Identifying the sex of archaeological turkey remains using ancient DNA techniques

Abstract

ABSTRACT'!Accurate sex identification of archaeological turkey remains is important for deciphering hunting and husbandry practices in pre-contact North America, particularly in the Southwest United States and Mesoamerica where domestic turkeys were raised. Although the sexual dimorphism of turkeys means that relatively complete elements can be distinguished using osteometric approaches, sexing fragmentary or juvenile remains is challenging. Here, we propose a simple and highly-sensitive coamplification approach which targets highly-repetitive DNA (hrDNA) sequences on the turkey Wchromosome. This technique simultaneously co-amplifies both hrDNA and mitochondrial DNA (mtDNA) fragments: the amplification of the W chromosome identifies the heterogametic sex (females), while the mtDNA fragment acts as an internal positive control to monitor for false negative results. To demonstrate the sensitivity and accuracy of this technique, we applied it to 20 modern turkeys and 117 archaeological turkey bones from 25 sites (ca. AD700-1700), including 32 samples from Sand Canyon Pueblo (AD1250-1300). We amplified ancient DNA from 86% of the ancient remains, demonstrating the sensitivity of the technique for targeting nuclear DNA. The correspondence between morphological size and the genetic sex identification for 100% of the complete skeletal elements demonstrates the accuracy and robusticity of this approach. Although within the larger regional assemblage, more males than females were identified (61% vs 39%), the site-specific analysis at Sand Canyon Pueblo suggests that adult male and female turkeys were present in a relatively even ratio. !

An efficient and reliable DNA-based sex identification method for archaeological Pacific salmonid (Oncorhynchus spp.) remains

“…Our method is potentially susceptible to sdY dropout related to this issue as the IPCs in both the Clock1a / sdY and D-loop/ sdY assays have higher copy numbers than sdY . However, we reduced the potential for sdY dropout and erroneous sex identifications caused by the IPCs outnumbering and outcompeting sdY by designing both assays to favor the amplification of sdY [ 18 ]. Both assays were designed to preferentially amplify sdY by skewing the primer ratio in favour of the sdY primers and targeting an sdY fragment shorter than the IPCs [ 18 ].…”

“…However, we reduced the potential for sdY dropout and erroneous sex identifications caused by the IPCs outnumbering and outcompeting sdY by designing both assays to favor the amplification of sdY [ 18 ]. Both assays were designed to preferentially amplify sdY by skewing the primer ratio in favour of the sdY primers and targeting an sdY fragment shorter than the IPCs [ 18 ]. Among the male samples, the stronger amplifications obtained for sdY relative to those obtained for the IPC, particularly D-loop, indicates sdY was indeed preferentially amplified (Figs 1 and 2 and S1 Fig ).…”

“…The IPC acts as a proxy for the X chromosome, which was not directly targeted due to a lack of data regarding X-linked markers conserved across Pacific salmonids. The IPC is also used to assess whether the failure to amplify sdY is due to its biological absence or a lack of amplifiable template DNA [ 18 ].…”

“…This D-loop fragment was amplified with primers (Smc7 and Smc8) previously published in Yang et al [ 19 ] ( Table 1 ). Following Speller and Yang [ 18 ], we set up the Clock1a / sdY and D-loop/ sdY co-amplifications to preferentially amplify sdY by targeting IPCs longer than the sdY fragment and weighting the primer ratios in favour of the sdY primers. A primer ratio of 1.5:1 ( sdY : Clock1a primers) was used in the Clock1a / sdY assay while a primer ratio of 6:1 ( sdY :D-loop primers) was used in D-loop/ sdY assay.…”

Sexual dimorphism among Mesoamerican turkeys: A key for understanding past husbandry

“…Turkeys show a clear sexual dimorphism enabling an analysis of sex-ratio from archaeological bone sample. It has been studied in Southwestern USA (Badenhorst et al, 2012;Munro, 1994;Speller and Yang, this volume), but Mesoamerica lacks similar studies.…”