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Effects of ancient anthropogenic clam gardens on the growth, survival, and transcriptome of Pacific littleneck clams (Leukoma staminea)

Monique R. Raap, Helen J. Gurney-Smith, Sarah E. Dudas, Christopher M. Pearce, Jong S. Leong, Ben J.G. Sutherland, View ORCID ProfileBen F. Koop
doi: https://doi.org/10.1101/2022.09.09.507365
Monique R. Raap
1Department of Biology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
2Hakai Institute, Quadra Island, British Columbia, Canada, V0P 1H0
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Helen J. Gurney-Smith
1Department of Biology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
2Hakai Institute, Quadra Island, British Columbia, Canada, V0P 1H0
3Department of Biology and Department of Fisheries and Aquaculture, Vancouver Island University, Nanaimo, British Columbia, Canada, V9R 5S5
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Sarah E. Dudas
1Department of Biology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
2Hakai Institute, Quadra Island, British Columbia, Canada, V0P 1H0
3Department of Biology and Department of Fisheries and Aquaculture, Vancouver Island University, Nanaimo, British Columbia, Canada, V9R 5S5
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Christopher M. Pearce
4Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada, V9T 6N7
5Department of Geography, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
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Jong S. Leong
1Department of Biology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
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Ben J.G. Sutherland
1Department of Biology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
6Sutherland Bioinformatics, Lantzville, British Columbia, Canada, V0R 2H0
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  • For correspondence: Helen.Gurney-Smith@dfo-mpo.gc.ca
Ben F. Koop
1Department of Biology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
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  • ORCID record for Ben F. Koop
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Abstract

Clam gardens are habitat modifications established by coastal Indigenous Peoples of northwest North America to enhance intertidal clam habitat productivity to provide secure and reliable local food resources. These gardens were established long ago and are mostly unmaintained in present times. To determine whether unmaintained clam gardens still provide a more productive and beneficial habitat than unmodified clam beaches, Pacific littleneck clams (Leukoma staminea) were transplanted to unmaintained clam gardens or unmodified reference beaches and then evaluated for growth, survival, and transcriptomic signatures of the gill and digestive gland after 16 weeks. All beaches in the study were characterized for sediment grain-size distribution, carbonate concentration, and organic content to identify sediment characteristics that may differ between clam garden and reference sites, as well as potentially contribute to differences in clam productivity. Clam growth and survival, sediment grain-size distribution, and carbonate and organic content were not significantly affected by unmaintained clam gardens. Wide variations in survival, growth, and sediment characteristics were observed among beaches. Examining across beach location resulted in the identification of significant negative effects of small rocks (2.00 – 4.75 mm), and silt (< 63 µm) on both growth and survival. Sand (250 – 500 µm) had a significant positive influence on both growth and survival while fine sand (125 – 250 µm) had a significant positive effect only on growth. Coarse sand (0.50 – 1.00 mm) had a significant positive effect on survival, while very fine sand (63 – 125 µm), carbonate, and organic content all had significant negative effects. To evaluate transcriptomic effects, a de novo transcriptome for L. staminea was assembled. The final assembly contained 52,000 putative transcripts and those specific to each of the two tissues were identified. This revealed that similar functional categories were enriched in tissue-specific genes, but each tissue had its own transcripts comprising the categories. Transcriptomic analysis revealed differential expression in individuals from clam gardens, and although this effect was small in terms of the numbers of genes, specific response genes were identified consistently in both tissues. In summary, while the unmaintained clam gardens did not impact clam growth and survival over the 16 weeks of the study, it did have an effect at the level of the transcriptome. Furthermore, correlations of transcripts associated with either high or low survival provide new insights into ecological associations of these genes in this non-model organism. In summary, localized environmental factors are likely to have a greater influence on Pacific littleneck clam physiology, growth, and survival than the presence/absence of unmaintained clam gardens.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Data Deposition: Raw RNA-sequencing data have been uploaded to SRA under BioProject PRJNA818991, BioSamples SAMN26893882–SAMN26893909.

  • https://github.com/bensutherland/Simple_reads_to_counts

  • https://github.com/raapm/ms_clam_garden

  • https://doi.org/10.6084/m9.figshare.19735753

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 13, 2022.
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Effects of ancient anthropogenic clam gardens on the growth, survival, and transcriptome of Pacific littleneck clams (Leukoma staminea)
Monique R. Raap, Helen J. Gurney-Smith, Sarah E. Dudas, Christopher M. Pearce, Jong S. Leong, Ben J.G. Sutherland, Ben F. Koop
bioRxiv 2022.09.09.507365; doi: https://doi.org/10.1101/2022.09.09.507365
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Effects of ancient anthropogenic clam gardens on the growth, survival, and transcriptome of Pacific littleneck clams (Leukoma staminea)
Monique R. Raap, Helen J. Gurney-Smith, Sarah E. Dudas, Christopher M. Pearce, Jong S. Leong, Ben J.G. Sutherland, Ben F. Koop
bioRxiv 2022.09.09.507365; doi: https://doi.org/10.1101/2022.09.09.507365

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