readme update citations

README.md

@@ -6,8 +6,7 @@ Scripts for FIU-led manuscript *Ecological roles and importance of sharks in the
 
 ![](./figures/fig1a.png)
 
-
-Powers Figure 1A: Millennial-scale changes in relative reef shark abundance. i: Perceived abundance of sharks off Caribbean Panama inferred from archaeological, historical, ecological, and fisheries records divided into cultural periods in Panama’s history (based on data in Dillon et al 2021. ii: Falling dermal denticle accumulation rates (proxy for relative abundance) suggest 71% (Caribbean Panama, black circles) and 756% (Dominican Republic, gray circles) declines in reef shark abundances since the mid-Holocene. Modified from Dillon et al 2021.
+Figure 1A: Millennial-scale changes in relative reef shark abundance. i: Perceived abundance of sharks in Caribbean Panama inferred from archaeological, historical, ecological, and fisheries records divided into cultural periods in Panama’s history (based on data in (18). ii: Falling dermal denticle accumulation rates (proxy for relative abundance) suggest 71% (Caribbean Panama, black circles) and 75% (Dominican Republic, gray circles) declines in reef shark abundances since the mid-Holocene. Modified from Dillon et al 2021.
 
 ### Data-specific information for Fig1A
 
@@ -65,14 +64,20 @@ Kittinger, J. N., J. M. Pandolfi, J. H. Blodgett, T. L. Hunt, H. Jiang, K. Maly,
 
 ![](./figures/fig1b.png)
 
-powers Figure 1B: Shark landings, relative effort, and CPUE through time. Uses "/data/FAO catch by nation and year.csv"" and "/data/TotalEffortby_FishingCountry_LengthBoat_Gear_Sector.csv". Written by Matias Braccini, [email protected], 2023, edited & packaged by Simon Dedman, [email protected], 2023.
+Figure 1B: Shark landings (Y1; blue area), relative effort (Y2; lines), and CPUE (Y2; dashed line) through time.
+
+Uses "/data/FAO catch by nation and year.csv"" and "/data/TotalEffortby_FishingCountry_LengthBoat_Gear_Sector.csv". Written by Matias Braccini, [email protected], 2023, edited & packaged by Simon Dedman, [email protected], 2023.
 
 ## Counterfactual plots, 1C & 1D
 
 ![](./figures/fig1c.png)
 
+Figure 1C: Reef shark relative abundance (MaxN per drop; Y1; blue line with 95% confidence interval; (MacNeil et al 2020)) and number of global coral reefs (Y2; green histogram; vertical dotted lines are quartiles, SERF (Cinner et al 2016)) along a gradient of human pressure (total gravity (Cinner et al 2018); SERF (Cinner et al 2016)). Shark abundances are highest on remote reefs, which are rare.
+
 ![](./figures/fig1d.png)
 
+Figure 1D: Counterfactual predictions of relative abundance of reef sharks with (status-quo) and without humans (SERF (Cinner et al 2016) models set human-related variables to zero). Expected relative abundance was estimated using MaxN measurements in a global study from 371 reefs (MacNeil et al 2020)).
+
 Code and data to reproduce counterfactual model analyses. Written, edited, & packaged by Natalie Klinnard, [email protected] & [email protected], 2023.
 
 Main data file is available as part of MacNeil et al. 2020 "Global status and conservation potential of reef sharks" here: https://www.dropbox.com/s/wjwld9lrfl1a7pk/FinPrint_Set_Data.csv?dl=0
@@ -81,14 +86,36 @@ Main data file is available as part of MacNeil et al. 2020 "Global status and co
 
 "/data/FinPrint_reefs_gravity.csv" and "/data/totgravity_data.csv" are used in "/R/EROS_gravity_maxN_plots.R" to produce Figure 1C: *Reef shark relative abundance and number of global coral reefs along a gradient of human pressure (total gravity)*. "/data/FinPrint_reefs_gravity.csv" contains the gravity and average MaxN values associated with all 371 reefs sampled as part of FinPrint data associated with MacNeil et al. 2020. "/data/totgravity_data.csv" contains total gravity decimal values for a global distribution of coral reefs created by Dr. Eva Maire, Lancaster University.
 
