Dataset Information

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

ABSTRACT: 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.

SUBMITTER: McKechnie I

PROVIDER: S-EPMC3948274 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature

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

McKechnie Iain I Lepofsky Dana D Moss Madonna L ML Butler Virginia L VL Orchard Trevor J TJ Orchard Trevor J TJ Coupland Gary G Foster Fredrick F Caldwell Megan M Lertzman Ken K

Proceedings of the National Academy of Sciences of the United States of America 20140218 9

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 ...[more]

PMID: 24550468

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Project description:BACKGROUND: The relationships between North Atlantic and North Pacific faunas through times have been controlled by the variation of hydrographic circumstances in the intervening Arctic Ocean and Bering Strait. We address the history of trans-Arctic connections in a clade of amphi-boreal pelagic fishes using genealogical information from mitochondrial DNA sequence data. The Pacific and Atlantic herrings (Clupea pallasii and C. harengus) have basically vicarious distributions in the two oceans since pre-Pleistocene times. However, remote populations of C. pallasii are also present in the border waters of the North-East Atlantic in Europe. These populations show considerable regional and life history differentiation and have been recognized in subspecies classification. The chronology of the inter-oceanic invasions and genetic basis of the phenotypic structuring however remain unclear. RESULTS: The Atlantic and Pacific herrings both feature high mtDNA diversities (large long-term population sizes) in their native basins, but an ocean-wide homogeneity of C. harengus is contrasted by deep east-west Pacific subdivision within Pacific C. pallasii. The outpost populations of C. pallasii in NE Europe are identified as members of the western Pacific C. pallasii clade, with some retained inter-oceanic haplotype sharing. They have lost diversity in colonization bottlenecks, but have also thereafter accumulated abundant new variation. The data delineate three phylogeographic groups within the European C. pallasii: herring from the inner White Sea; herring from the Mezen and Chesha Bays; and a strongly bottlenecked peripheral population in Balsfjord of the Norwegian Sea. CONCLUSIONS: The NE European outposts of C. pallasii are judged to be early post-glacial colonists from the NW Pacific. A strong regional substructure has evolved since that time, in contrast to the apparent broad-scale uniformity maintained by herrings in their native basins. The structure only partly matches the previous biological concepts based on seasonal breeding stocks or geographical subspecies designations. The trans-Arctic herring phylogeography is notably similar to those of the amphi-boreal mollusk taxa Macoma and Mytilus, suggesting similar histories of inter-oceanic connections. We also considered the time dependency of molecular rates, critical for interpreting timing of relatively recent biogeographical events, by comparing the estimates from coding and non-coding mitochondrial regions of presumably different mutation dynamics.

Project description:The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.

Dataset Information

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

Publications

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

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