References
Aalto, E. A., Lafferty, K. D., Sokolow, S. H., Grewelle, R. E., Ben-Horin, T., Boch, C. A., … De Leo, G. A. (2020). Models with environmental drivers offer a plausible mechanism for the rapid spread of infectious disease outbreaks in marine organisms. Scientific Reports , 10 (1), 5975. https://doi.org/10.1038/s41598-020-62118-4
Agnew, M. V., Friedman, C. S., Langdon, C., Divilov, K., Schoolfield, B., Morga, B., … Burge, C. A. (2020). Differential mortality and high viral load in naive pacific oyster families exposed to OsHV-1 suggests tolerance rather than resistance to infection.Pathogens , 9 (12), 1057. https://doi.org/10.3390/pathogens9121057
Aquino, C. A., Besemer, R. M., DeRito, C. M., Kocian, J., Porter, I. R., Raimondi, P. T., … Hewson, I. (2021). Evidence that microorganisms at the animal-water interface drive sea star wasting disease. Frontiers in Microbiology , 11 . https://doi.org/10.3389/fmicb.2020.610009
Bao, Z., & Eddy, S. R. (2002). Automated de novo identification of repeat sequence families in sequenced genomes. Genome Research ,12 (8), 1269–1276. https://doi.org/10.1101/gr.88502
Behringer, D. C., Silliman, B. R., & Lafferty, K. D. (Eds.). (2018).Marine Disease Ecology . Londong: Oxford University Press.
Benson, G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research , 27 (2), 573–580. https://doi.org/10.1093/nar/27.2.573
Burge, C. A., Mark Eakin, C., Friedman, C. S., Froelich, B., Hershberger, P. K., Hofmann, E. E., … Harvell, C. D. (2014). Climate Change Influences on Marine Infectious Diseases: Implications for Management and Society. Annual Review of Marine Science ,6 (1), 249–277. https://doi.org/10.1146/annurev-marine-010213-135029
Burt, J. M., Tinker, M. T., Okamoto, D. K., Demes, K. W., Holmes, K., & Salomon, A. K. (2018). Sudden collapse of a mesopredator reveals its complementary role in mediating rocky reef regime shifts.Proceedings of the Royal Society B: Biological Sciences ,285 (1883), 20180553. https://doi.org/10.1098/rspb.2018.0553
Catchen, J. M., Amores, A., Hohenlohe, P., Cresko, W., & Postlethwait, J. H. (2011). Stacks : Building and genotyping loci de novo from short-read sequences. G3 , 1 (3), 171–182. https://doi.org/10.1534/g3.111.000240
Catchen, J. M., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: an analysis tool set for population genomics.Molecular Ecology , 22 (11), 3124–3140. https://doi.org/10.1111/mec.12354
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., … Group, 1000 Genomes Project Analysis. (2011). The variant call format and VCFtools. Bioinformatics ,27 (15), 2156–2158. https://doi.org/10.1093/bioinformatics/btr330
Dégremont, L., Garcia, C., & Allen, S. K. (2015). Genetic improvement for disease resistance in oysters: A review. Journal of Invertebrate Pathology , 131 , 226–241. https://doi.org/10.1016/j.jip.2015.05.010
Eisenlord, M. E., Groner, M. L., Yoshioka, R. M., Elliott, J., Maynard, J., Fradkin, S., … Harvell, D. C. (2016). Ochre star mortality during the 2014 wasting disease epizootic: Role of population size structure and temperature. Philosophical Transactions of the Royal Society B: Biological Sciences , 371 (1689). https://doi.org/10.1089/rstb.2015.0212
Foll, M., & Gaggiotti, O. (2008). A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective. Genetics , 180 (2), 977–993. https://doi.org/10.1534/genetics.108.092221
Fuess, L. E., Eisenlord, M. E., Closek, C. J., Tracy, A. M., Mauntz, R., Gignoux-Wolfsohn, S., … Roberts, S. B. (2015). Up in arms: Immune and nervous system response to sea star wasting disease. PLoS ONE , 10 (7), e0133053. https://doi.org/10.1371/journal.pone.0133053
Gagnaire, P.-A., & Gaggiotti, O. E. (2016). Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches. Current Zoology , 62 (6), 603–616. https://doi.org/10.1093/cz/zow088
Gravem, S. A., Heady, W. N., Saccomanno, V. R., Alvastad, K. F., Gehman, A. L. M., Frierson, T. N., & Hamilton, S. L. (2021). Sunflower Sea Star (Pycnopodia helianthoides). IUCN Red List of Threatened Species .
