Phylogenetic analysis of the human ancient mitochondrial DNA

Adachi, Noboru; Umetsu, Kazuo; Takigawa, Wataru; Sakaue, Kazuhiro

doi:10.1016/j.jas.2004.02.011

Cited by 29 publications

(19 citation statements)

References 19 publications

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“…The quantity and purity of the DNA was evaluated by optical density (OD) 260 and OD 260/280 measurements using a spectrophotometer (NanoDrop 1000; Thermo Fisher Scientific Inc., Waltham, MA, USA). Their mtDNA haplogroups were confirmed to be F and M7a by combining data from a previously established APLP-method and direct sequencing of hypervariable region 1 [ 5 , 6 , 23 ]. This study was approved by the Ethics Committee of the University of Yamanashi.…”

Section: Methodsmentioning

confidence: 99%

A Unique Primer with an Inosine Chain at the 5′-Terminus Improves the Reliability of SNP Analysis Using the PCR-Amplified Product Length Polymorphism Method

et al. 2015

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Polymerase chain reaction-amplified product length polymorphism (PCR-APLP) is one of the most convenient and reliable methods for single nucleotide polymorphism (SNP) analysis. This method is based on PCR, but uses allele-specific primers containing SNP sites at the 3′-terminus of each primer. To use this method at least two allele-specific primers and one “counter-primer”, which serves as a common forward or reverse primer of the allele-specific primers, are required. The allele-specific primers have SNP sites at the 3′-terminus, and another primer should have a few non-complementary flaps at the 5′-terminus to detect SNPs by determining the difference of amplicon length by PCR and subsequent electrophoresis. A major disadvantage of the addition of a non-complementary flap is the non-specific annealing of the primer with non-complementary flaps. However, a design principle for avoiding this undesired annealing has not been fully established, therefore, it is often difficult to design effective APLP primers. Here, we report allele-specific primers with an inosine chain at the 5′-terminus for PCR-APLP analysis. This unique design improves the competitiveness of allele-specific primers and the reliability of SNP analysis when using the PCR-APLP method.

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Section: Methodsmentioning

confidence: 99%

A Unique Primer with an Inosine Chain at the 5′-Terminus Improves the Reliability of SNP Analysis Using the PCR-Amplified Product Length Polymorphism Method

et al. 2015

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“…The hypervariable region I (HVR-I) of the mitochondrial D-loop (368 bp, nucleotide positions 15999-16366) was amplified with three sets of overlapping primers (Adachi et al, 2004(Adachi et al, , 2013(Adachi et al, , 2014 (Table 1). This region also includes part of the tRNA Pro gene, although none of our samples exhibited mutations in this region, and thus this did not affect our results.…”

Section: Pcr Amplification and Direct Sequencingmentioning

confidence: 99%

Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the Late Neolithic-Chalcolithic Cucuteni–Tripolye culture

Schmidt

Wakabayashi

Waku

et al. 2020

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Verteba Cave (VC) in western Ukraine dates to the Eneolithic period (c. 5500 YBP), and contains the largest collection yet found of human skeletal remains associated with the Cucuteni-Tripolye culture. The subsistence economy of this people was based on agropastoralism, and included some of the largest and densest Middle Neolithic settlement sites in all of Europe. To understand further the evolutionary history of the Tripolye people, we examined population genetics patterns in mitochondrial DNA from ancient human remains excavated from VC chambers. From five commingled and secondary burial sites within the cave, we obtained 368 bp mtDNA HVR1 sequences from 22 individuals assignable to eight haplogroups: H (three haplotypes), HV (two haplotypes), W, K, and T. Overall nucleotide diversity is low (π = 0.00621). The two largest samples, from Chamber G3 and Site 7, were significantly differentiated with respect to haplotype composition: G3 (n = 8) is dominated by haplotype W (π = 0), whereas Site 7 (n = 15) is dominated by H haplotypes (π = 0.00439). Tajima's D as an indication of population expansion was not significantly negative for the complete sample (D = -1.37) or for sites G3 (D = -0.973) and 7 (D = -1.35), which were analyzed separately. Individuals from the Tripolye culture buried at VC c. 5500 YBP had predominantly haplogroup H and related haplotypes. This contrasts with predominantly haplogroup U individuals in preEneolithic peoples from the same area, which suggests lack of genetic continuity in a site that has been dated to the Mesolithic. Peoples of the Tripolye culture are more closely related to other early European farmers than to Mesolithic hunter-gatherers and/or pre-Eneolithic cultures.

