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Mitochondrial DNA sequence analysis of native Bolivians population

      Abstract

      Haplotypes of 111 individuals from La Paz have been studied by the analysis of the polymorphisms in mtDNA control region, HV1 and HV2 regions, in order to intend the genetic diversity. The aim was to created a population database, assess genetic interpopulation variability and classify haplogroups. We had identify 99 haplotypes with 125 polymorphic nucleotide positions, 93 haplotypes are unique. Nucleotide and sequence diversity are estimated in 0.016068 ± 0.008186 and 0.9988, respectively. Haplogroup distribution is as follows: 47.75% B; 14.41% C; 6.31% A; 4.5% D; 6.31% A, C, or D; 23.42% undetermined or compound haplogroups. Rate of heteroplasmy is 37.8% in HV1 and 53.2% in HV2.

      Keywords

      1. Introduction

      Andean region can reveal some history of Human migrations and the History of human colonization of the New World. MtDNA is remarkable useful for population genetics by its own characteristics: high copy number per cell, maternal inheritance, high mutation rate of evolution that confers highly polymorphism to the sequences and absence of recombination. The aim of this work was to create a population database of the variability of HV1 and HV2 segments in the population of La Paz, Bolivia; assess the genetic variability in the population; classify the population in to haplogroups; and make a comparison between the studied population and chosen populations from the five continents to discover the genetic variability of the population and infer about their past migrations.

      2. Methods

      The blood samples were obtained from 111, healthy and none related, individuals regarding the legal consentient in vigour in Bolivia. DNA was extracted using Chelex®100 method [
      • Walsh P.S.
      • Metzger D.A.
      • Higuchi R.
      Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material.
      ]. The HV1 and HV2 regions of the mtDNA were amplified using the primers L15997 and H16401 and the primers L408 and H048 [
      • Wilson M.R.
      • DiZinno J.A.
      • Polanksey D.
      • Replogle J.
      • Budowle B.
      Validation of mitochondrial DNA sequencing for forensic casework analysis.
      ], respectively. The two segments were sequenced, forward and reverse, using the sequencing chemistry ABI Prism® dRhodamine Terminator Cycle Sequencing Ready Reaction Kit that marks the terminators (ddNTP's). The sequences were analysed in the sequencers: 3100—Avant Genetic Analyser (ABI PRISM®) with the DNA Sequencing Analysis Software™ v.3.7 and the SeqScape® Software v.2.0; and in the 3130—Genetic Analyser (ABI PRISM®) with the ABI DNA Sequencing Analysis Software v.5.2 and the SeqScape® Software v.2.5. Comparison of the HV1 and HV2 regions of the mtDNA were effectuated with the Cambridge Reference Sequence (CRS) [
      • Anderson S.
      • Bankier A.T.
      • Barrel B.G.
      • De Bruijn M.H.
      • Coulson A.R.
      • Drouin J.
      • Eperon I.C.
      • Nierlich D.P.
      • Roe B.A.
      • Sanger F.
      • Schreier P.H.
      • Smith A.J.
      • Standen R.
      • Yoing I.G.
      Sequence and organization of the human mitochondrial genome.
      ]. The establishment of the haplogroups was made considering the HV1 segment [
      • Torroni A.
      • Schurr T.G.
      • Cabell M.F.
      • Brow M.D.
      • Neel J.V.
      • Larsen M.
      • Smith D.G.
      • Vullo C.M.
      • Wallace D.C.
      Asian affinities and continental radiation of the four founding native Americans mtDNAs.
      ]. The nucleotide diversity and the sequence diversity were calculated second Nei [
      • Nei M.
      Molecular Evolutionary Genetics.
      ]. The AMOVA was made with Arlequin 2000 [
      • Schneider S.
      • Roessli D.
      • Excoffier L.
      ARLEQUIN: A Software for Population Genetics Data Analysis.
      ].

      3. Results and discussion

      The HV1 and HV2 sequences were analysed between positions 16024–16390 and 73–340. In this study 99 haplotypes were identified with 125 polymorphic nucleotide positions, 93 haplotypes are unique. Nucleotide and sequence diversity are estimated in 0.016068 ± 0.008186 and 0.9988, respectively. Haplogroup distribution (Fig. 1) is as follows: 47.75% B; 14.41% C; 6.31% A; 4.5% D; 3.60% A, C or D; and 23.42% undetermined or compound haplogroups. Rate of heteroplasmy is 37.83% in HV1 and 53.15% in HV2. It should be notice that the high rate of length heteroplasmy that is found here is similar to others populations from South America and Southwester Asia. The phylogenetic tree obtained by the analysis of the molecular distances between the studied population and chosen populations from the five continents [

      M. Carvalho, H. Antunes, M.J. Anjos, L. Andrade, V. Lopes, F. Corte-Real, M.C. Vide, Estudo da Variabilidade do DNA Mitocondrial em Populações Africanas (Guiné e Cabo Verde). VII. Jornadas de Genética Forense, Reunião do Grupo Espanhol e Português da ISFG, Barcelona, 2002.

