Demographic and evolutionary processes in baleen whales inferred from ancient and modern DNA.

摘要

Over the past two centuries, human activities including overharvesting, increased use of fossil fuels, and coastal development have changed the state of the oceans. For many exploited marine species, little is known about population ecology prior to exploitation and other large-scale impacts on ocean ecosystems, and this lack of knowledge may hamper efforts to aid stock recovery and reconstruct damaged ecosystems. In the case of baleen whales, overhunting in the 19 th and 20th centuries decimated many populations, but our understanding of pre-whaling abundance, ecology, migration patterns, and habitat use is limited. However, recent advances in molecular biology and statistical inference have improved our ability to reconstruct demographic processes from genetic data. My dissertation research utilizes DNA data from modern and ancient sources in tandem with coalescent and statistical modeling to further our understanding of historical population ecology and molecular evolution in baleen whales.; First, I surveyed and analyzed DNA variation across the genome of gray whales (Eschrichtius robustus), and used data from nine nuclear introns and two mitochondrial markers to show that populations were three to five times larger in the past than today. In addition, I explored the effects of migration from other populations and pre-whaling population bottlenecks, and documented some of the potential ecological impacts of the inferred decline. Next, I compared rates and patterns of molecular evolution in the control region and cytochrome-b in three baleen whale species (gray whales, humpback whales (Megaptera novaeangliae), and Antarctic minke whales (Balaenoptera bonaerensis)). The mitochondrial control region has been frequently used in phylogeographic studies of whales despite uncertainty in mutation rate. I investigated the extent to which demography versus evolutionary processes may have caused significant variation in patterns between species, and present a new way of calibrating the molecular clock for the control region by constraining values using information from a linked gene. In order to determine current migration rates and population structure across different breeding grounds in gray whales, I collected microsatellite data from modem gray whales, and used demographic modeling to compare the results to the envelope of expectations under different rates and whaling histories. Slight departures from panmixia are apparent in the dataset, consistent with total disruption of migration patterns during whaling followed by reduced migration between breeding areas. Finally, I collected ancient genetic data from prehistoric whale specimens to better understand population dynamics and ecology prior to whaling. Coalescent analyses of ancient genetic data from gray whales show that data are consistent with a significant population bottleneck. Results suggest that a small part of this decline may have occurred in the last 600-700 years, but that the majority of the bottleneck occurred within the last 100-200 years, concurrent with industrial whaling. Ancient data show whaling may also have reduced regional genetic diversity and altered the geographic structuring of haplotypes in the case of North Pacific humpback whales: prehistoric samples show much higher genetic diversity and different spatial structuring of haplotypes compared to modern samples. In summary, these analyses illustrate the utility of genetic data in reconstructing population and evolutionary history in non-model organisms, provides insight into the impacts of whaling and climatic events on baleen whale populations, and demonstrate how multiple sources of data can be integrated to reconstruct the history of marine populations.