Oyster Genetic Diversity and Inbreeding Depressions: Using Mathematical Modeling to Guide Oyster Harvesters Practices Background Humans have been breeding crops for specific traits since prehistory, with remarkable examples documented in the eleventh, nineteenth, and twentieth centuries during shifts in agricultural practices (Wilczynski 1959, Darwin 1861). These practices, especially in the past two centuries, have caused some controversy within and between various groups with different political, social, and economic stakes in the industries (Costa­Font and Mossialos 2007, Murphy et al. 2007, Lammerts van Bueren et al. 2011). These anthropogenic genetic selective pressures have had some remarkable effects, though these effects have not been unanimously praised as beneficial. There has been substantial debate regarding the role of human meddling in the natural world, with topics ranging from the morality of social Darwinism (Jones 1980) to the use and/or mandates requiring children to be vaccinated before entering a public school (Gostin 2015). Biologists have been able to examine the effects and cascading consequences of selective breeding in multiple examples with various results. For instance, many aquaculture selection methods are producing their intended results (such as larger yields) (Gjedrem 1983) while some broiler chickens have been selectively bred to the point of joint immobility (Paxton et al. 2013). Negative effects of inbreeding have been observed extensively, both in and out of the laboratory. For example, white­footed mice experienced a sharp fitness decline (ie, lower survivorship and reproduction rates) after several generations of inbreeding (Paxton et al. 2013). Similarly, land snails fell victim to the same fate when mated with close relatives (Xiaofeng 1993). And, in humans, royalty are not immune: it is widely believed that inbreeding led to increased rates of hemophilia (a recessive disorder) among European royalty in the nineteenth century (Offner 2013). These populations either crashed or experienced decreased fitness because of a phenomenon referred to as ​
inbreeding depression​
, when a population accrues too many deleterious recessive alleles to live and reproduce as the population once was. Aquaculture’s vulnerability is a recently documented case regarding inbreeding and population crashes (Gjedrem and Baranski 2009). While some researchers have demonstrated some success with selective breeding (Langdon et al. 2003), long­term effects and sustainability have not been documented. Rather, newer research demonstrates a high degree of genetic similarity within Pacific oysters, which suggests that an inbreeding depression may be imminent (Plough and Hedgecock 2011). Willapa Bay is home to harvested Pacific oysters, which may also be highly genetically similar. Furthermore, controversy surrounding pesticide use in the region make the location a particularly fascinating and informative case study. Top of the Hour Glass Framing Question Is genetic diversity a good thing, and how do oyster farmers ensure genetic diversity within a population? This question deals with some general assumptions that are seen in public dialogue. While genetic diversity may be an important factor in ensuring a viable and productive population (Fred W. Allendorf 2012, Lauterbach, Ristow, and Gemeinholzer 2011, Boopathi 2013), the biological context of genetic diversity is absent or loosely/liberally described in general publications to promote the concept of biodiversity and genetic diversity as natural, healthy, and “wild” (Selge, Fischer, and van Der Wal 2011, “Why People Oppose GMOs Even Though Science Says They Are Safe” 2016). For instance, with the rise of monocultures, genetically modified foods, and pesticide use, all three examples of scientific and biological technologies are decontextualized, demonized, and portrayed as unnatural, a testament to human hubris (Pfund et al. 2011 (Frewer, Scholderer, and