Population Genetic Structure Is Unrelated to Shell Shape, Thickness and Organic Content in European Populations of the Soft-Shell Clam Mya Arenaria
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and DNA Extraction
2.2. Microsatellite Genotyping
2.3. Genetic Summary Statistics
2.4. Analysis of Population Structure
2.5. Elliptic Fourier Analysis of Shell Outlines
2.6. Analysis of Shell Thickness
2.7. Analysis of Organic Shell Content
2.8. Data accessibility
3. Results
3.1. Population Structure
3.2. Shell Shape Variation
3.3. Variation in Shell Thickness
3.4. Variation in Organic Content
4. Discussion
4.1. Population Genetic Structure
4.2. Shell Shape Variation
4.3. Variation in Shell Thickness, Microstructure and Organic Content
4.4. Genetic Versus Plastic Contributions
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Population ID | Location | Samples Used for Genetic Analysis | Samples Used for Shape Analysis | Samples Used for Thickness Analysis | Ho | He | Na | Ar |
---|---|---|---|---|---|---|---|---|
ITA | Comacchio (Italy) | 30 | 28 | 18 | 0.75 (0.13) | 0.76 (0.07) | 8.23 (2.37) | 6.24 (1.6) |
LIS | Lisbon (Portugal) | 28 | 29 | 21 | 0.67 (0.19) | 0.74 (0.18) | 8.36 (2.24) | 6.56 (1.73) |
BRE | Brest (France) | 32 | 35 | 19 | 0.76 (0.19) | 0.77 (0.12) | 9.54 (3.32) | 7.08 (2.56) |
PLY | Plymouth (UK) | 27 | 30 | 19 | 0.66 (0.13) | 0.75 (0.09) | 8.63 (3.44) | 6.6 (2.24) |
SAN | Saint Andrews (UK) | 23 | 22 | 20 | 0.74 (0.12) | 0.72 (0.1) | 5.91 (1.64) | 5.16 (1.45) |
LCR | Le Crotoy (France) | 31 | 40 | 21 | 0.71 (0.14) | 0.75 (0.08) | 8.18 (2.44) | 6.36 (1.54) |
TXL | Balgzand (Netherlands) | 30 | 30 | 21 | 0.71 (0.15) | 0.76 (0.1) | 8.72 (2.76) | 6.36 (1.65) |
SYL | Sylt (Germany) | 12 | 13 | 10 | 0.62 (0.14) | 0.73 (0.13) | 6.36 (2.65) | 6.63 (2.65) |
KIE | Kiel (Germany) | 34 | 35 | 18 | 0.59 (0.15) | 0.74 (0.11) | 8.91 (2.38) | 6.29 (1.52) |
Total | 247 | 262 | 167 | 0.69 (0.06) | 0.75 (0.02) | 8.09 (1.19) | 6.36 (0.52) |
Coefficient | Estimate | SE | 95% CI | t | p-Value |
---|---|---|---|---|---|
Shell shape GLMM † | |||||
(Intercept) | 0.002 | 0.11 | −0.37; 0.37 | 0.01 | 0.99 |
Shape (PC2) | −0.01 | 0.17 | −0.52; 0.49 | −0.07 | 0.94 |
Shape (PC3) | 0.02 | 0.19 | −0.51; 0.53 | 0.12 | 0.91 |
Latitude | −0.004 | 0.10 | −0.23; 0.22 | −0.03 | 0.97 |
Length × Shape (PC1) | −0.11 | 0.08 | −0.35; 0.13 | −1.27 | 0.20 |
Length × Shape (PC2) | −0.07 | 0.10 | −0.27; 0.13 | −0.70 | 0.49 |
Length × Shape (PC3) | 0.27 | 0.10 | 0.07; 0.45 | 2.70 | 0.0072 |
gPC1 | 0.03 | 0.06 | −0.09; 0.15 | 0.47 | 0.64 |
gPC2 | −0.01 | 0.06 | −0.13; 0.12 | −0.15 | 0.88 |
sMLH | 0.02 | 0.04 | −0.06; 0.11 | 0.55 | 0.58 |
Shell layers thickness GLMM * | |||||
(Intercept) | 274.60 | 7.15 | 257.38; 291.44 | 38.41 | <0.0001 |
Layer (CL) | −181.29 | 7.30 | −204.95; −158.30 | −24.82 | <0.0001 |
Layer (CCL) | −19.45 | 14.63 | −45.03; 5.82 | −1.33 | 0.18 |
Latitude × Layer (PR) | 24.30 | 7.36 | 9.02; 39.27 | 3.30 | 0.0010 |
Latitude × Layer (CL) | −2.68 | 3.40 | −17.10; 11.27 | −0.79 | 0.43 |
Latitude × Layer (CCL) | −23.72 | 13.36 | −37.43; −9.69 | −1.78 | 0.076 |
Length × Layer (PR) | 25.36 | 6.92 | 12.29; 38.93 | 3.66 | 0.0003 |
Length × Layer (CL) | 6.74 | 2.67 | −7.63; 21.44 | 2.53 | 0.012 |
Length × Layer (CCL) | 30.71 | 9.79 | 14.88; 46.79 | 3.14 | 0.0018 |
gPC1 | −0.98 | 2.65 | −9.80; 7.82 | −0.37 | 0.71 |
gPC2 | −1.62 | 2.45 | −10.62; 7.44 | −0.66 | 0.51 |
sMLH | 0.82 | 2.14 | −6.80; 8.64 | 0.38 | 0.70 |
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De Noia, M.; Telesca, L.; Vendrami, D.L.J.; Gokalp, H.K.; Charrier, G.; Harper, E.M.; Hoffman, J.I. Population Genetic Structure Is Unrelated to Shell Shape, Thickness and Organic Content in European Populations of the Soft-Shell Clam Mya Arenaria. Genes 2020, 11, 298. https://doi.org/10.3390/genes11030298
De Noia M, Telesca L, Vendrami DLJ, Gokalp HK, Charrier G, Harper EM, Hoffman JI. Population Genetic Structure Is Unrelated to Shell Shape, Thickness and Organic Content in European Populations of the Soft-Shell Clam Mya Arenaria. Genes. 2020; 11(3):298. https://doi.org/10.3390/genes11030298
Chicago/Turabian StyleDe Noia, Michele, Luca Telesca, David L. J. Vendrami, Hatice K. Gokalp, Grégory Charrier, Elizabeth M. Harper, and Joseph I. Hoffman. 2020. "Population Genetic Structure Is Unrelated to Shell Shape, Thickness and Organic Content in European Populations of the Soft-Shell Clam Mya Arenaria" Genes 11, no. 3: 298. https://doi.org/10.3390/genes11030298