Human auditory ossicles as an alternative optimal source of ancient DNA.

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

Heteroplasmy of Mitochondrial DNA Shown in Korean and Mongolian / 체질인류학회지

As characterization of mitochondrial DNA (mtDNA) shows maternal inheritance and exists as more than thousands copies per cell, it is widely used for population genetics and forensic scientific field. However, mitochondrial DNA study has difficulties because heteroplasmy of mtDNA is being reported from coding and control region. In this study, we have analyzed 200 samples to examine heteroplasmy in mitochondrial DNA of Korean and Mongolian. The control region and coding region in mtDNA of blood from Koreans and Mongolians were analyzed with PCR amplication and sequencing. As a result, several heteroplasmy was observed from total 10 positions including 5 positions in coding region and 5 positions in control region, respectively. Moreover, it showed more than one heteroplasmy in coding region from 6 samples in Korean and 17 samples in Mongolian. Interestingly, heteroplasmy at 5178 position was shown in 6 samples among 23 samples. Considering that the position is important for deciding haplogroup D, we suggest that additional analysis on 4883 position needs for correct haplogrouping. Beside, we also found heteroplasmy in the other positions of 204, 4853, or 16249. Therefore, we suggest that it is required of combinatory analysis on several key nucleotide positions to obtain good results when determining mitochondrial haplogroups.

Comparison of SNP Occurred in Coding Regions of Mitochondrial DNA Analyzed from Korean and Mongolian / 체질인류학회지

Even though mitochondrial DNA analysis is performed in the field of molecular genetics, differences of the results exist regarding which nucleotide positions are analyzed. In this study, we strategically analyzed to find ethnic specific SNP of coding regions of mitochondrial DNA of Korean and Mongolian. Mitochondrial DNA was analyzed with PCR amplification and sequencing with 112 blood samples of Korean and 92 blood samples of Mongolian. As a result, the mutation which commonly appears both in Korean and Mongolian population is 17 nucleotide positions, and the one that shown in the only Korean is 13 nucleotide positions, the one that shown in the only Mongolian 26 nucleotide positions. However, it was thought as individual variation as most mutations are shown in a sample. Among them, it appears as 9% substitution rate in 10397, 4850 nucleotide position of Korean, whereas 12.3% or 15% substitution rate in 5108, 9950 nucleotide positions of Mongolian, respectively. Beside, we observed high level of heteroplasmy in 3546, 3553 nucleotide positions. Therefore, we suggest that these regions might be novel genetic markers for dividing mitochondrial haplogroup of Korean and Mongolian population, but additional analysis needs on several nucleotide positions in huge samples as analyzing on restricted nucleotide positions using restricted DNA samples.

Sex of Ancient Mongolian Human Bones Using Biallelic Marker RPS4Y for Y haplogroup / 대한해부학회지

Many data from ancient human remains became useful by molecular approach for ancient human DNA. In anthropology, genetic sex is essential to understand marriage and burial patterns, differential mortality rates between sexes, and differential patterns by sex of disease, diet, status, and material possessions. This study was designed to determine genotype sex of 52 ancient human bones with well preserved skulls, and to compare with the orphological sex. Parts of femur and other bones were used as ancient bones excavated in Mongolia aged between bronze and Mongol period. Morphological sex was determined by Mongolian scientist, and genotype sex was determined by using biallelic marker RPS4Y for Y haplogroup. Of 52 genetic males, 10 samples were morphologically female. In conclusion, biallelic marker RPS4Y. PCR amplication method will be useful in sex determination of ancient bones.

Development of Ancient DNA Isolation Method for Improved PCR Amplification / 체질인류학회지

Ancient DNA analyses are widely used for evolutionary and phylogenetic study of mankind in anthropology and archeology. However, the DNA extraction from particularly poorly preserved ancient human samples is often unsuccessful in these analyses. In the present study, to improve the success rate of ancient DNA analysis, we introduced a high grade ancient DNA purification method using ion-exchange columns. We compared the success rate of ancient DNA analysis of this new method with that of the two methods that have been used for ancient DNA extraction, GENECLEAN(R) kit (Qbiogene) and Qiaquick column (Qiagen). Twelve ancient bone samples from Korea and Mongolia that are about 500 to 5,000 years old by an archeological estimation were used. As the DNA analysis methods, polymerase chain reaction (PCR) methods for the amplification of a mitochondrial DNA HV1 segment, a male sex determination marker DNA and M175 marker DNA that is used for the determination of O haplogroup of Y chromosome that is reportedly a common one in modern Korean people. The method developed in this study remarkably increased the success rate of DNA analysis compared with the other two methods. Using the GENECLEAN(R) kit, only two samples were amplifiable for the mitochondrial DNA, no samples for the male sex determination marker and M175 marker DNAs. Using the Qiaquick columns, nine samples were amplifiable for mitochondirial DNA, nine samples for male sex determination marker and six samples for M175 marker. The developed method allowed for the amplification of mitochondrial DNA from all samples, male sex determination marker from eight samples and M175 marker from eight samples. The results demonstrate that ion-exchange columns can be useful for the improved ancient DNA extraction in anthropology and archeology.