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

Evaluating Native American Bird Use and Bird Assemblage Variability along the Oregon Coast

Native American use of birds on the Oregon coast is not well known and has never been synthesized to present a regional understanding. We rectify this by analyzing data from 26 zooarchaeological assemblages, including three previously unpublished bird assemblages: Umpqua/Eden (35DO83), Whale Cove (35LNC60), and the Dunes Site (35CLT27). We employ a series of non-parametric randomization tests to directly evaluate patterns of taxonomic diversity, correlations with nearby breeding colonies, and broader procurement strategies discussed in ethnohistorical accounts. We compare the assemblages to contemporary surveys of naturally beached birds as observed by COASST (Coastal Observation Seabird Survey Team) and evaluate whether archaeological specimens were scavenged from the beach. While 71% of the identified bird remains belong to just three families (Anatidae, Alcidae, and Procellariidae), closer analysis reveals the incredible diversity of birds used by Oregon coast Native Americans. The assemblages vary considerably in terms of taxonomic diversity and composition, leading us to conclude that people used birds opportunistically, likely incorporating multiple strategies, including hunting, collecting beached carcasses and targeting cormorant colonies. We hope that the methods and approaches employed here will inspire other archaeologists to devote more attention to bird assemblages, and how their study can inform conservation efforts

Early Holocene Adaptations on the Southern Northwest Coast

Rick Minor (1995, 1997) and R. Lee Lyman (1997) recently debated the archaeological evidence for a "pre-littoral" adaptive stage on the southern Northwest Coast. We review the evolution of the usage of the term "pre-littoral," trace its connections with the earlier works of Richard Ross and Clement Meighan, and argue that such terminology is problematic because its etymology is not consistent with its definition and use by Lyman (1991,1997). This has misled other workers who have taken the term more literally. To alleviate this confusion, we propose that one alternative is to abandon the term "pre-littoral" and use the more neutral "Early Holocene" for this period of southern Northwest Coast prehistory. We also discuss the limited archaeological data for this time period on the Oregon Coast and explain why available data are more accurately represented by an Early Holocene designation

Return to Chetlessenten: The Antiquity and Architecture of an Athabaskan Village on the Southern Northwest Coast

Radiocarbon dates for the historic village of Chetlessenten (the Pistol River site) suggest that the numerous features and artifacts excavated by Hefiin (1966) from this Oregon coast site date primarily between about A.D. 1600 and A.D. 1856. In this paper, we summarize the historical importance of this well-known site, describe poorly documented investigations of the site by University of Oregon archaeologists between 1960 and 1961, report on architectural details for a semisubterranean wood plankhouse that may have been typical of precontact dwellings at Chetlessenten, and discuss the evidence for the antiquity of the site

Investigating the Utility of Birds in Precontact Yup’ik Subsistence: A Preliminary Analysis of the Avian Remains from Nunalleq