Bredahl 2003, Mucci, Hough, and Ziliani 2004). These phenomena are situated at the top of the hourglass, and echo themes seen in many environmental movements, such as the “feminized fish” panic (Ahearn 2016) that still persists today despite the fact that hermaphroditic tendencies have been recorded for decades (Carruth and Bowker 2000, Gross­Sorokin, Roast, and Brighty 2006). Moving further down the hourglass, I will explain the biological significance of genetic diversity with studies regarding inbreeding depressions, genetic rescues, the fundamental concepts of genes, reproduction, polyploids, and the use of mathematical modeling to predict and ensure viable populations of harvested or farmed organisms. This is necessary for resource management, to avoid the irrevocable overexploitation of biological systems (Nilsson 2004), and ensure the economic viability of both small and larger oyster farming operations (Dornier and Dufay 2013, Casellas et al. 2009). These questions sit above the focus question, but establish the necessary foundation for understanding exactly what genetic diversity is, the effects of populations with high and low genetic diversities, and the consequences of inbreeding. These more specific details bring the research to the narrowest part of the hourglass, preparing readers for the focus question. Middle of the Hour Glass Focus Question Using DNA assays, genetic analysis, and mathematical models of inbreeding, how many generations can the oyster harvesters in Willapa Bay continue using natural sets with previously purchased diploid oysters? This question is obviously more specific in space and time with both temporal (oyster generations) and spatial scales (Southeast Washington Coast). Furthermore, the Willapa Bay oyster situation has received media coverage and public commentary following questions regarding the use of pesticides (“Oyster Growers Apply for New Pesticide Permit” 2016), environmental protection limitations (Press 2015), and invasive species regulations (Ludwig 2016). These qualities make the location both interesting and more situated and therefore more answerable. However, even in a situated context, there is foundational information to be conveyed regarding the oyster reproduction process, the use of polyploid oysters to circumvent the undesirable oyster qualities that result from the summer breeding period, the nature of biological policies and economic strategies used by Willapa Bay oyster harvesters, and recent events that have pushed oyster producers to use either naturally or artificially set generations. The below methodologies can be used to adequately answer the specific and refined focus question. ●
Testing genetic variation​
: random samples of individuals are selected within a population of oysters. DNA samples are taken from each individual, undergo polymerase chain reactions, analyzed, and compared to each other for genetic similarity (Wright et al. 2007). Software can be used to determine significant genetic differences in specific “marker” genes. Ideally, for comparison, the DNA of an oyster from a past generation would be used. The older oyster DNA would demonstrate how the populations have changed over time, in what genetic direction, and to what extent (that is, how much or what percentage of the population is homologous at ​
x​
number of marker genes) (Camara and Vadopalas 2009). ●
Determining inbreeding coefficient​
: This step can only be done when the DNA analysis has been performed and the frequency rates of homozygosity in marker genes have been identified. There’s a lot of complicated math involved in this step, but it ties back to the concept of populations accumulating deleterious recessive alleles over time (Plough and Hedgecock 2011). The rate at which this happens is determined by the degree of homozygosity, as determined by the next method. ●
Computing a mathematical model​
