Polymetamorphism in the Richmond Area, Vermont

Guidebook for field trips in Vermont: 64th annual meeting October 13, 14, 15, 1972 Burlington, Vermont: Trip B-1

Ecological impacts of non-native Pacific oysters (Crassostrea gigas) and management measures for protected areas in Europe

Pacific oysters are now one of the most ‘globalised’ marine invertebrates. They dominate bivalve aquaculture production in many regions and wild populations are increasingly becoming established, with potential to displace native species and modify habitats and ecosystems. While some fishing communities may benefit from wild populations, there is now a tension between the continued production of Pacific oysters and risk to biodiversity, which is of particular concern within protected sites. The issue of the Pacific oyster therefore locates at the intersection between two policy areas: one concerning the conservation of protected habitats, the other relating to livelihoods and the socio-economics of coastal aquaculture and fishing communities. To help provide an informed basis for management decisions, we first summarise evidence for ecological impacts of wild Pacific oysters in representative coastal habitats. At local scales, it is clear that establishment of Pacific oysters can significantly alter diversity, community structure and ecosystem processes, with effects varying among habitats and locations and with the density of oysters. Less evidence is available to evaluate regional-scale impacts. A range of management measures have been applied to mitigate negative impacts of wild Pacific oysters and we develop recommendations which are consistent with the scientific evidence and believe compatible with multiple interests. We conclude that all stakeholders must engage in regional decision making to help minimise negative environmental impacts, and promote sustainable industry development

Supplement 1. Detailed worked tutorials of analyses performed in this paper, including R code for mixed effects models and example data.

<h2>File List</h2><div> <p><a href="S1_tutorial.pdf">S1_tutorial.pdf</a> (MD5: b9ce89e5e69463afbfc055a2943824e6)  --  worked examples for the analysis of growth variation within and among individuals and populations</p> <p><a href="S2_R_code.txt">S2_R_code.txt</a> (MD5: 6028e6cddbdf1473a4eef0faa8bd310a)  --  R code to perform analyses in S1</p> <p><a href="S3_within_zone_example_data.csv">S3_within_zone_example_data.csv</a> (MD5: ab86c1dd8ca7bcd2115f23a14b746bd8)  --  within-zone fish growth data</p> <p><a href="S4_among_zone_example_data.csv">S4_among_zone_example_data.csv</a> (MD5: d601bea4192d1f1c4c513fac34e39306)  --  among-zone fish growth data</p> <p><a href="S5_example_temperature.csv">S5_example_temperature.csv</a> (MD5: f7ae18b64af07ec4b4d7ff94966bbf46)  --  temperature data used in among-zone analyses</p> </div><h2>Description</h2><div> <p>These supplements are designed to assist the reader to implement hierarchical growth models using the statistical software R. The first supplement (S1_tutorial.pdf) provides detailed model descriptions, formulations and analytical steps used in the paper, complementing models presented in Table 3. The second supplement (S2_R_code.txt) provides executable R code for analyses in S1. The third, fourth, and fifth supplements (S3_within_zone_example_data.csv, S4_among_zone_example_data.csv, and S5_example_temperature.csv) are example data sets. </p> <p>Our analyses rely heavily on the R packages lme4, AICcmodavg, effects, lattice and plyr, all available on the comprehensive R archive network (CRAN; cran.r-project.org). </p> <p>Each row in S3_within_zone_example_data.csv and S4_among_zone_example_data.csv represents a measurement of growth in mm (Increment). These observations are associated with an Age (in years) and belong to a fish (FishID) of a given sex (M or F). Each fish has an age-at-capture (ACC, in years). Associated with each Increment is its year of deposition (Year) and the annual bottom temperature (Temp) experienced by the individual at this time. In addition, the S4_among_zone_example_data.csv and S5_example_temperature.csv files contain a variable called zone that assigns each fish to a fictitious fishing area. See Table 2 for additional descriptions of these parameters.</p> </div

Appendix A. Supplementary results: Age-class specific fish length ~ otolith radius relationships.

Supplementary results: Age-class specific fish length ~ otolith radius relationships

Appendix D. Intraclass correlation coefficient (ICC) and R2 equations for mixed models.

Intraclass correlation coefficient (ICC) and R2 equations for mixed models

Appendix G. Within vs. among individual supplementary results: result descriptions.

Within vs. among individual supplementary results: result descriptions

Appendix B. Supplementary methods and results: Estimation of spatially resolved annual bottom temperature from SynTS and the HadISST1 modelled products.

Supplementary methods and results: Estimation of spatially resolved annual bottom temperature from SynTS and the HadISST1 modelled products

Appendix E. Within-area supplementary results: result descriptions, model selection tables and within-area intrinsic effect plots.

Within-area supplementary results: result descriptions, model selection tables and within-area intrinsic effect plots

Appendix C. Supplementary methods and results: Calculation of relative abundance indices using fishery-derived CPUE estimates.

Supplementary methods and results: Calculation of relative abundance indices using fishery-derived CPUE estimates