Birds have been an integral part of traditional Yup’ik lifeways in the Yukon–Kuskokwim Delta, southwest Alaska, both economically and symbolically. From a subsistence point of view, the rich ethnographic record for the region highlights the importance of this resource as a critical seasonal food and a source of raw materials for clothing and tools. Little is known of bird exploitation in precontact Yup’ik society, however, as a result of limited archaeological research in the region, which thus constrains our ability to understand subsistence strategies prior to Euro-American contact. Recent excavations at the Nunalleq site (sixteenth to seventeenth century AD) have yielded a well-preserved avian assemblage that provides the opportunity to explore the use of birds during the late prehistoric period in the region. In this paper, we present the results of our preliminary zooarchaeological and technological analyses of this material. These new data demonstrate that a relatively wide range of taxa were harvested by precontact Yupiit, reflecting their multiple uses of birds. People not only exploited birds for their meat but also targeted specific taxa for the qualities of their skins for making parkas, their feathers as adornments or for fletching arrows, and their bones for making needles and other tools. Though this study shows a certain degree of continuity between precontact and historic Yup’ik subsistence practices, it also highlights a gradual decline in the non-dietary use of birds and the gradual increase in the intake of birds primarily targeted as sources of food in more recent times.Les oiseaux ont été une partie intégrante des modes de vie traditionnels yup’ik dans le Delta du Yukon-Kuskokwim et le sud-ouest de l’Alaska, autant économiquement que symboliquement. Du point de vue de la subsistance, les riches données ethnographiques pour la région montrent l’importance de cette ressource comme un aliment critique saisonnier et une source de matériaux bruts pour la fabrication de vêtements et d’outils. L’exploitation aviaire dans la société yup’ik precontact est cependant peu connue en raison du manque de recherches archéologiques dans la région, ce qui limite notre aptitude à comprendre les stratégies de subsistance avant le contact euro-américain. Des fouilles récentes sur le site de Nunalleq (XVIe-XVIIe siècles après J.C.) ont mis au jour un assemblage aviaire bien préservé procurant l’opportunité d’explorer l’utilisation des oiseaux pendant la période préhistorique tardive dans la région. Dans cet article, nous présentons les résultats de nos analyses archéozoologique et technique préliminaires de ce matériel. Ces nouvelles données indiquent qu’une relativement grande variété d’oiseaux était exploitée par les Yupiit precontacts, reflétant ainsi l’usage diversifié qu’ils en faisaient. Les oiseaux étaient non seulement exploités pour leur viande mais certains taxons étaient également chassés pour la qualité de leurs peaux dans la fabrication de parkas, de leurs plumes comme parure ou pour l’empennage de flèches, ainsi que de leurs os pour la production d’aiguilles et autres outils. Bien que cette étude montre un certain degré de continuité entre les pratiques de subsistance des Yupiit précontact et historiques, elle souligne un déclin graduel dans l’utilisation non-carnée des oiseaux et une croissance progressive, plus récemment, de l’exploitation d’espèces principalement chassées pour la consommation

An Early Holocene/Late Pleistocene Archaeological Site on the Oregon Coast? Comments on Hall et al. (2005)

In the journal Radiocarbon, Hall et al. (2005:383) claim that 35-CS-9, located in Bandon Ocean Wayside State Park on the southern Oregon coast, is one of the few Oregon coast sites that includes sediments and artifacts dating to the early Holocene and possibly to the late Pleistocene. Their claim for an early Holocene or late Pleistocene human occupation rests on a single radiocarbon date of 11,000 +/140 BP (12,710-12,680 cal BP) taken from charcoal found at least 20 cm below the nearest artifact. Although Hall et al. Compile various kinds of geoarchaeological evidence to support this claim, their case is not convincing. While we applaud aspects of their analyses, the inferences they have drawn are not substantiated by the evidence they present. We agree that 35-CS-9 is a significant site but believe claims for the antiquity of its human use have been exaggerated.The Radiocarbon archives are made available by Radiocarbon and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform February 202

Local and Traditional Knowledge and the Historical Ecologyof Pacific Herring in Alaska

The article focuses on the historical ecology of the Pacific herring, a marine food web resource, in the Gulf of Alaska. It states the hearing conducted by the Alaska Legislature\u27s House special committee on fisheries on the status and management of herring in Southeast Alaska during which Tlingit fisherman Clarence Jackson of Kake notes the disappearance of herring in his lifetime. Information on herring ecology based from Native and non-Native individuals from Southeast communities and archaeological site reports reveal that non-Natives in Southeast Alaska have exploited herring with the development of a herring reduction plant. It underscores the need for conservative management of herring populations, monitoring of herring spawning areas, and conducting otolith and ancient DNA studies

Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics

Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies, and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (i) the efficacy of bleach decontamination, (ii) the effect of decontamination on RAD genotypes, and (iii) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and non-spawning (uncontaminated) herring. Samples were soaked for 10 minutes in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction-site associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes, and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes, and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data, and can impact downstream analyses