: Using the inbreeding coefficient, we can determine how many generations until enough genetic deformations will accrue making enough of the offspring unviable and leading to the inbreeding depression we would expect in an inbred population (Paige 2010). There should be several models in this situation with the following circumstances, or some permutation of them: no gene flow from an outside source, 10% new individuals, 25% new individuals, and 50% new individuals. These individuals need not be 100% genetically different than the original population; this is impossible, but we can determine a benchmark that we determine is sufficiently or substantially different across ​
x​
% marker genes. So long as this percentage is the same in each model, we have broken no assumptions of gene flow. ●
Interviewing people involved in the oyster harvesting business​
: While most of the data collected is fairly technical, it is important not to ignore the less­numeric narrative that can be collected. The following questions could be asked to several people in the oyster business. ○
How has oyster production been in the past 2, 3, 5, 10, 20 years? ○
How often do you supplement your harvest with artificial set? ○
Have there been phenotypic changes in the oysters in the past 6 months, 1 year, 2 years, 3 years? ○
How often do you use triploid oysters to ensure a more reliable harvest during summer months? This data, while anecdotal, still reveals important trends about the oyster situation. By asking fairly vague questions and performing in­person interviews, the various actors could feel more empowered to disclose only what they wish (Paige 2010), which could foster a positive relationship with the researchers and oyster harvesters. Through this positive relationship, it is possible the actors would be more receptive to advice following the findings of our study. Furthermore, accessing financial records would allow mathematical models to be more successful by allowing the model to take into account the “leverage” (or lack thereof) or profit the harvesters could lose before the entire operation becomes a net cost. However, I suspect people might not be too keen on letting some nerds into their valuable and classified financial records for the sake of a more accurate model. But, it never hurts to ask. Results The results would demonstrate how fragile or resilient the current strategies oyster farms are using. The initial method would yield a percentage or ratio of (functionally) genetically identical individuals within the population at the various loci/genes. This in itself is useful because it demonstrates the lack of genetic diversity within the population, but the project goes further by establishing the inbreeding coefficient under a variety of strategies available to oyster harvesters. Beyond the inbreeding coefficient, by using mathematical models, we can predict the number of generations until the inbreeding depression either diminishes the population to the point of extinction or the point of financial inviability. The number of generations is dependent on a number of variables, but by utilizing explicit functional definitions of “different,” “variable,” “similar,” and “identical,” we can provide the most precise and consistent models to yield a more accurate time of economic collapse. Bottom of the Hourglass Larger implications Within the idea of promoting and protecting diversity, this research has the chance to interact with theories regarding what is “wild,” “natural,” “correct,” “proper,” and socially and/or politically acceptable. Incorporating this research into a larger school of thought that blindly trumps genetic and biological diversity would provide concrete examples and methodology that demonstrate the importance of having a genetically heterogeneous population, allowing us to ask the question “How can we ensure genetic diversity within a population?” with a broader understanding of ​
why​
and ​
how​
