Mitochondrial DNA preservation across 3000-year-old northern fur seal ribs is not related to bone density: Implications for forensic investigations § Jodi Lynn Barta a,b,c , Cara Monroe a,b,d , Susan J. Crockford e,f , Brian M. Kemp a,b, * a School of Biological Sciences, Washington State University, Pullman, WA 99164, USA b Department of Anthropology, Washington State University, Pullman, WA 99164, USA c Department of Biological and Health Sciences, Madonna University, Livonia, MI 48150, USA d Department of Anthropology, University of California-Santa Barbara, Santa Barbara, CA 93106, USA e Pacific Identifications Inc., 6011 Oldfield Road, R.R. #3, Victoria, BC V9E 2J4, Canada f Department of Anthropology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada 1. Introduction It has been over two decades since DNA was first recovered from ancient bones [1] and DNA has since proved invaluable for forensic identification [2–4]. Reflecting upon the first successful genetic identification of murder victims’ skeletal remains, Hagel- berg et al. [2, p. 429] noted that, ‘‘first, it is unclear what proportion of skeletal remains will yield sufficient human DNA. . .’’ and, ‘‘second, in the case of an apparent exclusion based on bone DNA analysis, it may be impossible to determine whether the exclusion is authentic or is inadvertently derived from contaminating material.’’ These possible drawbacks stem from the fact that DNA preserved in ancient and degraded remains are generally recovered in low copy number and are short with regards to strand length [5–7]. Molecules may also exhibit some additional chemical modifications (i.e., ‘‘miscoding lesions’’) [6,8–10]. Consequently, retrieval of ancient and degraded DNA is challenging, and attempts to authenticate human data can be compromised both by contamination, and by miscoding lesions that can appear as ‘‘mutations’’, when in fact they are artifacts. It is interesting to note that, as these challenges were encountered in forensic and ancient DNA (aDNA) investigations, remarkably similar protocols for minimizing contamination [11,12] were developed for field workers in the respective disciplines (e.g., local law enforcement and archeologists). Following Hagelberg et al.’s [2] assertion that not all skeletal remains may contain enough DNA for successful typing, forensic research has sought to determine which skeletal elements are superior in their preservation of DNA, regardless of postmortem interval, depositional and taphonomic history, and/or difficulty associated with processing of the material [13–17]. Despite forensic genetic analyses of over 31,000 skeletal elements that date as early as AD 1941 (summarized in Table 1), the Forensic Science International 239 (2014) 11–18 A R T I C L E I N F O Article history: Received 25 January 2013 Received in revised form 4 February 2014 Accepted 25 February 2014 Available online 12 March 2014 Keywords: Quantitative PCR Ancient DNA Bone density A B S T R A C T While recent forensic research has focused on determining which skeletal elements are superior in their preservation of DNA over the long term, little focus has been placed on measuring intra-element variation. Moreover, there is a general belief that dense (cortical) bone material will contain better- preserved DNA than does spongy (cancellous) bone. To address these ideas, quantitative PCR was used to estimate the degree of mitochondrial DNA (mtDNA) preservation variance across sections of 19 northern fur seal ribs (Callorhinus ursinus) that date to 3000 years before present. Further, we developed a measure called the ‘‘density index’’ that was used to gauge the relative densities of the rib sections studied here to determine if density was an appropriate predictor of preservation. The average preservation among the samples was significantly different (ANOVA, p = 1.9  10 9 ) with only 15% of the total variance observed within samples. However, 12 of the 19 specimens (63.2%) exhibited at least an order of magnitude difference in mtDNA preservation across the whole. Regression of the amount of mtDNA extracted per gram of bone material against the density index of the bone from which it was extracted demonstrates no relationship between these variables (R 2 = 0.03, p = 0.28). ß 2014 Elsevier Ireland Ltd. All rights reserved. § The opinions, findings, and conclusions or recommendations expressed in this publication/program/exhibition are those of the authors and do not necessarily reflect those of the Department of Justice. * Corresponding author at: Department of Anthropology, Washington State University, Pullman, WA 99164, USA. Tel.: +1 509 335 7403; fax: +1 509 335 3999. E-mail address: bmkemp@wsu.edu (B.M. Kemp). Contents lists available at ScienceDirect Forensic Science International jou r nal h o mep age: w ww.els evier .co m/lo c ate/fo r sc iin t http://dx.doi.org/10.1016/j.forsciint.2014.02.029 0379-0738/ß 2014 Elsevier Ireland Ltd. All rights reserved.