      ,
      • Carvalho M.
      • Mendes C.
      • Antunes H.
      • Anjos M.J.
      • Andrade L.
      • Lopes V.
      • Vieira D.N.
      • Vide M.C.
      mtDNA analysis in Portuguese populations (Central Portugal and Azores Islands): polymorphic sites in control region sequences.
      ,
      • Carvalho M.
      • Balsa F.
      • Lopes V.
      • Anjos M.J.
      • Andrade L.
      • Serra A.
      • Oliveira C.
      • Batista L.
      • Corte-Real F.
      • Vieira D.N.
      • Vide M.C.
      Mitochondrial DNA analusis in a population from Angola.
      ,
      • Pereira L.
      • Macaulay V.
      • Torroni A.
      • Scozzari R.
      • Prata M.J.
      • Amorim A.
      Prehistoric and historic traces in the mtDNA of Mozambique: insights into the Bantu expansions and the slave trade.
      ,
      • Trovoada M.J.
      • Pereira L.
      • Gusmão L.
      • Abade A.
      • Amorim A.
      • Prata M.J.
      Pattern of mtDNA variation in three populations from Sao Tome e Príncipe.
      ,
      • Crespillo M.
      • Luque J.A.
      • Paredes M.
      • Fernández R.
      • Ramírez E.
      • Valverde J.L.
      Mitochondrial DNA sequences for 118 individuals from northeastern Spain.
      ,
      • Lutz S.
      • Weisser H.-J.
      • Heizmann J.
      • Pollak S.
      Location and frequency of polymorphic positions in the mtDNA control region of individuals from Germany.
      ,
      • Parson W.
      • Parsons T.J.
      • Scheithauer R.
      • Holland M.M.
      Population data for 101 Austrian Caucasian mitochondrial DNA d-loop sequences: application of mtDNA sequence analysis to a forensic case.
      ,
      • Piercy R.
      • Sullivan K.M.
      • Benson N.
      • Gill P.
      The application of mitochondrial DNA typing to the study of white Caucasian genetic identification.
      ,
      • Rousselet F.
      • Mangin P.
      Mitochondrial DNA polymorphisms: a study of 50 French Caucasian individuals and application to forensic casework.
      ,
      • Ingman M.
      • Gullensten U.
      mtDB: human mitochondrial genome database, a resource for population genetics and medical sciences.
      ,
      • Shin M.-G.
      • Levin B.C.
      • Kim H.-R.
      • Lee I.-K.
      • Cho D.
      • Kee S.J.
      • Shin J.-H.
      • Suh S.-P.
      • Ryang D.-W.
      Profiling of length heteroplasmies in the human mitochondrial DNA control regions from blood cells in the Korean population.
      ,
      • Torres M.M.
      • Bravi C.M.
      • Bortolini M.-C.
      • Duque C.
      • Callergari-Jacques S.
      • Ortiz D.
      • Bedoya G.
      • Groot de Restrepo H.
      • Ruiz-Linares A.
      A revertant of the major founder native American haplogroup C common in populations from Northern South America.
      ,
      • Moraga M.L.
      • Rocco P.
      • Miquel J.J.
      • Nervi F.
      • Llop E.
      • Chakraborty R.
      • Rothhammer F.
      • Carvallo P.
      Mitochondrial DNA polymorphisms in Chilean aboriginal populations: implications for the peopling of the southern cone of the continent.
      ,
      • Vona G.
      • Falchi A.
      • Moral P.
      • Calò C.M.
      • Varesi L.
      Mitochondrial sequence variation in the Guahibo Amerindian population from Venezuela.
      ,
      • Budowle B.
      • Allard M.W.
      • Fisher C.L.
      • Isenberg A.R.
      • Monson K.L.
      • Stenwrt J.E.
      • Wilson M.R.
      • Miller K.P.
      HVI and HVII mitochondrial DNA in Apaches and Navajos.
      ] is illustrated in Fig. 2.
      Figure thumbnail gr1
      Fig. 1MtDNA haplogroups distribution of mtDNA in La Paz, Bolivia.
      Figure thumbnail gr2
      Fig. 2Phylogenetic tree, genetic distances between populations.

      4. Conclusion

      Due to the high frequency of unique haplotypes, the studied population has a great interpopulation genetic variability. The nucleotide and sequence diversity are high and similar to the ones found in other populations of South America. Native Bolivians exhibited haplotypes from four haplogroups observed in Native Americans. Genetic variability is high, suggesting isolation after an early colonization of the population.

      Conflict of interest

      None.

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