genetic diversity can influence a suite of ecological services and processes. The location of this study enables it to serve as an example with many third variables (introduced/non­native species, climate change and ocean acidification, pesticide use, and political/media coverage) that cannot be considered in a scientific manner, but influence the ecosystem nonetheless. In the case of Willapa Bay, we can answer some questions, ask others, establish a greater understanding of terms that are vaguely defined, and offer predictions based on our results. In response to the focus question, we answer this question in a very direct way and can provide some insight into the possibilities of what may happen under current policy. While it would certainly be stress­relieving if climate change and its associated biological, chemical, social, and geologic repercussions were not reality, ignoring these very real threats is impractical and simply foolish. This study does not directly discuss or consider the other anthropogenic effects that have applied selective pressure and/or genetic bottlenecking. Further studies could relate the impacts of ocean acidification on the production and viability of natural sets, the use of pesticides on regulating gene expression, and the cascading effects of oyster absence from its ecological niche within the marine ecosystem. Ahearn, Asheley. 2016. “Feminized Fish: A Side Effect Of Emerging Contaminants.” Accessed March 9. http://www.opb.org/news/article/clean­water­the­next­act­emerging­contaminants­fem/. Boopathi, N. Manikanda. 2013. ​
Genetic Mapping and Marker Assisted Selection Basics, Practice and Benefits​
. Dordrecht: Springer. Bubley, W. J., and O. Pashuk. 2010. “Life History of a Simultaneously Hermaphroditic Fish, Diplectrum Formosum.” ​
Journal of Fish Biology​
77 (3): 676–91. doi:10.1111/j.1095­8649.2010.02710.x. Bucklin, Katherine Adelaide. 2002. ​
Analysis of the Genetic Basis of Inbreeding Depression in the Pacific Oyster Crassostrea Gigas​
. Thesis PhD­­University of California, Davis. Camara, Mark D., and Brent Vadopalas. 2009. “Genetic Aspects of Restoring Olympia Oysters and Other Native Bivalves: Balancing the Need for Action, Good Intentions, and the Risks of Making Things Worse.” ​
Journal of Shellfish Research​
28 (1): 121–45. doi:10.2983/035.028.0104. Carruth, Laura L., and R. G. Bowker. 2000. “Freshwater Cichlid Crenicara Punctulata Is a Protogynous Sequential Hermaphrodite.” ​
Copeia​
2000 (1): 71–82. doi:10.1643/0045­8511(2000)2000[0071:FCCPIA]2.0.CO;2. Casellas, J., J. Piedrafita, G. Caja, and L. Varona. 2009. “Analysis of Founder­Specific Inbreeding Depression on Birth Weight in Ripollesa lambs.(Author abstract)(Report).” ​
Journal of Animal Science​
87 (1): 72. Costa­Font, Joan, and Elias Mossialos. 2007. “Are Perceptions of ‘risks’ and ‘benefits’ of Genetically Modified Food (in)dependent?.” ​
Food Quality and Preference​
18 (2): 173–82. doi:10.1016/j.foodqual.2005.09.013. De Rada, V. D. 2015. “Quality of Data from Matrix Questions in Face­to­Face Surveys: A Compared Study Using Paper and Electronic Questionnaires.” ​
Revista Espanola De Investigaciones Sociologicas​
, no. 152: 167–78. doi:10.5477/cis/reis.152.167. Dornier, Antoine, and Mathilde Dufay. 2013. “HOW SELFING, INBREEDING DEPRESSION, AND POLLEN LIMITATION IMPACT NUCLEAR‐CYTOPLASMIC GYNODIOECY: A MODEL.” ​
Evolution​
67 (9): 2674–87. doi:10.1111/evo.12142. Fred W. Allendorf. 2012. ​
Conservation and the Genetics of Populations​
. 2nd ed. Hoboken: Wiley. Frewer, Lynn J., Susan Miles, and Roy Marsh. 2002. “The Media and Genetically Modified Foods: Evidence in Support of Social Amplification of Risk.” ​
Risk Analysis​
22 (4): 701–11. Frewer, Lynn J., Joachim Scholderer, and Lone Bredahl. 2003. “Communicating about the Risks and Benefits of Genetically Modified Foods: The Mediating Role of Trust.” ​
Risk Analysis​
23 (6): 1117–33. Gjedrem, Trygve, and Matthew Baranski. 2009. ​
Selective Breeding in Aquaculture: An Introduction​
