crespillo et al., 2000; Pereira et al., 2000; Mogentale-Profizi et al., 2001; Brehm et al., 2003; Poetsch et al., 2003; Picornell et al., 2005; Pichler et al., 2006). Most of these haplotypes (25; 71%) perfectly matched more than one of the European populations. Four (lineages #12, #13, #38 and #68), three (#36, #62 and #63), two (#2 and #38), and one (#14) of the haplotypes found in Porto Alegre (Table 2) exclusively matched those found in the Azores, Portugal, Spain, and Italy, respectively. Only two lineages of European origin (#49 and #50) present in Porto Alegre blacks were not observed in whites from the same city or in any of the European populations considered here. As with the Y markers, the mtDNA data also revealed that the Azorian presence in Porto Alegre was clearly detectable regardless of the demographic and cultural changes that occurred after the initial foundation/colonization of the city.The same analysis with the 14 lineages of African origin found in the white sample revealed that 57% of them had perfect matches with those found in the regions of slave importation to Brazil (West, West-Central, and Southeast Africa; Salas et al., 2002; Plaza et al., 2004; Rosa et al., 2004; Beleza et al., 2005; Coia et al., 2005; Jackson et al., 2005). Three lineages (# 103, #104, and #116) exclusively matched those found in Angola, Cabinda, and Mozambique, countries inhabited by peoples who speak Bantu languages (Salas et al., 2002; Plaza et al., 2004; Beleza et al., 2005). Another lineage (#110) was also probably of Bantu origin since it occurs in Mozambique and in the Bassa ethnic group of Cameroon. Lineage #113 matched one found only in Guinea Bissau, whereas # 106 matched another found in Sierra Leone, both of which are West African countries (Rosa et al., 2004; Jackson et al., 2005). Two lineages (#108 and #109) had a geographical origin that was difficult to define since they occur in all sub-Saharan Africa. Only four African lineages were shared between the black and white Porto Alegre groups, with all four occurring in Africa and/or other Brazilian populations (Salas et al., 2002; Plaza et al., 2004; Rosa et al., 2004; Beleza et al., 2005; Coia et al., 2005; Jackson et al., 2005; Gonçalves et al., 2008).The four major Amerindian haplogroups were detected among Porto Alegre whites (A = 28%; B = 22%, C = 47%, D = 3%), whereas haplogroup A was absent among blacks (B = 19%, C = 69% and D = 12%). Lineage #87 was the most common in both samples. Since this lineage contained the mutations that defined the C nodal branch, it matched several sequences found in admixed populations from southern Brazil, and in individuals from the Tupian and Jêan tribes; these different matches precluded identification of the precise origin of this lineage (Alves-Silva et al., 2000; Marrero et al., 2005, 2007a,b). On the other hand, the Guarani contribution was clearly detected through the presence of lineages such as #75 (Marrero et al., 2007b). However, most of the Amerindian lineages found in Porto Alegre did not match and/or cluster with Guarani mtDNA sequences. These results support the idea that the present Guarani mitochondrial genome may be a poor representative of that found at colonial times (Marrero et al., 2007a). This finding also suggests that other tribes may have made a more significant contribution, through their women, to the formation of the contemporary admixed Porto Alegre population.Ancestral contributionsTable 3 summarizes the continental origins of the two Porto Alegre samples based on the mtDNA and Y-chromosome haplogroups. Although there was a significant introduction of non-European mtDNA sequences (Amerindian = 21%; African = 10%) among whites, Europe was still the major contributor in both genetic systems (mtDNA = 69%; Y-chromosome = 99%). This finding supported the general correspondence between physical appearance and maternal or paternal ancestry at the population level. In contrast, a completely different picture emerged when the black group was considered. Most of the mtDNA sequences (79%) had an African origin, but 56% of the Y-chromosomes were of European origin, while the Amerindian contribution involved both paternal and maternal inheritance.These results for the black group can be partly explained by the fact that mulatos and pardos, who showed visible signs of admixture, were included in this sample. However, history and the dynamics of admixture could also have played an important role. In the early centuries of colonization, almost only European men migrated to Brazil, and for different reasons, African males were brought preferentially to Brazil during the slave trade (Mattoso, 1982). This initial demographic asymmetry, and compulsory restrictions to the African male slaves