Appendix B. Eight tables presenting proxy diversity estimates, data and model characteristics, and statistical results.
TABLE B1. Estimated proxy gamma diversity (gp) slopes for the (a) reef within atoll and (b) atoll levels for atolls within the Tuamotu Archipelago.
Factor |
SE |
t |
P |
||||
a) Reef within atoll |
|
|
|
|
|||
Gamma diversity proxy |
|
|
|
||||
|
Fixed effects |
|
|
|
|
||
Intercept |
6.43 |
3.01 |
2.07 |
0.05 |
|||
pr,gp |
0.242 |
0.036 |
6.77 |
<0.001 |
|||
Observed gamma diversity |
|
|
|
||||
|
Fixed effects |
|
|
|
|
||
Intercept |
8.27 |
4.50 |
1.84 |
0.075 |
|||
pr,ob |
0.207 |
0.051 |
4.09 |
<0.001 |
|||
b) Atoll |
|
|
|
|
|||
Gamma diversity proxy |
|
|
|
||||
|
Fixed effects |
|
|
|
|
||
|
Intercept |
-6.54 |
7.96 |
-0.82 |
0.448 |
||
|
pa,gp |
0.646 |
0.054 |
11.88 |
<0.001 |
||
Observed gamma diversity |
|
|
|
||||
|
Fixed effects |
|
|
|
|
||
|
Intercept |
0.59 |
9.73 |
0.06 |
0.95 |
||
|
pa,ob |
0.575 |
0.069 |
8.37 |
<0.001 |
||
TABLE B2. Habitat factors used to derive habitat Shannon diversity, H'.
Measure |
Description |
Mud |
Silts and clays; very fine particles |
Fine sand |
Small grains; silica and carbonate particles |
Coarse sand |
Large grains; silica and carbonate particles |
Gravel |
Small rock pieces; no fine particles present |
Debris |
Uneven bottom with mixed rocks and rubble |
Small blocks |
Consistent carbonate rubble below 20 cm3 |
Large blocks |
Consistent carbonate rubble above 20 cm3 |
Rocks |
Rock pieces above 10 cm3 |
Rock slab |
Smooth rock face |
Coral structure |
Dead coral; structurally intact |
Filamentous algae |
Fine turf algae dominates |
Macroalgae |
Large algae dominates |
Live coral |
Live complex coral structures |
Large rocks |
Boulders >300 cm in diameter |
Meuble |
Soft bottoms; mixed composition |
Detritus |
High proportion of dead organic material |
TABLE B3. Reef type definitions from the Typatoll program (see Appendix A: Variable selection for more complete descriptions).
Reef type | Description |
Motu |
Lagoon areas adjacent to emerged vegetated sand islets |
Hoa |
Lagoon areas edging shallow reef flat spillways |
Reef rim |
Areas usually submerged at high tide and devoid of vegetation |
Pinnacle |
Coral structures inside the lagoon |
Pass |
Reef rim aperture |
Other |
Atypical areas |
TABLE B4. Number of transects Nt, reef types Nr, and mean (range) of selected characteristics for sampled atolls within the Tuamotu Archipelago.