. Vol. 10. Reviews: Methods and Technologies in Fish Biology and Fisheries. Dordrecht: Springer Netherlands. http://link.springer.com/10.1007/978­90­481­2773­3. Gostin, Lawrence O. 2015. “Law, Ethics, and Public Health in the Vaccination Debates: Politics of the Measles Outbreak.” ​
JAMA​
313 (11): 1099–1100. doi:10.1001/jama.2015.1518. Gross­Sorokin, Melanie Y., Stephen D. Roast, and Geoffrey C. Brighty. 2006. “Assessment of Feminization of Male Fish in English Rivers by the Environment Agency of England and Wales.” ​
Environmental Health Perspectives​
114 (Suppl 1): 147–51. doi:10.1289/ehp.8068. “Heredity ­ Abstract of Article: Comparison of Inbreeding and Outbreeding in Hermaphroditic Arianta Arbustorum (L.) (land Snail).” 1993. Heredity​
71 (5): 456–61. Jimenez, J. A., K. A. Hughes, G. Alaks, L. Graham, and R. C. Lacy. 1994. “An Experimental Study of Inbreeding Depression in a Natural Habitat.” ​
Science​
266 (5183): 271–73. doi:10.1126/science.7939661. Jones, Greta. 1980. ​
Social Darwinism and English Thought : The Interaction between Biological and Social Theory​
. Harvester Studies in Philosophy ; 20. Brighton, Sussex: Harvester Press ; Atlantic Highlands, NJ. Kause, Antti, Ossi Ritola, Tuija Paananen, Heli Wahlroos, and Esa A. Mäntysaari. 2005. “Genetic Trends in Growth, Sexual Maturity and Skeletal Deformations, and Rate of Inbreeding in a Breeding Programme for Rainbow Trout (Oncorhynchus Mykiss).” ​
Aquaculture​
, Genetics In Aquaculture VIIIEighth International Symposium on Genetics in Aquaculture, 247 (1–4): 177–87. doi:10.1016/j.aquaculture.2005.02.023. Lammerts van Bueren, E. T., S. S. Jones, L. Tamm, K. M. Murphy, J. R. Myers, C. Leifert, and M. M. Messmer. 2011. “The Need to Breed Crop Varieties Suitable for Organic Farming, Using Wheat, Tomato and Broccoli as Examples: A Review.” ​
NJAS ­ Wageningen Journal of Life Sciences​
, Improving Production Efficiency, Quality and Safety in Organic and “Low­Input” Food Supply Chains, 58 (3–4): 193–205. doi:10.1016/j.njas.2010.04.001. Langdon, Chris, Ford Evans, Dave Jacobson, and Michael Blouin. 2003. “Yields of Cultured Pacific Oysters Crassostrea Gigas Thunberg Improved after One Generation of Selection.” ​
Aquaculture​
220 (1–4): 227–44. doi:10.1016/S0044­8486(02)00621­X. Lauterbach, D., M. Ristow, and B. Gemeinholzer. 2011a. “Genetic Population Structure, Fitness Variation and the Importance of Population History in Remnant Populations of the Endangered Plant Silene Chlorantha (Willd.) Ehrh. (Caryophyllaceae).” ​
Plant Biology (Stuttgart, Germany)​
13 (4): 667–777. doi:10.1111/j.1438­8677.2010.00418.x. ———. 2011b. “Genetic Population Structure, Fitness Variation and the Importance of Population History in Remnant Populations of the Endangered Plant Silene Chlorantha (Willd.) Ehrh. (Caryophyllaceae).” ​
Plant Biology (Stuttgart, Germany)​
13 (4): 667–777. doi:10.1111/j.1438­8677.2010.00418.x. Ludwig, Mike. 2016. “Special Investigation: The Pesticides and Politics of America’s Eco­War.” ​
Truthout​
. Accessed March 9. http://www.truth­out.org/news/item/1515:special­investigation­the­pesticides­and­politics­of­americas­ecowar. M L Johnson, and M. S. Gaines. 1990. “Evolution of Dispersal: Theoretical Models and Empirical Tests Using Birds and Mammals.” ​
Annual Review of Ecology and Systematics​
21 (1): 449–80. doi:10.1146/annurev.es.21.110190.002313. Mucci, Andrea, and Guillermo Hough. 2004. “Perceptions of Genetically Modified Foods by Consumers in Argentina.” ​
Food Quality and Preference​
15 (1): 43–51. Mucci, Andrea, Guillermo Hough, and Cesar Ziliani. 2004. “Factors That Influence Purchase Intent and Perceptions of Genetically Modified Foods among Argentine Consumers.” ​
Food Quality and Preference​
15 (6): 559–67. Murphy, Kevin M., Kimberly G. Campbell, Steven R. Lyon, and Stephen S. Jones. 2007. “Evidence of Varietal Adaptation to Organic Farming Systems.” ​
Field Crops Research​
