Journal of Archaeological Science 99 (2018) 143–152

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Journal of Archaeological Science

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Human use of small forage fish: Improved ancient DNA species identification T techniques reveal long term record of sustainable mass harvesting of fishery in the northeast Pacific Rim ∗ Erica Palmera, Shannon Tushinghamb, , Brian M. Kempa,c a Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, USA b Department of Anthropology, Washington State University, USA c Department of Anthropology, University of Oklahoma, USA

ARTICLE INFO ABSTRACT

Keywords: The bulk storage and mass capture of small forage fish has played a primary role in the cultural traditions and Smelt subsistence practices of many ancient and modern indigenous communities throughout the world. aDNA Archaeologists are improving their recognition of human interaction with these fisheries through the application Species identification of fine-mesh screening techniques and ichthyofaunal analysis of fish bone. Because of the differing lifehistories Northern California of many of these fish, determining their species from archaeological contexts can improve our resolution ofpast Ichythyarchaeology harvesting and consumption patterns. This has remained a challenge for many categories of fish, such as and smelt. Here, we present an improved genetic species identification process that utilizes ancient DNA am- plification techniques involving a reagent-rich PCR protocol (i.e., “Rescue PCR”) and a PCR Enhancer CocktailP (i.e., PEC-P) to identify smelt and other forage fish bone from five archaeological sites located along the northern California (United States) Pacific coast dating to the Late Period (after 1300 cal BP). Through the application of these novel techniques, our species identification success rate increased to 71.2% overall, with some sites having a remarkable 100% success rate. We identified the species of 104 of 146 fish vertebrae, and determined that inhabitants at these sites harvested primarily surf smelt with potentially less emphasis on night smelt. Observations of herring, perch, sculpin and rainbow trout/steelhead were also made. Along with these small surf fish, we found evidence of larger fish such as shark and Pacific hake (common predatory fishinthearea).The study demonstrates a significant breakthrough in ancient DNA identification techniques that resulted inin- formation that speak to the long term continuity of use of mass harvested forage fish by indigenous peoples. The results of this project help establish a better understanding of subsistence and cultural traditions of northern California indigenous communities, with the potential to provide a more global understanding of fishing tech- nologies, sustainability, and mass harvesting of small fishes.

1. Introduction Kaplan et al., 2013; Pikitch et al., 2012; Smith et al., 2011). Archae- ologists are well-positioned to contribute to our understanding of past Small forage fish include a wide variety of pelagic schooling species populations of these fisheries and their use by people over substantial such as smelt, herring, anchovies, and sardines, that are found in the time scales. As archaeological techniques and analyses have become world's oceans. There is a growing appreciation among scientists for the more intricate, small fish vertebrae have been recovered in larger critical importance of these fisheries–not only in terms of their con- quantities at many sites in coastal and island settings reflecting an tribution to the diet of ancient and modern peoples throughout the antiquity for the mass harvest of small fish that has largely remained globe (e.g., Barrett et al., 2004; Biagi et al., 1984; Marcus et al., 1999; unrecognized. Due to the varied life histories and composition of many McKechnie et al., 2014; Moss et al., 2011; Moss et al. 2016; Rodrigues of these fish, species identification can provide a finer grained under- et al. 2018; Tushingham and Christiansen, 2015; Tushingham et al., standing their use by people, who may have targeted certain species 2016; Van Neer et al., 2017), but also as a keystone species that are a depending on an array of factors (seasonal occurrence, fat or other marker of the health of marine environments (e.g., Hall et al., 2012; nutritional content, co-occurrence with other species, etc.). In many