|
|
|
Transect-level |
||||
Atoll |
Nt |
Nr |
Depth (m) |
Habitat diversity H' |
Exposure (rad) |
E–W (°) |
N–S (°) |
Haraiki |
44 |
6 |
3.12 (0.38, 9.40) |
1.42 (0.66, 2.06) |
1.50 (0.0, 3.14) |
0.0 (-0.16, 0.03) |
0.0 (-0.28, 0.02) |
Hikueru |
70 |
6 |
3.35 (0.50, 14.8) |
1.38 (0.40, 1.90) |
1.13 (0.0, 3.14) |
0.0 (-0.07, 0.07) |
0.0 (-0.05, 0.03) |
Hiti |
52 |
3 |
6.18 (0.66, 13.02) |
1.37 (0.22, 2.08) |
1.57 (0.0, 2.36) |
0.0 (-0.02, 0.03) |
0.0 (-0.02, 0.02) |
Kauehi |
68 |
5 |
6.37 (1.54, 14.62) |
1.45 (0.10, 2.12) |
1.39 (0.0, 3.14) |
0.0 (-0.13, 0.78) |
0.0 (-0.47, 0.12) |
Marokau |
72 |
4 |
6.81 (0.40, 22.38) |
1.53 (0.06, 2.08) |
1.31 (0.0, 3.14) |
0.0 (-0.09, 0.11) |
0.0 (-0.07, 0.11) |
Nihiru |
72 |
4 |
6.30 (1.02, 15.18) |
1.35 (0.22, 2.04) |
1.35 (0.0, 3.14) |
0.0 (-0.06, 0.05) |
0.0 (-0.06, 0.05) |
Reka-Reka |
23 |
3 |
1.01 (0.50, 2.02) |
0.85 (0.0, 1.58) |
0.96 (0.0, 2.36) |
0.0 (-0.004, 0.004) |
0.0 (-0.06, 0.06) |
Taiaro |
36 |
2 |
4.21 (1.30, 10.28) |
1.54 (0.95, 2.08) |
1.75 (0.0, 3.14) |
0.0 (-0.09, 0.03) |
0.0 (-0.03, 0.06) |
Tekokota |
36 |
4 |
2.26 (1.00, 4.90) |
1.46 (0.68, 1.89) |
1.40 (0.0, 3.14) |
0.0 (-0.02, 0.02) |
0.0 (-0.01, 0.01) |
Tepoto |
36 |
3 |
3.05 (0.86, 6.16) |
1.22 (0.23, 1.96) |
1.48 (0.0, 3.14) |
0.0 (-0.01, 0.01) |
0.0 (-0.01, 0.01) |
|
|
|
|
||||
|
|
|
Atoll-level |
||||
|
|
|
Archipelago position (PCA) |
Fishing pressure (persons/km2 reef) |
Lagoon size (km2) |
Connectedness (km2) |
|
Haraiki |
|
|
-0.22 |
0.03 |
10.43 |
0.50 |
|
Hikueru |
|
|
-0.99 |
0.002 |
82.47 |
0.44 |
|
Hiti |
|
|
0.72 |
0.00 |
15.28 |
2.50 |
|
Kauehi |
|
|
2.09 |
0.001 |
315.12 |
3.60 |
|
Marokau |
|
|
-1.53 |
0.004 |
217.50 |
5.22 |
|
Nihiru |
|
|
-0.32 |
0.007 |
79.51 |
0.74 |
|
Reka-Reka |
|
|
-1.16 |
0.00 |
0.74 |
0.10 |
|
Taiaro |
|
|
1.70 |
0.00 |
11.84 |
0.63 |
|
Tekokota |
|
|
-0.88 |
0.00 |
5.11 |
0.60 |
|
Tepoto |
|
|
0.83 |
0.00 |
1.56 |
2.03 |
|
TABLE B5. Candidate factors used to evaluate the inference weights for potential reef processes at the regional (atoll) and local (transect) scales. Singlefactor models were considered to represent hypothesis with which they are associated in multiple factor model.
Model |
Regional |
Local factor |
Biological interpretation (hypothesis) |
Spatial |
Atoll position |
Transect |
Biogeographic positions of atolls and local spatial position determine community structure, due to underlying, scale-wide gradients |
Habitat |
Lagoon size |
Habitat |
Habitat diversity and larger reef areas create more potential niches for fish communities |
Dispersal potential |
Atoll |
Transect |
Size and proximity of adjacent atolls and |
TABLE B6. Hierarchical intercept-model comparisons for best-fit models of species richness, abundance, and biomass in reef fishes from the Tuamotu Archipelago. Model criteria include AIC and log-likelihood (log-L); best-fitting hierarchical structures to predict group means are highlighted in boldface. Three-level hierarchical model (Mart) groupings were transect (t, level-1), reef type (r, level-2), and atoll (a, level-3); two-level hierarchical model (Ma.r) groupings were transect (t, level-1) and atoll (a, level-2); and the basic linear model (M..t) was at the transect level only. Net ΔAIC values are given in parentheses.
|
Richness |
log(Abundance) |
log(Biomass) |
DCAa |
M.t |
|
|
|
|
log-L |
-2023.1 |
-794.5 |
-1146.6 |
-615.6 |
AIC |
4052.1 |
1594.9 (279.6) |
2299.2 (319.6) |
1237.2 (307.0) |
Ma.t |
|
|
|
|
log-L |
-1949.1 |
-690.1 |
-999.0 |
-478.1 |
AIC |
3904.3 |
1386.2 (70.9) |
2003.9 (24.3) |
962.3 (32.1) |
Mart |
|
|
|
|
log-L |
-1891.1 |
-653.6 |
-985.8 |
-461.1 |
AIC |
3790.3 |
1315.3 (0.0) |
1979.6 (0.0) |
930.2 (0.0) |
TABLE B7. Results for the top AIC-ranked models for species richness, log(biomass), and DCAa of reef fishes in the Tuamotu Archipelago. Results include slope estimates
(), standard errors [], and confidence intervals (CI). Note that random-effect estimates are variance components.