reproduction, determined that the first Brazilians were born mostly from the union between European males and Amerindian or African females. Later, social practices determined that a child with more pronounced physical African features would be considered black, while those with more pronounced European features would be considered white. This situation created ample opportunity for the introduction of African mtDNA lineages and European Y-chromosomes into the white and black segments, respectively (Parra et al., 2003; Gonçalves et al., 2007). A second major European migratory movement during the 19th century that was particularly important for southern Brazil involved couples and families, not just males. This migration resulted in many white persons/populations with complete European genomes, whereas others are phenotypically white but show non-European admixture signs at the genome level (Marrero et al., 2005; Zembrzuski et al., 2006).To investigate whether these differences between the two skin color groups were peculiar to Porto Alegre or whether they represented a more general tendency, we compiled the literature data for all of the estimates of African, European and Amerindian contributions in black and white Brazilian populations from different geographical regions. Table 4 shows that the pattern described above occurs throughout southern Brazil, but not in other regions of the country. In blacks from the Southeast, for example, the African component predominates in both paternal and maternal data sets, whereas among whites in this region the European contribution is particularly frequent when only Y chromosome markers are considered. Table 4 also show that the whites from the North and South present large differences, basically related to the Amerindian and European women contribution; the extensive admixture between Indians and non-Indians ended in southern Brazil at least 170 years ago, whereas in northern Brazil, especially in the Amazon basin, Amerindian genes are still being introduced into non-native urban and rural populations. The results of these discontinuous vs. continuous patterns of gene flow can be seen by comparing the mtDNA results mentioned above with the biparental loci admixture values (21% vs. 54% and 13% vs. 44% for the Amerindian component in white samples from the South and North, respectively). In contrast, groups or populations identified as white in the Northeast and Southeast had very similar proportions of Amerindian, European and African ancestries in all of the genetic systems investigated. Since European colonization started almost simultaneously in the Northeast and Southeast, this similarity suggests that the dynamics of admixture were similar in both regions.These striking differences between and within the skin color groups in Brazilian regions can be due to several factors, and some can be the same as those presented for the Porto Alegre case. The type of classification employed to classify the samples in the different studies is also important. Both self and interviewer classifications are full of subjectivities (Salzano and Bortolini, 2002). Distinct admixture dynamics due to historical events and social practices should also be considered. Overall, our results corroborate the idea that, despite some general trends, there is a notable heterogeneity in the pattern of admixture within and among populations/groups in Brazil (Bortolini et al., 1999; Alves-Silva et al., 2000; Marrero et al., 2005). Our findings also highlight the intricacies of past and present patterns of mating in a complex society with a relatively recent multiethnic origin, and the relative instability of phenotypic classifications within this society.AcknowledgmentsThis work was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Fundação de Amparo à Pesquisa do Rio Grande do Sul (FAPERGS), Pró-Reitoria de Pesquisa da Universidade Federal do Rio Grande do Sul (PROPESQ-UFRGS), and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the Institutos do Milênio and Apoio a Núcleos de Excelência programs. We thank the 203 volunteers who provided blood and saliva samples that made this study possible. M.H. Hutz and E. Bandinelli donated some samples, and S.D.J. Pena and J.C. 