∗ Corresponding author. E-mail address: [email protected] (S. Tushingham). https://doi.org/10.1016/j.jas.2018.09.014 Received 25 June 2018; Received in revised form 30 September 2018; Accepted 30 September 2018 0305-4403/ © 2018 Elsevier Ltd. All rights reserved. E. Palmer et al. Journal of Archaeological Science 99 (2018) 143–152 cases, however, due to the small size and morphological similarity 2001; Moyle, 2002; Borgeld et al., 2007; Tushingham et al., 2013; between the skeletal features of many of these fishes, identification of Tushingham et al., 2018; Newland et al., 2016; Department of Fish and certain species has been difficult or impossible through osteometric Wildlife Marine Region, 2016). Such declines in smelt impact both the faunal analysis alone. Recent strides in ancient DNA (aDNA) analysis, native cultural traditions, as well as the local ecosystem. Therefore, it is however, have allowed researchers to identify greater numbers of fish important to determine harvesting and collection patterns of smelt in bones to the species level, providing critical information for further the past and compare them to present practices making it possible to refining our understanding of prehistoric fishing practices (Jordan monitor temporal changes in surf fish populations. et al., 2010; Moss et al. 2016; Rodrigues et al. 2018; Speller et al., There are seven different species of smelt present in northern 2012). These data can be used to evaluate hypotheses regarding mass California having a wide range of life histories, from spending their harvesting techniques, reliance on storage, contribution of particular entire lives in freshwater to partially in marine environments and only species to the diet, and species presence through time and across space, moving to freshwater habitats to , as well as some species among other topics. spending their entire lives in marine ecosystems (Sweetnam et al., In this paper we report the results of a large scale aDNA study of 2001). Due to their particular taste and usefulness in providing food for species identification of small fish bone from sites in the northeastern marine mammals, birds and aquarium fish, many smelt species have Pacific Rim. We focus on smelt—a family (Osmeridae) of small forage supported sport or commercial fisheries at some point in their history fish found globally with increasing evidence to be a critical resource for (Sweetnam et al., 2001; Moyle, 2002). For instance, in 1995 over two many indigenous groups in the region. The fish bone analyzed in this million pounds of smelt were collected for a value of over $600,000 study are from five sites in northwestern California, USA, where ar- (Sweetnam et al., 2001). Smelt are also key species in their ecosystems, chaeologists have recently demonstrated smelt specifically were used supporting wild predatory populations of marine mammals, birds and by regional native groups for centuries (Tushingham and Christiansen, fish (including salmon and cod) (Sweetnam et al., 2001). The seven 2015; Tushingham et al., 2013; Tushingham et al. 2018). With at least species present in northern California today include: (Hy- seven species of native smelt in this region, each with varying life pomesus transpacificus), wakasaki ( nipponensis), surf smelt histories and patterns of indigenous use and consumption, under- (Hypomesus pretiosus), night smelt (Sprinchus starksi), longfin smelt standing their past use has implications for understanding prehistoric (Spirinchus thaleichthys), eulachon (Thaleichthys pacificus), and whitebait economies, as well as overall historic impacts on local fish populations. smelt (Allosmerus elongatus), each with varying habitat characteristics, Exactly which of these species was harvested by Native Americans re- life histories, and current population status (Text S1). mained elusive because identification to species based on osteometerics is challenging at best, impossible at worst (Tushingham et al., 2017). In 1.2. Northwestern California indigenous groups and use of smelt this study we address this problem through the application of novel aDNA species identification techniques that were developed overa At contact, Native American groups in northwestern California lived period of several years to better understand ancient use of the smelt in permanent Pacific Northwest Coast-style plank house villages along fishery. the coast and rivers of the region for at least 1300 years (Tushingham In particular, our study of fish vertebrae rarely exceeding 5 mgwas 2009; Tushingham, 2013). Key dietary staples included acorns, salmon, made possible by the use of two novel treatments for DNA amplification sea mammals, shellfish, and small surf fish(Gould 1966, 1975; from largely degraded, and particularly small, archaeological samples. Tushingham and Bencze, 2013). After the formation of plank house First, we employed PEC-P, a polymerase chain reaction (PCR) enhancer villages, people became more dependent on the mass extraction of re- cocktail, innovated by Zhang et al. (2010) for DNA Polymerase Tech- sources, complex curated technology, bulk storage methods, and col- nology. Composed of a trehalose sugar, L-carnetine salt, and a de- lector-type strategies (Tushingham 2009; Tushingham, 2013). Storage tergent, PEC-P buffer aids in overcoming PCR inhibition associated with of front-loaded staples such as smelt and salmon became a key over- plant tissues, bile salts and fecal samples when used in conjunction with wintering strategy that developed in concert with lowered mobility OmniKlentaq DNA Polymerase [which has been determined useful in associated with sedentary plank house village life (Tushingham 2009; the study of ancient DNA (Monroe et al., 2013) and is the polymerase Tushingham and Bettinger, 2013). used in our study]. But, as demonstrated in our study, PEC-P has ad- Although salmon have been emphasized as being a fundamental ditional potential in increasing successful ancient DNA amplification. “prime mover” of the culture and economies of indigenous peoples of Each sample was also processed with “Rescue PCR” as described by the northeastern Pacific Rim, the narrow focus on salmon as staple has Johnson and Kemp (2017). In Rescue PCR, all reagents are increased come under increased scrutiny, as regional patterns of subsistence re- proportionally, in this case by 25%. Use of a reagent-rich PCR protocol inforce a more complex scenario (e.g., Butler and Campbell, 2004; such as this can increase amplification presumably through cir- Monks, 1987; Rodrigues et al. 2018; Tushingham and Bettinger, 2013; cumventing the effects of PCR inhibitors (Johnson and Kemp, 2017). Tushingham and Christiansen, 2015). Greater dietary diversity has been Many studies analyzing bulk fish bone composition from primarily recognized through recent methodological advances, such as fish bone small, fragmented bones are unable to establish an accurate composi- analysis, archaeobotanical research, and the application of fine grained tion since abundance is difficult to calculate, however, here we con- archaeological techniques employing small screen sizes and flotation. trolled for this through the use of identifiable fragments (i.e., fish ver- As zooarchaeological recovery techniques and analysis have become tebrae). As demonstrated here, the ability to study DNA from such small more systematic and intricate (i.e., fine mesh sieving and flotation), specimens leads to greater possibilities in the study of archaeological small fish vertebrae have been recovered in larger quantities, sug- DNA all over the world. gesting mass harvest of these fish contributed largely to local pre-con- tact indigenous economies (McKechnie et al., 2014; Moss et al., 2011; 1.1. Smelt species and life histories Moss et al. 2016; Rodrigues et al. 2018; Tushingham et al., 2016, 2017, 2013, 2018). Modern Osmeridae fish populations in northern California include As attested by the ethnographic record, a variety of smelt species species in the following genera: Hypomesus, Allosmerus, Thaleichthys and were, and often continue to be, harvested by indigenous groups along Spirinchus. Surf smelt (Hypomesus pretiosus) and night smelt (Sprinchis the US Pacific Coast from California to British Columbia, Canada. Surf starksi) are the most prevalent species collected by the tribes, re- smelt were of particular importance to Tolowa, Yurok and Wiyot peo- creationalists, and commercial fisheries today. However, in recent ples in northern California, and most ethnographic data about in- decades, surf fish populations have been declining in size, making digenous use of this fishery come from this area (Gould, 1975; species distribution different from that of the past(Sweetnam et al., Tushingham et al., 2013). According to ethnographic data, every year

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