Cross-Shelf Habitat Occupancy Probabilities for Juvenile Groupers in the Florida Keys Coral Reef Ecosystem

Figures & data

FIGURE 1. Map of the Florida Keys coral reef tract. Reef strata are described in Table 1.

TABLE 1. Physical and biological habitat characteristics of primary sampling units (PSUs) during 2003–2011. Abbreviations are as follows: n = the number of PSUs sampled, min = the minimum value, max = the maximum value, and avg = the mean value.

			Bottom depth (m)			Vertical relief (m)			% Coral cover			Latitude (decimal degrees)			% Hard bottom
Habitat stratum type	Rugosity	n	Min	Avg	Max	Min	Avg	Max	Min	Avg	Max	Min	Avg	Max	Min	Avg	Max
i. Inshore patch	Low–med	99	1.8	3.5	7.8	0.10	1.16	3.12	0	13.8	45.6	24.51	24.96	25.74	17.5	75.6	100
ii. Midchannel patch	Low–med	390	1.5	5.3	12.6	0.12	1.37	4.27	0	10.7	52.2	24.46	25.03	25.52	10.7	77.1	100
iii. Offshore patch	Low–med	228	2.1	7.0	13.5	0.10	1.08	4.00	0.2	6.2	32.2	24.44	24.91	25.55	12.5	73.2	100
iv. Offshore patch	High	45	2.2	6.2	12.4	0.90	2.41	3.97	2.2	9.0	26.0	25.10	25.11	25.29	35.0	79.2	98.2
v. Outer fore reef	Low–med	1,184	2.1	9.0	18.0	0.10	0.79	3.20	0	3.3	25.0	24.43	24.97	25.74	0	70.6	100
vi. Outer fore reef	High	279	2.8	6.6	17.1	0.32	2.19	4.42	0.6	5.3	36.8	24.43	24.76	25.58	23.7	74.2	100

TABLE 2. Variable inclusion probabilities and coefficient means for Red Grouper statistical models. Asterisks indicate variables included in resource selection functions; values in parentheses are standard errors; na = not applicable.

	Variable inclusion probability		Site occupancy coefficient means
Parameter	Logistic regression	Site occupancy	Base diffuse priors	t-distribution diffuse priors
Occurrence submodel
Mean slope ()
Depth	0.02	0.13	na	na
Vertical relief	0.91*	0.27	na	na
% Coral cover	0.01	0.03	na	na
Latitude	0.01	0.03	na	na
% Hard bottom	0.00	0.02
Random slopes ()
Depth	0.14	0.16	na	na
Vertical relief	0.16	0.27	na	na
% Coral cover	0.11	0.44	na	na
Latitude	0.61	0.57	na	na
% Hard bottom	0.02	0.07	na	na
Reef stratum (s)	1.00*	1.00*	0.71 (0.75)	0.66 (0.75)
Strata i to vi			0.92 (0.68)	0.80 (0.69)
			0.86 (0.70)	0.75 (0.69)
			0.35 (1.05)	0.41 (1.05)
			–0.49 (0.65)	–0.58 (0.65)
			–2.31 (0.72)	–2.44 (0.75)
Grand mean ()	na	na	–0.06 (0.65)	0.04 (0.66)
Conditional submodel
Mean slope ()
Depth	na	0.13	na
Vertical relief	na	0.78*	–0.52 (0.08)	–0.53 (0.07)
% Coral cover	na	0.01	na
Grand mean ()	na	na	–0.88 (0.11)	–0.89 (0.11)

FIGURE 2. Goodness-of-fit plots for Red Grouper resource selection functions. Shown are the observed and replicated discrepancy measures calculated from the squared Pearson residuals for each binomial model formulation.

FIGURE 3. Intercept odds ratios of Red Grouper occurrence in each reef stratum. Odds ratios were calculated relative to reference stratum i, defined as low–medium relief inshore patch reefs. The circles denote means, and the lines are centered 95% confidence intervals.

TABLE 3. Variable inclusion probabilities and coefficient means for Black Grouper statistical models. Asterisks indicate variables included in resource selection functions; values in parentheses are standard errors; na = not applicable.

	Variable inclusion probability		Site occupancy coefficient means
Parameter	Logistic regression	Site occupancy	Base diffuse priors	t-distribution diffuse priors
Occurrence submodel
Mean slope ()
Depth	0.02	0.09	na	na
Vertical relief	0.90*	0.04	na	na
% Coral cover	0.29	0.04	na	na
Latitude	0.98*	0.80*	–1.10 (0.15)	–1.09 (0.15)
% Hard bottom	0.01	0.10	na	na
Random slopes ()
Depth	0.99*	1.00*	–1.02 (0.66)	–0.99 (0.63)
Strata i to vi			–1.21 (0.32)	–1.20 (0.32)
			0.07 (0.41)	0.06 (0.41)
			–1.14 (0.70)	–1.12 (0.68)
			0.20 (0.14)	0.20 (0.14)
			2.19 (0.49)	2.15 (0.49)
Vertical relief	0.36	0.11	na	na
% Coral cover	0.05	0.05	na	na
Latitude	0.05	0.39	na	na
% Hard bottom	0.03	0.18	na	na
Reef stratum (s)	0.31	0.05	na	na
Grand mean ()	na	na	0.17 (0.19)	0.15 (0.19)
Observation submodel
Mean slope ()
Depth	na	0.06	na	na
Vertical relief	na	1.00*	0.61 (0.06)	0.61 (0.06)
% Coral cover	na	0.04	na	na
Grand mean ()	na	na	–1.23 (0.09)	–1.22 (0.09)

FIGURE 4. (A) Red Grouper responses to maximum vertical relief from the occurrence submodel () and (B) the observation submodel (p). The solid (1) and dashed (2) lines correspond to the logistic regression and site occupancy formulations, respectively.

FIGURE 5. Black Grouper responses to (A) latitude and (B) maximum vertical relief from the occurrence submodel () and (C) vertical relief from observation submodel (p). The solid (1) and dashed (2) lines correspond to the logistic regression and site occupancy formulations, respectively.

FIGURE 6. Conditional responses in Black Grouper occurrence probability () to depth within each reef stratum for the logistic regression and site occupancy model formulations. Reef strata (i–vi) are described in Table 1. Only reef strata with statistically significant slope coefficients are shown.