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October5,2007 from: http://www.ibge.gov.br/home/estatistica/populacao/censo2000/populacao/censo2000_populacao.pdf.Network 4.2.0.0 ProgramAvailable at May 29, 2007, from: http://www.fluxus-engineering.comTablesTable 1- Y-SNP haplogroup frequencies in Porto Alegre residents classified as white or black compared with individuals from another Brazilian city (Rio de Janeiro) and European populations.aPresent study; bSilva et al. (2006); cGonçalves et al. (2005); dMontiel et al. (2005); eBeleza et al. (2006); fFlores et al. (2003); gCapelli et al. (2006, 2007); hKayser et al. (2005).Table 2- mtDNA haplotypes and haplogroups in Porto Alegre residents classified as black or white.LineageNumber of sequencesHVS-I mutationsaHaplogroupbOrigin#WhiteBlackc1222rCRSHEuropean24126HEuropean33153HEuropean42261HEuropean52354HEuropean62311HEuropean7183HEuropean8193HEuropean91114HEuropean101168HEuropean111189HEuropean121240HEuropean131124 354HEuropean14193 304HEuropean151209HEuropean161233HEuropean171189 300 325HEuropean181361HEuropean192162H1aEuropean201304H5European211129 223IEuropean22269 126 192JEuropean23169 126 193 300 309JEuropean24169 126 366JEuropean25169 126 222JEuropean26269 126 145 231 261J2aEuropean27169 93 126 261 274 355J2aEuropean28169 126 261J2aEuropean29169 126 145 172 222 261J1b1European30169 126 145 172 222 261 305TJ1b1European31369 126 193 278J1cEuropean32169 111 126J1cEuropean331188 224 311KEuropean3431224 311KEuropean35183 224 311KEuropean36186 224 311KEuropean371193 224 290 311KEuropean38193 224 311KEuropean391129 223 291 298M or IEuropean401129 183C 189 249 311M1 or U1aEuropean411126 145 176G 223 260N1bEuropean421145 176G 223N1bEuropean431126 292 294TEuropean44151 126 294TEuropean453126 163 186 189 284 294T1European461126 254 294 296 304T2bEuropean473126 294 296 304T2bEuropean481126 294 296 304 360T2bEuropean491126 193 294 296 304 357T2bEuropean501126 294 296 311T2bEuropean511126 193 294 296 304T2bEuropean522126 220 292 294T3European531126 163 186 189 294T3European54151 129C 183C 189U2eEuropean551189 319 356U4European562270U5European572192 256 270U5European581192 270U5European591256 270U5European604167 192 256 270 311 318U5aEuropean611189 256 362U5aEuropean621256 270 342U5aEuropean632172 183C 189 219 278U6aEuropean641172 183C 189 278U6aEuropean653153 298VEuropean663298VEuropean671187 298 311VEuropean681291 298VEuropean691189 223 278XEuropean703126 223 278 290 319 362AAmerindian711111 223 290 319 362AAmerindian721111 223 290 319AAmerindian731111 129 223 290 319 362AAmerindian741111 126 223 259 290 319 362AAmerindian751111 223 266 290 319 362AAmerindian761111 223 269 290 319 360 362AAmerindian77192 111 223 290 319 362AAmerindian782178 183C 189 217BAmerindian7911189 217BAmerindian801178 183C 189 217 311BAmerindian811178 183C 189 217BAmerindian82183 189 217BAmerindian831183C 189 217BAmerindian841189 217 249 312 344BAmerindian851189 217 311 319BAmerindian861189 217 311BAmerindian87105223 298 325 327CAmerindian881114 123 298 325 327CAmerindian891223 224 298 311 325 327 356CAmerindian901223 270 298 325 327CAmerindian911126 207 223 298 325 327CAmerindian921051 172 223 295 298 325 327 335CAmerindian931185 209 223 327CAmerindian941187 223 290 325CAmerindian952051 223 298 325 327CAmerindian961223 298 325 327 356CAmerindian971051 223 287 298 311 325 327CAmerindian981223 298 325 327 362CAmerindian991223 325 327CAmerindian1001223 239 288 325 362DAmerindian1011189 223 325 362DAmerindian1021223 325 362DAmerindian1033148 172 187 188G 189 223 230 311 320L0a2African10413129 148 168 172 187 188G 189 223 230 278 293 311 320L0a1African105166 129 179 187 189 218 223 230 243 290 311L0dAfrican1062111 126 187 189 223 239 270 278 293 311L1bAfrican107183 126 187 189 215 223 264 270 278 293 311L1bAfrican10812126 187 189 223 264 270 278 293 311L1bAfrican10912126 187 189 223 264 270 278 311L1bAfrican1101129 187 189 223 274 278 293 294 311 360L1c1African1111134 187 213 223 265C 274 278 286G 360L1c2African1121189 223 265C 278 286G 294 311 343T 360L1c2African1131193 213 223 239 278 294 309 390L2a1β1African1141223 292 320L3e2African115186 149T 152A 223 248 320 355L3e2African11612209 223 311L3fAfrican76SeveralcSeveralcAfrican172107aThe nucleotide positions considered for the analyses were from 16,050 to 16,391. Note that a value of 16,000 has been subtracted from each nucleotide position to make this column easier to read. Sequences were aligned with the revised reference sequence (rCRS; Andrews et al., 1999). bHaplogroup nomenclature is that recommended in the literature (see text). Those cases in which HVS-I information alone did not allow the identification of specific haplogroups were classified based on probabilities. cComplete information about the African lineages observed in Porto Alegre blacks can be found in Hünemeier et al. (2007).Table 3- Estimates of parental contribution based on mtDNA and Y-chromosome markers in whites and blacks from Porto Alegre.Table 4- Estimates of parental contribution using three set of markers and considering persons classified as white or black in different regions of Brazil. aND = No data available; bHVS-I sequences and SNPs in the mtDNA codifying region; cSNPs in the non-recombining region of the Y-chromosome; dClassic blood group plus protein polymorphisms. Associate Editor: Paulo A. Otto