11,500 y of human-clam relationships provide long-term context for intertidal management in the Salish Sea, British Columbia.

Historical ecology can provide insights into the long-term and complex relationships between humans and culturally important species and ecosystems, thereby extending baselines for modern management. We bring together paleoecological, archaeological, and modern clam records to explore the relationship between humans and butter clams (Saxidomus gigantea) throughout the Holocene in the northern Salish Sea of British Columbia, Canada. We compare butter clam size and growth patterns from different temporal, environmental, and cultural contexts spanning 11,500 y to present. Butter clam size and growth were restricted in early postglacial times but increased over the next few millennia. During the early-Late Holocene, humans took increasing advantage of robust clam populations and after 3.5 ka, began constructing clam gardens (intertidal rock-walled terraces). Environmental and cultural variables, including coarse substrate, stabilized sea surface temperature, and the presence of a clam garden wall, increased clam growth throughout the Holocene. Measurements of clams collected in active clam gardens and deposited in middens suggest that clam gardens as well as other mariculture activities enhanced clam production despite increased harvesting pressure. Since European contact, decline of traditional management practices and increases in industrial activities are associated with reduced clam size and growth similar to those of the early postglacial clams. Deeper-time baselines that more accurately represent clam population variability and allow us to assess magnitudes of change throughout time as well as the complex interactions among humans and clams are useful for modern marine resource management.

Archaeological data provide alternative hypotheses on Pacific herring (Clupea pallasii) distribution, abundance, and variability.

Pacific herring (Clupea pallasii), a foundation of coastal social-ecological systems, is in decline throughout much of its range. We assembled data on fish bones from 171 archaeological sites from Alaska, British Columbia, and Washington to provide proxy measures of past herring distribution and abundance. The dataset represents 435,777 fish bones, dating throughout the Holocene, but primarily to the last 2,500 y. Herring is the single-most ubiquitous fish taxon (99% ubiquity) and among the two most abundant taxa in 80% of individual assemblages. Herring bones are archaeologically abundant in all regions, but are superabundant in the northern Salish Sea and southwestern Vancouver Island areas. Analyses of temporal variability in 50 well-sampled sites reveals that herring exhibits consistently high abundance (>20% of fish bones) and consistently low variance (<10%) within the majority of sites (88% and 96%, respectively). We pose three alternative hypotheses to account for the disjunction between modern and archaeological herring populations. We reject the first hypothesis that the archaeological data overestimate past abundance and underestimate past variability. We are unable to distinguish between the second two hypotheses, which both assert that the archaeological data reflect a higher mean abundance of herring in the past, but differ in whether variability was similar to or less than that observed recently. In either case, sufficient herring was consistently available to meet the needs of harvesters, even if variability is damped in the archaeological record. These results provide baseline information prior to herring depletion and can inform modern management.

The global relevance of locally grounded ethnobiology.

While ethnobiology is a discipline that focuses on the local, it has an outstanding, but not yet fully realized potential to address global issues. Part of this unrealized potential is that universalistic approaches often do not fully recognize culturally grounded perspectives and there are multiple challenges with scaling up place-based research. However, scalability is paramount to ensure that the intimate and context-specific diversity of human-environmental relationships and understandings are recognized in global-scale planning and policy development. Here, we identify four pathways to enable the scalability of place-based ethnobiological research from the ground up: local-to-global dialogues, aggregation of published data, multi-sited studies, and geospatial analyses. We also discuss some major challenges and consideration to encourage continuous reflexivity in these endeavours and to ensure that scalability does not contribute to unnecessarily decontextualizing, co-opting, or overwriting the epistemologies of Indigenous Peoples and local communities. As ethnobiology navigates multiple scales of time and space and seeks to increase its breadth, this study shows that the use of deliberately global approaches, when carefully nested within rich field-based and ecological and ethnographically grounded data, can contribute to: (1) upscaling case-specific insights to unveil global patterns and dynamics in the biocultural contexts of Indigenous Peoples and local communities; (2) bringing ethnobiological knowledge into resolutions that can influence global environmental research and policy agendas; and (3) enriching ethnobiology's field-based ethos with a deliberate global analytical focus.

Ancient DNA reveals phenological diversity of Coast Salish herring harvests over multiple centuries.

Phenological diversity in food resources prolongs foraging opportunities for consumers and buffers them against environmental disturbances. Such diversity is particularly important in forage fish such as Pacific herring (Clupea pallasii), which are foundational to coastal food webs and fisheries. While the importance of phenological diversity is well-known from contemporary studies, the extent to which different populations contribute to fisheries over long time scales is mostly unknown. In this study, we investigated the relative contributions of genetically and phenologically distinct herring populations to Indigenous Peoples' food systems over multiple centuries, using ancient DNA extracted from archaeological herring bones. These bones were excavated from two Coast Salish archaeological sites (Burton Acres Shell Midden and Bay Street Shell Midden) in the Puget Sound region, USA. Using genetic stock identification from seven nuclear DNA markers, we showed that catches at the two sites in central Puget Sound were dominated by January-February and March-April spawners, which are the contemporary spawning groups in the vicinity of the sites. However, May spawners were detected in the older Burton Acres assemblage (dated to 910-685 cal BP), and a mixed stock analysis indicated that catches at this site consisted of multiple populations. These results suggest that Coast Salish ancestors used a portfolio of herring populations and benefited from the ecological resource wave created by different spawning groups of herring. This study of ancient DNA allowed us to glimpse into Indigenous traditional food and management systems, and it enabled us to investigate long-term patterns of biodiversity in an ecologically important forage fish species.