|
Factor |
90% CI |
|||
Richness |
|
|
|
||
HSTA,mixed |
|
|
|||
|
Fixed effects |
|
|
|
|
|
Intercept |
12.79 |
2.43 |
(8.80, 16.79) |
|
|
Lagoon size |
0.06 |
0.01 |
(0.04, 0.08) |
|
|
Habitat diversity |
4.88 |
1.09 |
(3.08, 6.68) |
|
|
Random effects |
|
|
|
|
|
Interceptreef |
8.37 |
- |
(6.26, 11.87) |
|
|
Interceptatoll |
0.002 |
- |
(0.00, 0.01) |
|
log(Biomass) |
|
|
|
||
HSTA,mixed |
|
|
|||
|
Fixed effects |
|
|
|
|
|
Intercept |
6.61 |
0.66 |
(5.53, 7.70) |
|
|
Lagoon size |
0.008 |
0.004 |
(0.00, 0.02) |
|
|
Habitat diversity |
0.72 |
0.19 |
(0.41, 1.03) |
|
|
Random effects |
|
|
|
|
|
Interceptreef |
1.49 |
- |
(0.98, 2.26) |
|
|
Interceptatoll |
0.66 |
- |
(0.45, 0.99) |
|
|
|
|
|
|
|
HST,mixed |
|
|
|||
|
Fixed effects |
|
|
|
|
|
Intercept |
7.27 |
0.63 |
(6.23, 8.30) |
|
|
Habitat diversity |
0.72 |
0.19 |
(0.41, 1.03) |
|
|
Random effects |
|
|
|
|
|
Interceptreef |
1.75 |
- |
(1.18, 2.61) |
|
|
Interceptatoll |
0.66 |
- |
(0.44, 0.98) |
|
DCAa |
|
|
|
||
HST,mixed |
|
|
|||
|
Fixed effects |
|
|
|
|
|
Intercept |
2.24 |
0.22 |
(1.81, 2.68) |
|
|
Habitat diversity |
-0.20 |
0.07 |
(-0.34, -0.07) |
|
|
Random effects |
|
|
|
|
|
Interceptreef |
0.61 |
- |
(0.37, 0.99) |
|
|
Interceptatoll |
0.25 |
- |
(0.16, 0.37) |
TABLE B8. Results for the top AIC-ranked models of functional-group log(abundance) for reef fishes in the Tuamotu Archipelago. Results include slope estimates (), standard errors [], and confidence intervals (CI). Note that random-effect estimates are variance components.
|
Factor |
90% CI |
||
Detritivores |
|
|
|
|
DPT,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
1.26 |
0.25 |
(0.77, 1.75) |
|
Exposure |
0.30 |
0.06 |
(0.18, 0.41) |
|
Random effects |
|
|
|
|
Interceptreef |
0.62 |
- |
(0.32, 1.21) |
|
Interceptatoll |
0.70 |
- |
(0.47, 1.05) |
|
|
|
|
|
DPTA,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
1.20 |
0.35 |
(0.51, 1.88) |
|
Connectedness |
0.04 |
0.15 |
(-0.30, 0.38) |
|
Exposure |
0.30 |
0.06 |
(0.18, 0.41) |
|
Random effects |
|
|
|
|
Interceptreef |
0.63 |
- |
(0.32, 1.21) |
|
Interceptatoll |
0.70 |
- |
(0.47, 1.05) |
Grazers |
|
|
|
|
DPT,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
1.88 |
0.29 |
(1.30, 2.45) |
|
Exposure |
0.32 |
0.06 |
(0.20, 0.43) |
|
Random effects |
|
|
|
|
Interceptreef |
0.75 |
- |
(0.38, 1.50) |
|
Interceptatoll |
0.85 |
- |
(0.59, 1.22) |
|
|
|
|
|
DPTA,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
1.85 |
0.42 |
(1.03, 2.67) |
|
Connectedness |
0.02 |
0.18 |
(-0.39, 0.42) |
|
Exposure |
0.32 |
0.06 |
(0.20, 0.43) |
|
Random effects |
|
|
|
|
Interceptreef |
0.75 |
- |
(0.38, 1.50) |
|
Interceptatoll |
0.85 |
- |
(0.60, 1.22) |