+### Citations
+
+J. E. Cinner, C. Huchery, M. A. MacNeil, N. A. Graham, T. R. McClanahan, J. Maina, E. Maire, J. N. Kittinger, C. C. Hicks, C. Mora, E. H. Allison, S. D’Agata, A. Hoey, D. A. Feary, L. Crowder, I. D. Williams, M. Kulbicki, L. Vigliola, L. Wantiez, G. Edgar, R. D. Stuart-Smith, S. A. Sandin, A. Green, M. J. Hardt, M. Beger, A. Friedlander, S. J. Campbell, K. E. Holmes, S. K. Wilson, E. Brokovich, A. J. Brooks, J. J. Cruz-Motta, D. J. Booth, P. G. C. Chabanet, M. Tupper, S. C. Ferse, U. R. Sumaila, D. Mouillot, Bright spots among the world’s coral reefs. Nature. 535, 416–419 (2016).
+
+J. E. Cinner, E. Maire, C. Huchery, M. A. MacNeil, N. A. Graham, C. Mora, T. R. McClanahan, M. L. Barnes, J. N. Kittinger, C. C. Hicks, S. D’Agata, A. S. Hoey, G. G. Gurney, D. A. Feary, I. D. Williams, M. Kulbicki, L. Vigliola, L. Wantiez, G. J. Edgar, R. D. Stuart-Smith, S. A. Sandin, A. Green, M. J. Hardt, M. Beger, A. M. Friedlander, S. K. Wilson, E. Brokovich, A. J. Brooksa, J. J. Cruz-Mottab, D. J. Boothc, P. Chabanetd, C. Goughe, M. Tupperf, S. C. Ferseg, U. R. Sumailah, S. Pardede, D. Mouillot, Gravity of human impacts mediates coral reef conservation gains. Proceedings of the National Academy of Sciences. 115, E6116–E6125 (2018).
+
+M. A. MacNeil, D. D. Chapman, M. Heupel, C. A. Simpfendorfer, M. Heithaus, M. Meekan, E. Harvey, J. Goetze, J. Kiszka, M. E. Bond, L. M. Currey-Randall, C. W. Speed, C. S. Sherman, M. J. Rees, V. Udyawer, K. I. Flowers, G. Clementi, J. Valentin-Albanese, T. Gorham, M. S. Adam, K. Ali, F. Pina-Amargós, J. A. Angulo-Valdés, J. Asher, L. García Barcia, O. Beaufort, C. Benjamin, A. T. Bernard, M. L. Berumen, S. Bierwagen, E. Bonnema, R. M. Bown, D. Bradley, E. Brooks, J. J. Brown, D. Buddo, P. Burke, C. Cáceres, D. Cardeñosa, J. C. Carrier, J. E. Caselle, V. Charloo, T. Claverie, E. Clua, J. E. Cochran, N. Cook, J. Cramp, B. D’Alberto, M. de Graaf, M. Dornhege, A. Estep, L. Fanovich, N. F. Farabaugh, D. Fernando, A. L. Flam, C. Floros, V. Fourqurean, R. Garla, K. Gastrich, L. George, R. Graham, T. Guttridge, R. S. Hardenstine, S. Heck, A. C. Henderson, H. Hertler, R. Hueter, M. Johnson, S. Jupiter, D. Kasana, S. T. Kessel, B. Kiilu, T. Kirata, B. Kuguru, F. Kyne, T. Langlois, E. J. Lédée, S. Lindfield, Luna-Acosta, J. Maggs, B. M. Manjaji-Matsumoto, A. Marshall, P. Matich, E. McCombs, D. McLean, L. Meggs, S. Moore, S. Mukherji, R. Murray, M. Kaimuddin, S. J. Newman, J. Nogués, C. Obota, O. O’Shea, K. Osuka, Y. P. Papastamatiou, N. Perera, B. Peterson, A. Ponzo, A. Prasetyo, L. S. Quamar, J. Quinlan, A. Ruiz-Abierno, E. Sala, M. Samoilys, M. Schärer-Umpierre, A. Schlaff, N. Simpson, A. N. Smith, L. Sparks, A. Tanna, R. Torres, M. J. Travers, M. van Zinnicq Bergmann, L. Vigliola, J. Ward, A. M. Watts, C. Wen, E. Whitman, A. J. Wirsing, A. Wothke, E. Zarza-Gonzâlez, J. E. Cinner, Global status and conservation potential of reef sharks. Nature. 583, 801–806 (2020).
+
 ## SankeyAlluvial.R
 
 ![](./figures/fig3b.png)
 
-powers Figure 3B, Sankey/Alluvial plot, uses "/data/SankeyAlluvial.csv". Written, edited, & packaged by Simon Dedman, [email protected], 2023.
+Figure 3B: Alluvial plot of studied sharks’ ecotypes, ecological roles, and strength of evidence from table S1 studies. Competition and/or bottom-up processes binned due to small sample size. Effect size and strength of evidence rated by 30 investigators’ expert opinions scoring source paper metrics on a low/medium/high scale. * = Macropredatory sharks: Pelagic. BU = bottom up, NVS = nutrient vector / storage, SAF = sharks as food, EAE = excretion and egestion.
+
+Uses "/data/SankeyAlluvial.csv". Written, edited, & packaged by Simon Dedman, [email protected], 2023.
 