Groner, M. L., Maynard, J., Breyta, R., Carnegie, R. B., Dobson, A., Friedman, C. S., … Harvell, C. D. (2016). Managing marine disease emergencies in an era of rapid change. Philosophical Transactions of the Royal Society B: Biological Sciences , 371 (1689), 20150364. https://doi.org/10.1098/rstb.2015.0364
Gudenkauf, B. M., & Hewson, I. (2015). Metatranscriptomic analysis of Pycnopodia helianthoides (Asteroidea) affected by sea star wasting disease. PLoS ONE , 10 (5). https://doi.org/10.1371/journal.pone.0128150
Harvell, D. C., Aronson, R., Baron, N., Connell, J., Dobson, A., Ellner, S., … Ward, J. (2004). The rising tide of ocean diseases: unsolved problems and research priorities. Frontiers in Ecology and the Environment , 2 (7), 375–382.
Harvell, D. C., Mitchell, C. E., Ward, J. R., Altizer, S., Dobson, A. P., Ostfel, R. S., & Samuel, M. D. (2002). Climate warming and disease risks for terrestrial and marine biota. Science ,296 (5576), 2158–2162.
Harvell, D. C., Montecino-Latorre, D., Caldwell, J. M., Burt, J. M., Bosley, K., Keller, A., … Gaydos, J. K. (2019). Disease epidemic and a marine heat wave are associated with the continental-scale collapse of a pivotal predator (Pycnopodia helianthoides). Science Advances , 5 (1), eaau7042. https://doi.org/10.1126/sciadv.aau7042
Hewson, I., Bistolas, K. S. I., Quijano Cardé, E. M., Button, J. B., Foster, P. J., Flanzenbaum, J. M., … Lewis, C. K. (2018). Investigating the complex association between viral ecology, environment, and northeast Pacific Sea Star Wasting. Frontiers in Marine Science , 5 (MAR). https://doi.org/10.3389/fmars.2018.00077
Hewson, I., Button, J. B., Gudenkauf, B. M., Miner, B., Newton, A. L., Gaydos, J. K., … Harvell, D. C. (2014). Densovirus associated with sea-star wasting disease and mass mortality. Proceedings of the National Academy of Sciences of the United States of America ,111 (48), 17278–17283. https://doi.org/10.1073/pnas.1416625111
Holt, C., & Yandell, M. (2011). MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.BMC Bioinformatics , 12 (1), 491. https://doi.org/10.1186/1471-2105-12-491
Jombart, T. (2015). An introduction to adegenet 2.0.0. Retrieved from http://adegenet.r-forge.r-project.org/files/tutorial-basics.pdf
Jombart, T., Devillard, S., & Balloux, F. (2010). Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics , 11 (1), 94. https://doi.org/10.1186/1471-2156-11-94
Kohl, W. T., McClure, T. I., & Miner, B. G. (2016). Decreased Temperature Facilitates Short-Term Sea Star Wasting Disease Survival in the Keystone Intertidal Sea Star Pisaster ochraceus. PLoS ONE ,11 (4), e0153670. https://doi.org/10.1371/journal.pone.0153670
Korf, I. (2004). Gene finding in novel genomes. BMC Bioinformatics , 5 , 59. https://doi.org/10.1186/1471-2105-5-59
Lloyd, M. M., & Pespeni, M. H. (2018). Microbiome shifts with onset and progression of Sea Star Wasting Disease revealed through time course sampling. Scientific Reports , 8 (1), 16476. https://doi.org/10.1038/s41598-018-34697-w
MCCALLUM, H., KURIS, A., HARVELL, C., LAFFERTY, K., SMITH, G., & PORTER, J. (2004). Does terrestrial epidemiology apply to marine systems? Trends in Ecology & Evolution , 19 (11), 585–591. https://doi.org/10.1016/j.tree.2004.08.009
Menge, B. A., Cerny-Chipman, E. B., Johnson, A., & Sullivan, J. (2016). Correction: Sea Star Wasting Disease in the Keystone Predator Pisaster ochraceus in Oregon: Insights into Differential Population Impacts, Recovery, Predation Rate,. PloS One , 11 (6), e0157302. Retrieved from http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0153994
Menge, B. A., Cerny-Chipman, E. B., Johnson, A., Sullivan, J., Gravem, S., & Chan, F. (2016). Sea Star Wasting Disease in the Keystone Predator Pisaster ochraceus in Oregon: Insights into Differential Population Impacts, Recovery, Predation Rate, and Temperature Effects from Long-Term Research. PLoS ONE , 11 (6), e0157302. https://doi.org/10.1371/journal.pone.0153994
Miner, C. M., Burnaford, J. L., Ambrose, R. F., Antrim, L., Bohlmann, H., Blanchette, C. A., … Raimondi, P. T. (2018). Large-scale impacts of sea star wasting disease (SSWD) on intertidal sea stars and implications for recovery. PLoS ONE , 13 (3), e0192870. https://doi.org/10.1371/journal.pone.0192870
Montecino-Latorre, D., Eisenlord, M. E., Turner, M., Yoshioka, R., Harvell, C. D., Pattengill-Semmens, C. V., … Gaydos, J. K. (2016). Devastating transboundary impacts of sea star wasting disease on subtidal asteroids. PLoS ONE , 11 (10), e0163190. https://doi.org/10.1371/journal.pone.0163190
Mydlarz, L. D., Jones, L. E., & Harvell, C. D. (2006). Innate immunity, environmental drivers, and disease ecology of marine and freshwater invertebrates. Annual Review of Ecology, Evolution, and Systematics , 37 (1), 251–288. https://doi.org/10.1146/annurev.ecolsys.37.091305.110103
Nei, M., Maruyama, T., & Chakrabort, R. (1975). The bottleneck effect and genetic variability in populations. Evolution , 29 , 1–10.
