What’s all that racket! Soundscapes, phenology, and biodiversity in estuaries
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response to global warming? Proc. Natl. Acad. Sci. U.S.A 96, 5565–5569 (1999). https://doi.org/10. 1073/pnas.96.10.5565 PMID: 10318924 2. Root T. L., Price J. T., Hall K. R., Schneider S. H., Fingerprints of global warming on wild animals and plants (tier 2). Nature 421, 57–60 (2002). 3. Walther G., Post E., Convey P., Menzel A., Parmesan C., Beebee T. J., et al, Ecological responses to recent climate change. Nature 416, 389–395 (2002). https://doi.org/10.1038/416389a PMID: 11919621 4. Edwards M., Richardson A. J., Impact of climate change on marine phenology and tropic mismatch. Nature 430, 881–884 (2004). https://doi.org/10.1038/nature02808 PMID: 15318219 5. Carter S. K., Saenz D., Rudolf V. H. W., Shifts in phenological distributions reshape interaction potential in natural communities. Ecol. Lett. 21, 1143–1151 (2018). https://doi.org/10.1111/ele.13081 PMID: 29927047 6. Pijanowski B. C., Villanueva-Rivera L. J., Dumyahn S. L., Farina A A., Krause BL B. L., Napoletano B. M., et al, Soundscape ecology: The science of sound in the landscape. BioScience 61, 203–216 (2011). PLOS ONE Estuarine soundscapes and biodiversity PLOS ONE | https://doi.org/10.1371/journal.pone.0236874 September 3, 2020 16 / 18
7. Lieth H., (1974) “Purposes of a phenology book” in Phenology and Seasonality Modeling H Lieth, ed, ( Springer-Verlag, New York, NY, 1974), pp. 3–19. 8. Buxton R. T., Brown E., Sharman L., Gabriele C. M., Mckenna M. F., Using bioacoustics to examine shifts in songbird phenology. Ecol. Evol. 14, 1–14 (2016). 9. Sueur J., Pavoine S., Hamerlynck O., Duvail S., Rapid acoustic survey for biodiversity appraisal. PloS One 3, e4065 (2008). https://doi.org/10.1371/journal.pone.0004065 PMID: 19115006 10. Towsey M. W., Parsons S., Sueur J., (2014) Ecology and acoustics at a large scale. Ecol. Inform. 21, 1–3 (2014). 11. Staaterman E., Ogburn M. B., Altieri A. H., Brandl S. J., Whippo R., Seemann J., et al, Bioacoustic mea- surements complement visual biodiversity surveys: preliminary evidence from four shallow marine habi- tats. Mar. Ecol. Prog. Ser. 575, 207–215 (2017). 12. Desiderà E., Guidetti P., Panzalis P., Navone A., Boissery P., Gervaise C., et al, Acoustic fish communi- ties: sound diversity of rocky habitats reflects fish species diversity. Mar. Ecol. Prog. Ser. 608, 183–197 (2019). 13. MacGinitie G. E., Notes on the natural history of several marine Crustacea. Am. Midi. Natural. 18:1031–1036 (1937). 14. Guest W. C., Lasswell J. L., A note on courtship behavior and sound production of red drum. Copeia 1978, 337–338 (1978). 15. Luczkovich J. J., Pullinger R. C., Johnson S. E., Sprague M. W., Identifying sciaenid critical spawning habitats by the use of passive acoustics. Trans. Am. Fish. Soc. 137, 576–605 (2008).
