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

Abstract

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.

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany

“…Notwithstanding the use of a recently developed extraction protocol aimed to maximize endogenous DNA (54), this rate of success compares favorably to results from mammalian bones whereby the majority of samples-excluding petrous bonestypically yield a few percent endogenous DNA at most (55). Our positive results agree with studies using PCR-based methods that have reported successful amplification from fish bones (56)(57)(58)(59)(60) in some cases up to 10,000 y old (61). The observation that porous, light fish bones can yield whole genome shotgun libraries with high levels of endogenous DNA underscores our lack of understanding of DNA preservation in different types of animal bone.…”

Hair, Bone Plates and Coprolites: Ancient DNA Research on Rare Archaeological Materials

“…A r c h a e o g e n e t i c a n a l y s e s o f f i s h b o n e s Until now, fish remains have rarely been used for ancient DNA analyses, even though they can be found at archaeological sites in high numbers, and their potential in palaeoecological and palaeoeconomical questions has occasionally been demonstrated (Arndt et al 2003;Speller et al 2012;Shirak et al 2013; BALTICA 23 Hutchinson et al 2015). In the Baltic Sea region, during the last decade, it was sturgeon that came into the focus of genetic research.…”

Sustained prehistoric exploitation of a Marshall Islands fishery: ichthyoarchaeological approaches, marine resource use, and human-environment interactions on Ebon Atoll

“…The application of diversity indices, measures of trophic alteration, aDNA analysis, and stable isotope analysis not only track changes in fish community structure and range as represented in the archaeological record but contribute unique perspectives to modern fisheries research (e.g., Butler and Delacorte 2004;Pauly et al 1998;Van Neer and Ervynck 2009). A balance between marine research and social science datasets is required, but the emphasis on establishing multidisciplinary research projects (e.g., Sea Around Us Project and Oceans Past Platform; see also Barrett et al 2004a;Jackson et al 2001;Kittinger et al 2011;Miller et al 2011;Speller et al 2012) will continue to redirect this discourse and ideally provide holistic conservation and management outcomes (Christie 2011).…”

“…Stable isotope, aDNA, and DNA analysis have become critical components of interdisciplinary historical ecology research and provide insight into changes in population structure, interaction, adaptation, population size estimates, trophic ecology, and alterations to prey, habitat, and foraging preferences of taxa over time-also including humans. Speller et al (2012) used aDNA to study genetic diversity and population structure of prehistoric herring populations, research key to understanding temporal and spatial genetic variations in fish populations (see Pääbo et al 2004;Willerslev and Cooper 2005). aDNA can be utilised to identify species introductions and translocations, particularly relevant to island archaeology (Rick et al 2014: 688) Leach et al 1998Leach et al , 2003.…”

“…Globally, these approaches have provided insights into long-term anthropogenic and climatic alterations to marine ecosystems, population baseline data, and generated key directives for restoration frameworks (e.g., Barrett et al 2004;Jackson et al 2001;McClanahan and Omukoto 2011;Miller et al 2011;Speller et al 2012;Thornton et al 2010;Wake et al 2013). Similar research agendas have been implemented within the Pacific (e.g., Dalzell 1998;Kittinger et al 2011;, however, these themes are yet to be considered using ichthyoarchaeological data from the Republic of the Marshall Islands (RMI).…”