Paine, R. T. (1966). Food web complexity and species diversity.The American Naturalist , 100 (910), 91–75.
Paine, R. T. (1969). A note on trophic complexity and community stability. The American Naturalist , 103 , 91–93.
Paine, R. T. (1974). Intertidal community structure. Oecologia ,15 , 93–120.
Price, A. L., Jones, N. C., & Pevzner, P. A. (2005). De novo identification of repeat families in large genomes.Bioinformatics , 21 , 351–358. https://doi.org/10.1093/bioinformatics/bti1018
Ruiz‐Ramos, D. V., Schiebelhut, L. M., Hoff, K. J., Wares, J. P., & Dawson, M. N. (2020). An initial comparative genomic autopsy of wasting disease in sea stars. Molecular Ecology , 29 (6), 1087–1102. https://doi.org/10.1111/mec.15386
Rumble, S. M., Lacroute, P., Dalca, A. V., Fiume, M., Sidow, A., & Brudno, M. (2009). SHRiMP: Accurate mapping of short color-space reads.PLoS Computational Biology , 5 (5), e1000386. https://doi.org/10.1371/journal.pcbi.1000386
Schiebelhut, L. M., Puritz, J. B, & Dawson, M. N. (2018. Decimation by sea star wasting disease and rapid genetic change in a kystone species, Pisaster ochraceus. Proceedings of the National Academy of Sciences of the United States of America , 115 , 7069-7074. https://doi.org/10.1073/pnas.1800285115
Schultz, J. A., Cloutier, R. N., & Côté, I. M. (2016). Evidence for a trophic cascade on rocky reefs following sea star mass mortality in British Columbia. PeerJ , 4 , e1980. https://doi.org/10.7717/peerj.1980
Shapiro, M. D., Kronenberg, Z., Li, C., Domyan, E. T., Pan, H., Campbell, M., … Wang, J. (2013). Genomic diversity and evolution of the head crest in the rock pigeon. Science , 339 (6123), 1063–1067. https://doi.org/10.1126/science.1230422
Slater, G. S. C., & Birney, E. (2005). Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics , 6 (31). https://doi.org/10.1186/1471-2105-6-31
Smit, A., & Hubley, R. (2014). RepeatModeler Open-1.0.
Stanke, M., & Morgenstern, B. (2005). AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.Nucleic Acids Research , 33 , 465–467. https://doi.org/10.1093/nar/gki458
Tracy, A. M., Pielmeier, M. L., Yoshioka, R. M., Heron, S. F., & Harvell, D. C. (2019). Increases and decreases in marine disease reports in an era of global change. Proceedings of the Royal Society B: Biological Sciences , 286 (1912), 20191718. https://doi.org/10.1098/rspb.2019.1718
Tracy, A. M., Weil, E., & Harvell, D. C. (2020). Warming and pollutants interact to modulate octocoral immunity and shape disease outcomes.Ecological Applications , 30 (2), e02024. https://doi.org/10.1002/eap.2024
Weir, B. S., & Cockerham, C. C. (1984). Estimating F-Statistics for the Analysis of Population Structure. Evolution , 38 (6), 1358–1370. https://doi.org/10.2307/2408641
Zenger, K. R., Richardson, B. J., & Vachot-Griffin, A.-M. (2003). A rapid population expansion retains genetic diversity within European rabbits in Australia. Molecular Ecology , 12 (3), 789–794. https://doi.org/10.1046/j.1365-294X.2003.01759.x