Ancient DNA analysis of northeast Pacific humpback whale (Megaptera novaeangliae)

The main goal of this ancient DNA-based study was to analyze archaeological whale skeletal remains from the west coast of Vancouver Island, British Columbia to investigate population genetic diversities of humpback whales pre-dating industrial whaling. This study also examined whale hunting practices of early indigenous people by revealing potential species selections. Nuu-chah-nulth people are believed to have hunted whales for millennia and numerous whale bones have been recovered from archaeological middens from the region. Whale skeletal remains (N=264) from two archaeological sites (Ts’ishaa and Huu7ii) were analyzed using ancient DNA techniques, with 84% of the samples yielding amplifiable DNA. Nearly 79% of the samples were identified as humpback whale based on cytochrome b and D-loop regions of mtDNA. The analysis was carried out in a dedicated ancient DNA facility, including strict contamination controls and multiple repeats of both PCR and sequencing. No systematic contamination was detected over the course of this study, further supporting the authenticity of the ancient DNA data obtained. The mtDNA haplotypes of 105 of the humpback whales was determined using a 344bp D-loop sequence assembled from multiple overlapping DNA fragments. The genetic diversity of ancient humpback whales (π=0.0147 and h=0.804) falls within the range of modern Pacific humpback whales. Since some of the major genetic signatures can still be observed in today’s populations, results indicate a strong resilience despite industrial whaling during the 19th century. The majority of whale remains in this study were identified as humpback whale and to a lesser degree as grey whale (13%), supporting the notion that the ancestors of the Nuu-chah-nulth people probably practised whaling almost 5000 years ago. Humpback whale could be more easily targeted using traditional techniques based on the whale’s speed and proximity to the shore. Other species such as finback and right whale (among others) only appear in archaeological records younger than 2000BP, which may indicate an improvement of hunting techniques over time.