Antonia T. Rodrigues

High Potential for Using DNA from Ancient Herring Bones to Inform Modern Fisheries Management and Conservation

Pacific herring (Clupea pallasi) are an abundant and important component of the coastal ecosystems for the west coast of North America. Current Canadian federal herring management assumes five regional herring populations in British Columbia with a high degree of exchange between units, and few distinct local populations within them. Indigenous traditional knowledge and historic sources, however, suggest that locally adapted, distinct regional herring populations may have been more prevalent in the past. Within the last century, the combined effects of commercial fishing and other anthropogenic factors have resulted in severe declines of herring populations, with contemporary populations potentially reflecting only the remnants of a previously more abundant and genetically diverse metapopulation. Through the analysis of 85 archaeological herring bones, this study attempted to reconstruct the genetic diversity and population structure of ancient herring populations using three different marker systems (mitochondrial DNA (mtDNA), microsatellites and SNPs). A high success rate (91%) of DNA recovery was obtained from the extremely small herring bone samples (often <10 mg). The ancient herring mtDNA revealed high haplotype diversity comparable to modern populations, although population discrimination was not possible due to the limited power of the mtDNA marker. Ancient microsatellite diversity was also similar to modern samples, but the data quality was compromised by large allele drop-out and stuttering. In contrast, SNPs were found to have low error rates with no evidence for deviations from Hardy-Weinberg equilibrium, and simulations indicated high power to detect genetic differentiation if loci under selection are used. This study demonstrates that SNPs may be the most effective and feasible approach to survey genetic population structure in ancient remains, and further efforts should be made to screen for high differentiation markers.This study provides the much needed foundation for wider scale studies on temporal genetic variation in herring, with important implications for herring fisheries management, Aboriginal title rights and herring conservation.

Early human use of anadromous salmon in North America at 11,500 y ago.

Significance Fish bones from the 11,500-y-old Upward Sun River site in interior Alaska represent the oldest evidence for salmon fishing in North America. We used ancient DNA analysis to identify the fish specimens as chum salmon (Oncorhynchus keta), and stable isotope analysis to confirm that the salmon were anadromous (sea-run). The exploitation of salmon at this early date is noteworthy because Paleoindians are traditionally portrayed as big-game hunting specialists. Furthermore, the presence of salmon at Upward Sun River over 1,400 km upriver from the coast shows that spawning runs had been established by the end of the last Ice Age. The early availability and use of anadromous salmon has important implications for understanding Paleoindian economies and expansion into North America. Salmon represented a critical resource for prehistoric foragers along the North Pacific Rim, and continue to be economically and culturally important; however, the origins of salmon exploitation remain unresolved. Here we report 11,500-y-old salmon associated with a cooking hearth and human burials from the Upward Sun River Site, near the modern extreme edge of salmon habitat in central Alaska. This represents the earliest known human use of salmon in North America. Ancient DNA analyses establish the species as Oncorhynchus keta (chum salmon), and stable isotope analyses indicate anadromy, suggesting that salmon runs were established by at least the terminal Pleistocene. The early use of this resource has important implications for Paleoindian land use, economy, and expansions into northwest North America.

Evaluating Ancient Whale Exploitation on the Northern Oregon Coast Through Ancient DNA and Zooarchaeological Analysis

ABSTRACT Whales have long been an important part of Pacific Northwest Coast human subsistence and lifeways. Native peoples on the Oregon Coast were not known to hunt whales, but a humpback whale phalange with an embedded bone harpoon at the Par-Tee site (35CLT20) and ethnographic accounts raised the possibility of opportunistic whale hunting. We analyzed a suite of whale remains from Par-Tee and performed ancient DNA-based species identifications on 30 specimens. The assemblage includes gray whales (Eschrichtius robustus, 60.7% of the assemblage), humpbacks (Megaptera novaeangliae, 32.1%), minkes (Balaenoptera acutorostrata, 3.6%), and orcas (Orcinus orca, 3.6%). While the species composition is similar to those found in archaeological deposits from systematic whaling areas in Washington and Vancouver Island, bone modification patterns and element representation reveal important differences. Our analysis demonstrates that whales were likely a supplementary part of human subsistence at Par-Tee and, while opportunistic whale hunting likely occurred, it may have been secondary to scavenging and utilization of beached and/or drift whales.

Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations

Anthropogenic habitat alterations can drive phenotypic changes in wild populations. However, the underlying mechanism (i.e., phenotypic plasticity and/or genetic evolution) and potential to recover previous phenotypic characteristics are unclear. Here we investigate the change in adult migration characteristics in wild salmon populations caused by dam construction and other anthropogenic habitat modifications. Strikingly, we find that dramatic allele frequency change from strong selection at a single locus explains the rapid phenotypic shift observed after recent dam construction. Furthermore, ancient DNA analysis confirms the abundance of a specific adaptive allele in historical habitat that will soon become accessible through a large restoration (i.e., dam removal) project. However, analysis of contemporary samples suggests the restoration will be challenged by loss of that adaptive allele from potential source populations. These results highlight the need to conserve and restore critical adaptive genetic variation before the potential for recovery is lost.

Cheek Tooth Morphology and Ancient Mitochondrial DNA of Late Pleistocene Horses from the Western Interior of North America: Implications for the Taxonomy of North American Late Pleistocene Equus

Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to the end-Pleistocene extinction. Based on the morphological and molecular data analyzed, a caballine (Equus ferus) and a non-caballine (E. conversidens) species were identified from different localities across most of the Western Interior. A second non-caballine species (E. cedralensis) was recognized from southern localities based exclusively on the morphological analyses of the cheek teeth. Notably the separation into caballine and non-caballine species was observed in the Bayesian phylogenetic analysis of ancient mtDNA as well as in the geometric morphometric analyses of the upper and lower premolars. Teeth morphologically identified as E. conversidens that yielded ancient mtDNA fall within the New World stilt-legged clade recognized in previous studies and this is the name we apply to this group. Geographic variation in morphology in the caballine species is indicated by statistically different occlusal enamel patterns in the specimens from Bluefish Caves, Yukon Territory, relative to the specimens from the other geographic regions. Whether this represents ecomorphological variation and/or a certain degree of geographic and genetic isolation of these Arctic populations requires further study.

Ancient DNA analysis of Indigenous rockfish use on the Pacific Coast: Implications for marine conservation areas and fisheries management

Rockfish (Sebastes spp.) are a common marine fish in nearshore and continental shelf environments in the North Pacific Ocean. They are frequently identified in coastal archaeological sites in western North America; however, the morphological similarity of rockfish species limits conventional zooarchaeological identifications to the genus level. This study applies ancient DNA analysis to 96 archaeological rockfish specimens from four sites on separate islands in an archipelago on western Vancouver Island, British Columbia, Canada. Two of the archaeological sites are located within a marine protected area specifically designed to facilitate the recovery of inshore rockfish populations; two sites are located outside this boundary and remain subject to considerable fishing pressure. Using mitochondrial 16S and control region DNA sequences, we identify at least twelve different rockfish species utilized during the past 2,500 years. Identification of rockfish at closely spaced and contemporaneously occupied sites confirms that a variety of Sebastes species were consistently exploited at each site, with more exposed areas having a higher number of species present. Identification results indicate that four of the twelve species did not occur within the conservation area boundary and, instead, were found in sites where commercial and recreational fishing continues to be permitted. This study demonstrates that ancient DNA identifications of archaeological assemblages can complement and expand perspective on modern day fisheries conservation and management in this National Park Reserve and First Nations ancestral territory.