Efficacy of three methods of extracting DNA from skeletal remains obtained from three taphonomic contexts

Abstract

Introduction

The extraction techniques of deoxyribonucleic acid (DNA) from old bone samples are based on the use of complex methodologies, which deal with the degradation of the sample, the low amount of DNA, and the presence of inhibitors that can be extracted simultaneously.

Objective

To compare the efficiency in obtaining DNA from the methods: organic extraction, commercial kit, and previous total demineralization, to obtain STR profiles of old bone samples from 3 taphonomic processes (alkaline, acid, and moist mitotic).

Materials and methods

29 skeletal remains from 3 different taphonomic contexts were processed: acidic, alkaline, and wet-fungal. The amount of DNA obtained from 3 methodologies was evaluated in a comparative manner: organic extraction method (phenol–chloroform–isoamyl alcohol) (SO), extraction by silica column KIT QIAamp® DNA Investigator of QIAgen® (KC), and the methodology of extraction by previous total demineralization (DP). Finally, the obtaining of the STR profiles from the methodology of greater performance was tested.

Results

The following quantification values were obtained: (i) alkaline medium: 0.068 ± 0.07 ng/μL (SO), 0.021 ± 0.01 ng/μL (KC), and 0.073 ± 0.052 ng/μL (DP); (ii) acidic medium: 0.098 ± 0.064 ng/μL (SO), 0.041 ± 0.029 ng/μL (KC), and 0.068 ± 0.042 ng/μL; (iii) wet-mitotic medium: 0.25 ± 0.061 ng/μL (SO), 0.04 ± 0.027 ng/μL (KC), and 0.15 ± 0.072 ng/μL (DP). Likewise, using the DNA samples obtained by the SO method, complete profiles were obtained for the wet taphonomic context while the alkaline taphonomic process proved to be the most drastic for DNA degradation, presenting a greater number of incomplete profiles.

Conclusions

The methodology of organic extraction was optimal in obtaining DNA from the 3 taphonomic processes evaluated. On the other hand, the wet-fungal taphonomic process is the one that produces the least negative impact on the preservation of DNA from skeletal remains.