4. Discussion
Genomic approaches are gaining importance in conservation biology. Lower costs of sequencing and improvements in data analysis in non-model organism has made these genetic tools more accessible. We present a gold-standard draft genome of a NA blue whale assembled using integrated second generation short-read and third generation long-read sequencing data. The genome was used herein to discern for the first time the population structure and demographic history of blue whales in the NA using samples from present-day whales and whales collected in the early 1900’s through the 20th century, with the earliest samples representing the blue whale population at the onset of industrial whaling. Additionally, we investigated genes that appear to be under positive selection in blue whales.
Our analysis of whole genome and mitochondrial DNA from present-day (latitudes ~ 44°N to 79°N) and historic samples revealed low population structuring among NA blue whales, indicating that the NA blue whales comprise a single panmictic population. This is in contrast to evidence gathered from satellite tracking and observational studies (Lesage et al., 2017; Ramp & Sears, 2013, Silva et al., 2013), and points to the complexities of studying large marine mammals in situ and the importance of whole genome analyses to better understand population structure. The full mitochondrial analysis suggests that the historical samples from the South Atlantic and Antarctica are not as genetically distinct from North Atlantic whales as nuclear DNA analyses suggest. Further studies, with larger sample sizes, particularly for Antarctic blue whales are needed including nuclear and mitochondrial DNA analyses allowing us to test different aspects of population demography
We observed relatively high genome-wide heterozygosity in present-day NA blue whales and one historical Antarctic whale sample, consistent with reports of high heterozygosity observed in Chilean and other Antarctic whales (Torres-Florez et al., 2014). Despite being hunted to the brink of extinction, with the population size being reduced by more than 96%, blue whales have retained high genetic variability. Thus, possible long-term effects of severe bottlenecking may not be fully evident in extant populations. High genetic diversity within the species is promising for species recovery, if low population numbers do not persist for an extended period of time. Similar high genetic diversity has been observed in other species that have experienced extreme overexploitation, such as Antarctic fur seals, but have since begun to recover through conservation efforts (Paijmans et al., 2020). Our examination of the demographic history of NA blue whales modeled on genome wide heterozygous sites found a decline in blue whale numbers in the North Atlantic over the last several hundreds of thousands of years during multiple periods of glaciation. The PSMC methodology loses resolution in relatively recent time periods and thus does not reveal the impact of 19th and 20th century whaling. Our results are similar to observations from an earlier study by Árnason et al., (2018), although use of our blue whale de novoassembly allowed for a better estimation of the effective population size at the end of the last glaciation providing an estimate of what the NA blue whale population size may have been prior to whaling.
Blue and fin whales are the two largest animals on earth and can hybridize even though they are not sibling species (~8.35 million years since divergence) (Árnason et al., 2018). Interspecific hybridization can occur naturally or result from disruption of breeding due to anthropogenic effects. Hybridization with introgression can in some cases lead to the extinction of distinct species through swamping of the genome of one of the hybrid pairs. We demonstrated gene flow between blue and fin whales in all of our present-day and four (of six) historical samples; two whales from the early 20th century lacked introgression. While our sample size is very limited, this possible increase in the rate of introgression might be related to reduced mate choice in blue whales due to their reduced population size after industrial whaling. This hypothesis should be further tested with larger sample sizes of whales from pre- and post-whaling. The gene flow that we recorded between fin whales and NA blue whales was not evident in previous studies (Árnason et al., 2018; Westbury et al., 2019) that were done without the blue whale genome as a reference. The direction of gene flow was fin to blue whale in all present-day blue whales analyzed from NA, consistent with the observation of several interspecific hybrids resulting from mating of a male fin whales and female blue whales (Pampoulie et al., 2020).
We also assembled and annotated the NA blue whale transcriptome, allowing for functional analysis of positively selected blue whale genes. We identified several nAChR signaling pathway genes that are associated with cancer development (Schuller, 2009) and also the selection of genes involved in apoptosis. Earlier studies of suppression of cancer in marine mammals detected positive selection of another apoptosis pathway gene (ETNK1 ) in humpback whales (Tollis et al., 2019) and positive selection of genes regulating nucleotide repair, chromatin structure and transcription in bowhead whales (Keane et al., 2015). Sperm whale gene analysis has revealed several cancer genes (MMP7, CASP12 and PRSS33 ) that were positively selected (Warren et al., 2017). Diseases like cancer which are associated with age and large body size, surprisingly do not affect large aquatic mammals (Keane et al., 2015; Tollis et al., 2019). The gene pathways involved are not fully understood. Our analysis indicates functional enrichment of genes in the nAChR pathway that might further elucidate the underlying mechanism of cancer suppression. This might be a useful tool in medical research.
In summary, the results from our study suggest that the blue whales in the NA comprise a single population. Thus, future conservation assessment and planning should be conducted in a holistic framework viewing NA blue whales as a single population. Hybridization of blue whales with fin whales is frequent in the NA and introgression might be increasing in the present population. Future rates of introgression should be monitored. The genetic variability in NA blue whales is high and the slow recovery of blue whales in the NA is not associated with reduction of heterozygosity via bottlenecking in extant populations. However, it may become a factor in the future if populations do not increase from their current low levels. Rates of introgression with fin whales should be monitored. Further studies with a larger sample size for present-day and historical blue whales from around the world could be used to examine changes in levels of heterozygosity and resolve questions regarding gene flow among populations of blue whales from different oceans to enhance conservation planning efforts.