 ## TraitsRidgeplot.R
 
 ![](./figures/fig5b.png)
 
-powers Figure 5B, traits ridge plot, uses "/data/Traitsridgeplot.xlsx". Written, edited, & packaged by Simon Dedman, [email protected], 2023. Panels arranged and annotated by Kylene Gilmore, kylenegilmoreart.com.
+Figure 5B: Species richness and abundance of sharks decreases along a gradient of market gravity (human impact), along with traits influencing shark movement and trophic interactions. Communities lose wide-ranging individuals that connect habitats, have flexible habitat adaptations that increase resilience, and feed at upper trophic levels. Data from (Simpfendorfer et al 2023, Dulvy et al 2021, Iliou et al 2023, Froese & Pauly 2023).
+
+Uses "/data/Traitsridgeplot.xlsx". Written, edited, & packaged by Simon Dedman, [email protected], 2023. Panels arranged and annotated by Kylene Gilmore, kylenegilmoreart.com.
+
+### Citations
+
+C. A. Simpfendorfer, M. R. Heithaus, M. R. Heupel, M. A. Macneil, M. Meekan, E. Harvey, C. S. Sherman, L. M. Currey-Randall, J. S. Goetze, J. J. Kiszka, M. J. Rees, C. W. Speed, V. Udyawer, M. E. Bond, K. I. Flowers, G. M. Clementi, J. Valentin-Albanese, M. S. Adam, K. Ali, J. Asher, E. Aylagas, O. Beaufort, C. Benjamin, A. T. F Bernard, M. L. Berumen, S. Bierwagen, C. Birrell, E. Bonnema, R. M. K Bown, E. J. Brooks, J. J. Brown, D. Buddo, P. J. Burke, C. Cceres, M. Cambra, D. Cardeosa, J. C. Carrier, S. Casareto, J. E. Caselle, V. Charloo, J. E. Cinner, T. Claverie, E. E. G Clua, J. E. M Cochran, N. Cook, J. E. Cramp, B. M. Dalberto, M. D. Graaf, M. C. Dornhege, M. Espinoza, A. Estep, L. Fanovich, N. F. Farabaugh, D. Fernando, C. E. L Ferreira, C. Y. A Fields, A. L. Flam, C. Floros, V. Fourqurean, L. Gajdzik, L. G. Barcia, R. Garla, K. Gastrich, L. George, T. Giarrizzo, R. Graham, T. L. Guttridge, V. Hagan, R. S. Hardenstine, S. M. Heck, A. C. Henderson, P. Heithaus, H. Hertler, M. H. Padilla, R. E. Hueter, R. W. Jabado, J.-C. Joyeux, V. Jaiteh, M. Johnson, S. D. Jupiter, M. Kaimuddin, D. Kasana, M. Kelley, S. T. Kessel, B. Kiilu, T. Kirata, B. Kuguru, F. Kyne, T. Langlois, F. Lara, J. Lawe, E. J. I Lde, S. Lindfield, A. Luna-Acosta, J. Q. Maggs, B. M. Manjaji-Matsumoto, A. Marshall, L. Martin, D. Mateos-Molina, P. Matich, E. Mccombs, A. Mcivor, D. Mclean, L. Meggs, S. Moore, S. Mukherji, R. Murray, S. J. Newman, J. Nogus, C. Obota, D. Ochavillo, O. O’Shea, K. E. Osuka, Y. P. Papastamatiou, N. Perera, B. Peterson, C. R. Pimentel, F. Pina-Amargs, H. T. Pinheiro, A. Ponzo, A. Prasetyo, L. M. Sjamsul Quamar, J. R. Quinlan, J. A. Reis-Filho, H. Ruiz, A. Ruiz-Abierno, E. Sala, P. S. De-Len, M. A. Samoilys, W. R. Sample, M. S.- Umpierre, A. M. Schlaff, K. Schmid, S. N. Schoen, N. Simpson, A. N. H Smith, J. L. Y Spaet, L. Sparks, T. Stoffers, A. Tanna, R. Torres, M. J. Travers, M. V. Zinnicq Bergmann, L. Vigliola, J. Ward, J. D. Warren, A. M. Watts, C. K. Wen, E. R. Whitman, A. J. Wirsing, A. Wothke, E. Zarza-Gonzlez, D. D. Chapman, Widespread diversity deficits of coral reef sharks and rays. Science. 380, 1155–1160 (2023).
+
+N. K. Dulvy, N. Pacoureau, C. L. Rigby, R. A. Pollom, R. W. Jabado, D. A. Ebert, B. Finucci, C. M. Pollock, J. Cheok, D. H. Derrick, K. B. Herman, C. S. Sherman, W. J. VanderWright, J. M. Lawson, R. H. Walls, J. K. Carlson, P. Charvet, K. K. Bineesh, D. Fernando, G. M. Ralph, J. H. Matsushiba, C. Hilton-Taylor, S. V. Fordham, C. A. Simpfendorfer, Overfishing drives over one-third of all sharks and rays toward a global extinction crisis. Current Biology (2021), doi:10.1016/j.cub.2021.08.062.
+
+A. S. Iliou, W. Vanderwright, L. Harding, D. M. Jacoby, N. L. Payne, N. K. Dulvy, Tail shape and the swimming speed of sharks. Royal Society Open Science. 10, 231127 (2023).
+
+R. Froese & D. Pauly. FishBase version 10/2023. www.fishbase.org. Fisheries Centre, University of British Columbia Vancouver, BC, Canada