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“…La amplificación por PCR de la RVHI se realizó en tres fragmentos solapados que comprenden las posiciones 15984 a 16411 del genoma mitocondrial, utilizando los cebadores: F15984 (5'-tag cac cca aag cta aga ttc taa t-3', modificado a partir de F15989, Gabriel et al, 2001) y H16167 (Ricaut et al, 2004); L16120 (Adachi et al, 2004) y R16239 (Ivanov et al, 1996); F16204 (5'-gca agt aca gca atc aac cct-3', diseñado por nuestro equipo de trabajo) y R16410 (Gabriel et al, 2001).…”

Section: Secuenciación De La Rhvi Del Adn Mitocondrialunclassified

Linajes Mitocondriales en Muestras De Esquina De Huajra (Jujuy, Argentina). Aportes Al Estudio De La Ocupación Incaica en La Región Y La Procedencia De Sus Habitantes

Russo¹,

Gheggi²,

Avena³

et al. 2016

Rev Arg Antrop Biol

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El sitio arqueológico Esquina de Huajra (centrosur de la Quebrada de Humahuaca) corresponde a una instalación ubicada cronológicamente en la Fase Inca (ca. 500-420 AP) y la tradicionalmente asignada en el noroeste argentino como Hispano Indígena o de primeros contactos con el español (ca. 420-320 AP). Enmarcado en la política económica incaica, habría sido clave en la explotación y distribución de bienes procedentes de las Yungas Orientales. Además, su cultura material sugiere importantes redes de interacción con las tierras altas, planteando interrogantes sobre la conformación poblacional de sus habitantes.En este trabajo se analizan los linajes maternos de individuos de Esquina de Huajra en comparación con otros sitios del centro-sur andino para evaluar su posible origen foráneo, considerando que el reasentamiento de poblaciones fue una práctica imperial recurrente. El ADN fue extraído de piezas dentales de 6 individuos. Se secuenció la Región Hipervariable I del ADN mitocondrial en cuatro individuos hallándose dos A2 y dos C1. La ausencia de B2 discrepa con lo descripto para gran parte de los sitios andinos, donde este haplogrupo es mayoritario. Dos de los cuatro haplotipos se comparten únicamente con otros sitios de la Quebrada de Humahuaca del Período de Desarrollos Regionales (Los Amarillos y San José); pero una variante nodal C1 fue reportada tanto en Juella como en sitios peruanos preincaicos e incaicos. Estos resultados representan un primer aporte al estudio genético de los habitantes de Esquina de Huajra y una evidencia más de los complejos procesos poblacionales en la región andina.

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Phylogenetic analysis of the human ancient mitochondrial DNA

Cited by 29 publications

References 19 publications

A Unique Primer with an Inosine Chain at the 5′-Terminus Improves the Reliability of SNP Analysis Using the PCR-Amplified Product Length Polymorphism Method

A Unique Primer with an Inosine Chain at the 5′-Terminus Improves the Reliability of SNP Analysis Using the PCR-Amplified Product Length Polymorphism Method

Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the Late Neolithic-Chalcolithic Cucuteni–Tripolye culture

Linajes Mitocondriales en Muestras De Esquina De Huajra (Jujuy, Argentina). Aportes Al Estudio De La Ocupación Incaica en La Región Y La Procedencia De Sus Habitantes

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