3500 years of shellfish mariculture on the Northwest Coast of North America.

Ancient systems of mariculture were foundations of social-ecological systems of many coastal Indigenous Peoples. However, since such systems either do not leave tangible remains in the archaeological record, and/or are hard to date, we know little about their development and use. Clam gardens, traditional mariculture features located within the intertidal zone along the Northwest Coast of North America, are composed of a rock wall positioned at the low tide mark and a flattened terrace on the landward side of the wall. Because these features are largely composed of rock and sediment, and have complex formation histories, they can be difficult to age. On northern Quadra Island, British Columbia, we identify three variations in clam garden form, constructed in different geomorphological settings, each of which require different sampling approaches to obtain ages on construction and ongoing use. To age the clam gardens, we consider radiocarbon dating of invertebrates that inhabit beach deposits (both pre- and post-garden construction), and the relationship of the gardens and clam samples to the local sea level history and taphonomic processes. Within our study area, we find clam gardens have been in use for 3500 years, likely corresponding to other social and ecological changes of the time. These data allow us to formulate guidelines on samples most suitable to constrain the age of initial and on-going wall construction and use of clam gardens, which can be extrapolated to dating other ancient mariculture features in other regions. Such dating programs are the foundation for understanding the long-term development of traditional marine management practices and how they are situated in broader social-ecological systems.

Intraspecific DNA contamination distorts subtle population structure in a marine fish: Decontamination of herring samples before restriction-site associated 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 (a) the efficacy of bleach decontamination, (b) the effect of decontamination on RAD genotypes and (c) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and nonspawning (uncontaminated) herring. Samples were soaked for 10 min 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.

Between a rock and a soft place: Using optical ages to date ancient clam gardens on the Pacific Northwest.

Rock-walled archaeological features are notoriously hard to date, largely because of the absence of suitable organic material for radiocarbon dating. This study demonstrates the efficacy of dating clam garden wall construction using optical dating, and uses optical ages to determine how sedimentation rates in the intertidal zone are affected by clam garden construction. Clam gardens are rock-walled, intertidal terraces that were constructed and maintained by coastal First Nation peoples to increase bivalve habitat and productivity. These features are evidence of ancient shellfish mariculture on the Pacific Northwest and, based on radiocarbon dating, date to at least the late Holocene. Optical dating exploits the luminescence signals of quartz or feldspar minerals to determine the last time the minerals were exposed to sunlight (i.e., their burial age), and thus does not require the presence of organic material. Optical ages were obtained from three clam garden sites on northern Quadra Island, British Columbia, and their reliability was assessed by comparing them to radiocarbon ages derived from shells underneath the clam garden walls, as well as below the terrace sediments. Our optical and radiocarbon ages suggest that construction of these clam garden walls commenced between ~1000 and ~1700 years ago, and our optical ages suggest that construction of the walls was likely incremental and increased sedimentation rates in the intertidal zone by up to fourfold. Results of this study show that when site characteristics are not amenable to radiocarbon dating, optical dating may be the only viable geochronometer. Furthermore, dating rock-walled marine management features and their geomorphic impact can lead to significant advances in our understanding of the intimate relationships that Indigenous peoples worldwide developed with their seascapes.

Ancient clam gardens increased shellfish production: adaptive strategies from the past can inform food security today.

Maintaining food production while sustaining productive ecosystems is among the central challenges of our time, yet, it has been for millennia. Ancient clam gardens, intertidal rock-walled terraces constructed by humans during the late Holocene, are thought to have improved the growing conditions for clams. We tested this hypothesis by comparing the beach slope, intertidal height, and biomass and density of bivalves at replicate clam garden and non-walled clam beaches in British Columbia, Canada. We also quantified the variation in growth and survival rates of littleneck clams (Leukoma staminea) we experimentally transplanted across these two beach types. We found that clam gardens had significantly shallower slopes than non-walled beaches and greater densities of L. staminea and Saxidomus giganteus, particularly at smaller size classes. Overall, clam gardens contained 4 times as many butter clams and over twice as many littleneck clams relative to non-walled beaches. As predicted, this relationship varied as a function of intertidal height, whereby clam density and biomass tended to be greater in clam gardens compared to non-walled beaches at relatively higher intertidal heights. Transplanted juvenile L. staminea grew 1.7 times faster and smaller size classes were more likely to survive in clam gardens than non-walled beaches, specifically at the top and bottom of beaches. Consequently, we provide strong evidence that ancient clam gardens likely increased clam productivity by altering the slope of soft-sediment beaches, expanding optimal intertidal clam habitat, thereby enhancing growing conditions for clams. These results reveal how ancient shellfish aquaculture practices may have supported food security strategies in the past and provide insight into tools for the conservation, management, and governance of intertidal seascapes today.

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.