Commercial whaling during the 20th century drastically reduced many populations of great whales in the Southern Hemisphere. The Antarctic blue whale, for example, is estimated to have been reduced to less than 0.1% of its original abundance based on catch records and population dynamic models. Despite this population bottleneck, several contemporary populations of great whales are characterized by a relatively high mitochondrial DNA (mtDNA) diversity, potentially as a result of the long life span and the short duration of the exploitation bottleneck. However, few studies have attempted to compare historical diversity from artifacts of early commercial whaling to contemporary samples of living populations of whales. In this dissertation, I explored the impact of 20th century commercial whaling on the genetic diversity of great whales in the South Atlantic, using bones from early whaling stations that operated around the Antarctic Peninsula and the South Atlantic island of South Georgia at the beginning of the 20th century. Over 200,000 whales were taken from these stations from 1904 to 1965. The number of most species in the vicinity of the former whaling stations still remains low today. In Chapter Two, I used ancient DNA methods to extract and amplify mtDNA control region sequences to identify the species of a collection of 94 whale bone samples from the Antarctic Peninsula and South Georgia. I successfully identified to species 67 of the 94 whale bones collected from 12 locations of former whaling stations; eight on the Antarctic Peninsula and four on South Georgia. The species composition of the bone collection from South Georgia and the Antarctic Peninsula was similar to the catch history of the early years of whaling in the Antarctic region, supporting my inference that these bones represent ‘pre-whaling’ diversity. I then added the sequences from the samples to a collection of 231 whale bones from a previous study to provide the largest collection to date of historical DNA from great whales. In Chapter Three, I compared historical and contemporary mtDNA control region diversity of three great whale species exploited at South Georgia during the 20th century: the blue, humpback and fin whale. For this, I also had access to mtDNA diversity estimates from contemporary whales in the South Atlantic and Southern Ocean. Comparisons of historical and contemporary mtDNA control region haplotypes identified maternal lineages not present in the contemporary populations that may have been lost due to exploitation. I identified a significant difference in mtDNA haplotype frequencies of contemporary and historical samples in the blue and humpback whale. These results combined with the lack of return of great whales to South Georgia suggested a loss of feeding aggregations from this region.
In Chapter Four, I used next-generation sequencing to assess the quality and quantity of endogenous DNA in the historical bone samples of Antarctic blue whales. I used a shotgun-sequencing approach to assess endogenous content in 30 samples. Eighteen of the 30 samples were sequenced using two different methods for ancient DNA extraction. The historical Antarctic blue whale bone samples had a variable endogenous DNA content as measured by reference mapping to the closest relative with a genome available, the North Pacific minke whale. The modified ancient DNA extraction protocol increased the endogenous content from an average of 6.26% to 15.69%. The highest endogenous content in an historical sample was ~48 %. I quantified the single-copy nuclear DNA in the extracts using 384 genomic loci described in a North Pacific blue whale to confirm the endogenous content in the extracts. The average mitochondrial DNA content within the samples was similar between extraction methods and accounts for 0.13% of the endogenous DNA. I reconstructed near-complete mitochondrial genomes for 20 bone samples, providing the first mitochondrial genome sequences of Antarctic blue whales at the onset of 20th century commercial whaling. A comparison of these to an unpublished collection of contemporary mitochondrial genome sequences showed no surviving maternal lineages. The description of mitochondrial and nuclear DNA in the historical Antarctic blue whale samples demonstrated the potential for future descriptions of historical Antarctic blue whale diversity using NGS. The research presented in this dissertation describes the historical genetic diversity of ‘pre-whaling’ populations in the Southern Hemisphere and provided the first evidence of a loss of mtDNA diversity in the South Atlantic humpback and Antarctic blue whales. The value of this ‘molecular archive’ preserved in these beached bones was further confirmed with the genomic sequencing described in Chapter Four and stressed the importance of preservation of this resource with the impending threat of climate change in the Antarctic.