Abstract
Pacific salmonid (Oncorhynchus spp.) remains are routinely recovered from archaeological sites in northwestern North America but typically lack sexually dimorphic features, precluding the sex identification of these remains through morphological approaches. Consequently, little is known about the deep history of the sex-selective salmonid fishing strategies practiced by some of the region’s Indigenous peoples. Here, we present a DNA-based method for the sex identification of archaeological Pacific salmonid remains that integrates two PCR assays that each co-amplify fragments of the sexually dimorphic on the Y chromosome (sdY) gene and an internal positive control (Clock1a or D-loop). The first assay co-amplifies a 95 bp fragment of sdY and a 108 bp fragment of the autosomal Clock1a gene, whereas the second assay co-amplifies the same sdY fragment and a 249 bp fragment of the mitochondrial D-loop region. This method’s reliability, sensitivity, and efficiency, were evaluated by applying it to 72 modern Pacific salmonids from five species and 75 archaeological remains from six Pacific salmonids. The sex identities assigned to each of the modern samples were concordant with their known phenotypic sex, highlighting the method’s reliability. Applications of the method to dilutions of modern DNA samples indicate it can correctly identify the sex of samples with as little as ~39 pg of total genomic DNA. The successful sex identification of 70 of the 75 (93%) archaeological samples further demonstrates the method’s sensitivity. The method’s reliance on two co-amplifications that preferentially amplify sdY helps validate the sex identities assigned to samples and reduce erroneous identifications caused by allelic dropout and contamination. Furthermore, by sequencing the D-loop fragment used as a positive control, species-level and sex identifications can be simultaneously assigned to samples. Overall, our results indicate the DNA-based method reported in this study is a sensitive and reliable sex identification method for ancient salmonid remains.
Highlights
Pacific salmonids (Oncorhynchus spp.) were and continue to be an important component of many Indigenous fisheries in northwestern North America [1,2]
Since sex among many salmonids is believed to be primarily genetically determined [12], ancient DNA analysis can potentially be used to identify the sex of archaeological salmonid bones
We developed and optimized a DNA-based method for the sex identification of archaeological Pacific salmonid remains that incorporates two PCR assays that co-amplify sexually dimorphic on the Y chromosome (sdY) and an internal positive control (IPC)
Summary
Pacific salmonids (Oncorhynchus spp.) were and continue to be an important component of many Indigenous fisheries in northwestern North America [1,2]. Ethnographic records indicate many Indigenous salmonid fisheries in the region likely employed sex-selective fishing strategies [3,4,5,6,7,8,9,10]. Among some groups, such as the Tlingit [7], sex-selective fishing was one of the resource management strategies used to cultivate salmonid stocks [11]. Documenting the deep history of these ethnographically-documented sex-selective salmonid fishing strategies and their use as a resource management strategy requires the accurate sex identification of archaeological salmonid remains. Since sex among many salmonids is believed to be primarily genetically determined [12], ancient DNA (aDNA) analysis can potentially be used to identify the sex of archaeological salmonid bones
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