Scrapevators |
|
|
|
|
HSTA,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
1.45 |
0.31 |
(0.85, 2.05) |
|
Lagoon size |
0.003 |
0.002 |
(-0.001, 0.007) |
|
Habitat diversity |
0.52 |
0.13 |
(0.26, 0.78) |
|
Random effects |
|
|
|
|
Interceptreef |
0.42 |
- |
(0.14, 1.30) |
|
Interceptatoll |
0.76 |
- |
(0.53, 1.10) |
|
|
|
|
|
HST,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
1.71 |
0.30 |
(1.14, 2.29) |
|
Habitat diversity |
0.52 |
0.13 |
(0.25, 0.78) |
|
Random effects |
|
|
|
|
Interceptreef |
0.57 |
- |
(0.26, 1.26) |
|
Interceptatoll |
0.76 |
- |
(0.53, 1.08) |
Planktivores |
|
|
|
|
HSTA,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
1.41 |
0.48 |
(0.47, 2.35) |
|
Lagoon size |
0.0098 |
0.003 |
(0.002, 0.017) |
|
Habitat diversity |
0.28 |
0.16 |
(-0.04, 0.60) |
|
Random effects |
|
|
|
|
Interceptreef |
0.99 |
- |
(0.57, 1.73) |
|
Interceptatoll |
0.70 |
- |
(0.46, 1.08) |
|
|
|
|
|
HSA,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
1.78 |
0.44 |
(0.93, 2.63) |
|
Lagoon size |
0.010 |
0.003 |
(0.002, 0.018) |
|
Random effects |
|
|
|
|
Interceptreef |
1.00 |
- |
(0.53, 1.86) |
|
Interceptatoll |
0.75 |
- |
(0.51, 1.12) |
Corallivores |
|
|
|
|
HST,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
0.14 |
0.16 |
(-0.16, 0.45) |
|
Habitat diversity |
0.35 |
0.08 |
(0.20, 0.51) |
|
Random effects |
|
|
|
|
Interceptreef |
0.19 |
- |
(0.04, 0.94) |
|
Interceptatoll |
0.50 |
- |
(0.35, 0.71) |
|
|
|
|
|
HSTA,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
0.04 |
0.18 |
(-0.29, 0.37) |
|
Lagoon size |
0.0013 |
0.0001 |
(-0.001, 0.003) |
|
Habitat diversity |
0.35 |
0.08 |
(0.19, 0.51) |
|
Random effects |
|
|
|
|
Interceptreef |
0.12 |
- |
(0.004, 3.57) |
|
Interceptatoll |
0.50 |
- |
(0.35, 0.71) |
Invertivores |
|
|
|
|
SST,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
4.03 |
0.26 |
(3.52, 4.53) |
|
Transect position (E) |
0.36 |
0.20 |
(-0.03, 0.74) |
|
Transect position (N) |
-0.84 |
0.51 |
(-1.83, 0.16) |
|
Random effects |
|
|
|
|
Interceptreef |
0.70 |
- |
(0.37, 1.24) |
|
Interceptatoll |
0.54 |
- |
(0.37, 0.78) |
Piscivores |
|
|
|
|
HSA,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
1.29 |
0.11 |
(1.07, 1.50) |
|
Lagoon size |
0.0033 |
0.0001 |
(0.002, 0.005) |
|
Random effects |
|
|
|
|
Interceptreef |
0.06 |
- |
(0.00, 10.00) |
|
Interceptatoll |
0.45 |
- |
(0.28, 0.64) |
|
|
|
|
|
HSTA,mixed |
|
|
||
|
Fixed effects |
|
|
|
|
Intercept |
1.15 |
0.16 |
(0.83, 1.47) |
|
Lagoon size |
0.0032 |
0.0001 |
(0.002, 0.005) |
|
Habitat diversity |
0.10 |
0.09 |
(-0.08, 0.28) |
|
Random effects |
|
|
|
|
Interceptreef |
0.06 |
- |
(0.00, 10.00) |
|
Interceptatoll |
0.41 |
- |
(0.27, 0.63) |