16. Montie E. W., Kehrer C., Yost J., Brenkert K., O’Donnell T., Denson M. R., Long–term monitoring of captive red drum Sciaenops ocellatus reveals that calling incidence and structure correlate with egg deposition. J. Fish. Biol. 88, 1776–1795 (2016). https://doi.org/10.1111/jfb.12938 PMID: 27170109 17. Montie E. W., Hoover M., Kehrer C., Yost J., Brenkert K., O’Donnell T., et al, Acoustic monitoring indi- cates a correlation between calling and spawning in captive spotted seatrout (Cynoscion nebulosus). PeerJ 5:e2944, (2017) https://doi.org/10.7717/peerj.2944 PMID: 28289557 18. Monczak A., Mueller C., Miller M., Ji Y., Borgianini S., Montie E. W., Sound patterns of snapping shrimp, fish, and dolphins in an estuarine soundscape of the southeastern USA. Mar. Ecol. Prog. Ser. 609, 49– 68 (2019). 19. Deegan L. A., Finn J. T., Ayvazian S. G., Ryder-Kieffer C. A., Buonaccorsi J., Development and valida- tion of an estuarine biotic integrity index. Estuaries 20, 601–617 (1997). 20. Harding L. W. Jr, Gallegos C. L., Perry E. S., Miller W. D., Adolf J. E., Mallonee M. E., et al, Long-term trends of nutrients and phytoplankton in Chesapeake Bay. Estuaries and Coasts 39, 664–681 (2015). 21. Harding L. W. Jr, Mallonee M. E., Perry E. S., Miller W. D., Adolf J. E., Gallegos C. L., et al, Variable cli- matic conditions dominate recent phytoplankton dynamics in Chesapeake Bay. Sci. Rep. 6, 23773 (2016). https://doi.org/10.1038/srep23773 PMID: 27026279 22. Curtis K. R., Howe B. M., Mercer J. A., Low-frequency ambient sound in the North Pacific: Long time
series observations. J. Acoust. Soc. Am. 106, 3189–3200 (1999). 23. Ma B. B., Nystuen J. A., Lien R. C., Prediction of underwater sound levels from rain and wind. J. Acoust. Soc. Am. 117, 3555–3565 (2005). https://doi.org/10.1121/1.1910283 PMID: 16018459 24. Haxel J. H., Dziak R. P., Matsumoto H., Observations of shallow water marine ambient sound: The low frequency underwater soundscape of the central Oregon coast. J. Acoust. Soc. Am. 133, 2586–2596 (2013). https://doi.org/10.1121/1.4796132 PMID: 23654367 25. Marley S. A., Erbe C., Salgado Kent C. P., Underwater sound in an urban estuarine river: Sound sources, soundscape contribution, and temporal variability. Acoustics Australia 44: 171–86 (2016). 26. Bohnenstiehl D. R., Lillis A., Eggleston D. B., The curious acoustic behavior of estuarine snapping shrimp: temporal patterns of snapping shrimp sound in sub–tidal oyster reef habitat. PloS One 11, 1– 21 (2016). 27. McQueen K., Marshall C. T., Shifts in spawning phenology of cod linked to rising sea temperatures. ICES J. Mar. Sci. 74, 1561–1573 (2017). 28. Monczak A., Berry A., Kehrer C., Montie E. W., Long–term acoustic monitoring of fish calling provides baseline estimates of reproductive time–lines in the May River estuary, southeastern USA. Mar. Ecol. Prog. Ser. 581, 1–19 (2017). 29. Luczkovich J. J., Sprague M. W., Johnson S. E., Pullinger R. C., Delimiting spawning areas of weakfish, Cynoscion regalis (family Sciaenidae) in Pamlico Sound, North Carolina using passive hydroacoustic surveys. Bioacoustics 10, 143–160 (1999).