102 (3): 172–77. doi:10.1016/j.fcr.2007.03.011. Nilsson, Torbjörn. 2004. “Integrating Effects of Hunting Policy, Catastrophic Events, and Inbreeding Depression, in PVA Simulation: The Scandinavian Wolf Population as an Example.” ​
Biological Conservation​
115 (2): 227–39. doi:10.1016/S0006­3207(03)00120­4. “No Consensus on the Definition of ‘native’ or ‘invasive’ Species.” 2014. ​
Death of a Million Trees​
. February 18. http://milliontrees.me/2014/02/18/no­consensus­on­the­definition­of­native­or­invasive­species/. Offner, Susan. 2013. “Royal Hemophilia.(cause of Hemophilia in European Royal Families).” ​
The American Biology Teacher​
75 (9): 652. “Oyster Growers Apply for New Pesticide Permit.” 2016. ​
KING5​
. Accessed March 9. http://www.king5.com/story/tech/science/environment/2016/01/08/oyster­growers­apply­new­pesticide­permit/78534562/. Paige, Ken N. 2010. “The Functional Genomics of Inbreeding Depression: A New Approach to an Old Problem.” ​
BioScience​
60 (4): 267–77. doi:10.1525/bio.2010.60.4.5. Paxton, Heather, Monica A. Daley, Sandra A. Corr, and John R. Hutchinson. 2013. “The Gait Dynamics of the Modern Broiler Chicken: A Cautionary Tale of Selective Breeding.” ​
Journal of Experimental Biology​
216 (17): 3237–48. doi:10.1242/jeb.080309. “[PDF] from Innocua.net.” 2016. Accessed March 8. http://www.innocua.net/web/download­1003/0272­4332.00062.pdf. Pfund, Jean­Laurent, John Daniel Watts, Manuel Boissière, Amandine Boucard, Renee Marie Bullock, Andree Ekadinata, Sonya Dewi, et al. 2011. “Understanding and Integrating Local Perceptions of Trees and Forests into Incentives for Sustainable Landscape Management.” Environmental Management​
48 (2): 334–49. doi:10.1007/s00267­011­9689­1. Plough, Louis V., and Dennis Hedgecock. 2011. “Quantitative Trait Locus Analysis of Stage­Specific Inbreeding Depression in the Pacific Oyster Crassostrea Gigas.” ​
Genetics​
189 (4): 1473–86. doi:10.1534/genetics.111.131854. Pons, O., and R. J. Petit. 1996. “Measuring and Testing Genetic Differentiation with Ordered versus Unordered Alleles.” ​
Genetics​
144 (3): 1237–45. PR.com (Press Releases)​
. 2015. “HAGA Uploads New Presentation About the Negative Effects of GMO Crops.” Press, The Associated. 2015. “Pesticide Spray Plan for Willapa Bay Oyster Beds Canceled after Public Expresses Concerns.” ​
OregonLive.com​
. May 3. http://www.oregonlive.com/pacific­northwest­news/index.ssf/2015/05/pesticide_spray_plan_for_willa.html. “PubMed Entry.” 2016. Accessed March 8. http://www.ncbi.nlm.nih.gov/pubmed/21940682. Selge, S., A. Fischer, and R. van Der Wal. 2011. “Public and Professional Views on Invasive Non­Native Species ­ A Qualitative Social Scientific Investigation.” ​
Biological Conservation​
144 (12): 3089–97. doi:10.1016/j.biocon.2011.09.014. “Snapshot.” 2016. Accessed March 8. http://onlinelibrary.wiley.com/doi/10.1111/0272­4332.00062/full;jsessionid=0C53553942FB2C1E94A4DE7B7A5DB5CC.f01t04?wol1UR
L=/doi/10.1111/0272­4332.00062/full&regionCode=US­OR&identityKey=733d1ec9­7a91­4593­95b1­4ff6ffbbd238. “‘The Trouble with the Word “invasive.”’” 2014. ​
Death of a Million Trees​
. January 28. http://milliontrees.me/2014/01/28/the­trouble­with­the­word­invasive/. “Tracking Oyster Restoration with Genetic Tests • Virginia Sea Grant : Virginia Sea Grant.” 2016. Accessed March 9. http://vaseagrant.vims.edu/tracking­oyster­restoration­genetic­tests/. “Why People Oppose GMOs Even Though Science Says They Are Safe.” 2016. ​
Scientific American​
. Accessed March 8. http://www.scientificamerican.com/article/why­people­oppose­gmos­even­though­science­says­they­are­safe/. Wilczynski, Jan Z. 1959. “On the Presumed Darwinism of Alberuni Eight Hundred Years before Darwin.” ​
Isis​
50 (4): 459–66. doi:10.1086/348801. Wright, Anita C., Victor Garrido, Georgia Debuex, Melissa Farrell­Evans, Archana A. Mudbidri, and W. Steven Otwell. 2007. “Evaluation of Postharvest­Processed Oysters by Using PCR­Based Most­Probable­Number Enumeration of Vibrio Vulnificus Bacteria.” ​
Applied and Environmental Microbiology​
73 (22): 7477–81. doi:10.1128/AEM.01118­07.