30. Mann D. A., Lobel P. S., Passive acoustic detection of sounds produced by the damselfish, Dascyllus albisella (Pomacentridae). Bioacoustics 6, 199–213 (1995). PLOS ONE Estuarine soundscapes and biodiversity PLOS ONE | https://doi.org/10.1371/journal.pone.0236874 September 3, 2020 17 / 18
31. Kharouba H. M., Ehrle´ n J., Gelman A., Bolmgren K., Allen J. M., Travers S. E., et al, Global shifts in the phenological synchrony of species interactions over recent decades. Proc. Natl Acad. Sci. USA, 115, 5211–5216 (2018). https://doi.org/10.1073/pnas.1714511115 PMID: 29666247 32. Visser M. E., Phenology: Interactions of climate change and species. Nature, 535, 236–237 (2016). https://doi.org/10.1038/nature18905 PMID: 27362228 33. Loman J., Breeding phenology in Rana temporaria. Local variation is due to pond temperature and pop- ulation size. Ecol Evol. 6(17):6202–6209 (2016). https://doi.org/10.1002/ece3.2356 PMID: 27648237 34. Van Buskirk J., Mulvihill R. S., Leberman R. C., Variable shifts in spring and autumn migration phenol- ogy in North American songbirds associated with climate change. Glob Chang Biol, 15: 760–771 (2009). 35. Vermeij M. J. A., Marhaver K. L., Huijbers C. M., Nagelkerken I., Stephen D D. (2010) Coral larvae move toward reef sounds. PloS One 5, 3–6 (2010). 36. Lillis A., Eggleston D. B., Bohnenstiehl D. R., Oyster larvae settle in response to habitat–associated underwater sounds. PloS One 8:e79337 (2013). https://doi.org/10.1371/journal.pone.0079337 PMID: 24205381 37. Lillis A., Apprill A., Suca J. J., Becker C., Llopiz J. K., Mooney T. A., Soundscapes influence the settle- ment of the common Caribbean coral Porites astreoides irrespective of light conditions. R. Soc. Open. Sci. 12(5), 181358 (2018). 38. Stanley J. A., Radford C. A., Jeffs A. G., Location, location, location–finding a suitable home in amongst
the noise. Proc. Royal Soc. 279: 3622–3631 (2012). 39. Oksanen J., Blanchet F. G., Friendly M., Kindt R., Legendre P., McGlinn D., et al, vegan: Community Ecology Package. R package version 2.5–4 (2019). 40. Kursa M. B., Rudnicki W. R., Feature selection with the Boruta package. J. Stat. Softw. 36, 1–13 (2010). 41. Kursa M. B., rFerns: an implementation of the random ferns method for general-purpose machine learn- ing. J. Stat. Softw. 61, 10 (2014). 42. Wright M. N., Ziegler A., Ranger: a fast implementation of random forests for high dimensional data in C ++ and R. J. Stat. Softw. 77, 1–17 (2017). 43. Degenhardt F., Seifert S., Szymczak S., Evaluation of variable selection methods for random forests and omics data sets. Brief Bioinform 22, 492–503 (2019). 44. Strobl A. L. Boulesteix, A. Zeileis, T. Hothorn, Bias in random forest variable importance measures: illustrations. Sources and a solution. BMC Bioinformatics 8, 25 (2007). https://doi.org/10.1186/1471- 2105-8-25 PMID: 17254353 45. Altmann A., Toloşi L., Sander O., Lengauer T., Permutation importance: a corrected feature importance measure. Bioinformatics 26, 1340–7 (2010). https://doi.org/10.1093/bioinformatics/btq134 PMID: 20385727 46. Nembrini S., Ko¨ nig I. R., Wright M. N., The revival of the Gini importance? Bioinformatics 34, 3711– 3718 (2018). https://doi.org/10.1093/bioinformatics/bty373 PMID: 29757357 47. Diaz-Uriarte R., de Andres S. A., Gene selection and classification of microarray data using random for- est. BMC Bioinformatics 7, 1–13 (2006). https://doi.org/10.1186/1471-2105-7-1
48. Li J., Siwabessy J., Tran M., Huang Z., Heap A., Predicting seabed hardness using Random Forest in R, in: Data mining applications with R, Zhao Y, Cen Y, Eds. Elsevier p. 299–329 (2013). 49. Breiman L., Random forests. Machine learning, 45, 5–32 (2001). 50. Lau M. K., DTK: Dunnett-Tukey-Kramer pairwise multiple comparison test adjusted for unequal vari- ances and unequal sample sizes. R package version 3.5 (2013). 51. Barry J. A. Hartigan, A Bayesian analysis for change point problems. J. Am. Stat. Assoc. 88, 309–319 (1993). 52. Erdman J. W. Emerson, bcp: an R Package for performing a Bayesian analysis of change point prob- lems. J. Stat. Softw. 23, 1–13 (2007). PLOS ONE Estuarine soundscapes and biodiversity PLOS ONE | https://doi.org/10.1371/journal.pone.0236874 September 3, 2020 18 / 18