Ecological Archives E090-016-A2

M. Aaron MacNeil, Nicholas A. J. Graham, Nicholas V. C. Polunin, Michel Kulbicki, René Galzin, Mireille Harmelin-Vivien, and Steven P. Rushton. 2009. Hierarchical drivers of reef-fish metacommunity structure. Ecology 90:252–264.

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
factor

Local factor

Biological interpretation (hypothesis)


Spatial
separation

Atoll position
in archipelago

Transect
position in atoll

Biogeographic positions of atolls and local spatial position determine community structure, due to underlying, scale-wide gradients

Habitat
specialization

Lagoon size

Habitat
diversity

Habitat diversity and larger reef areas create more potential niches for fish communities

Dispersal potential

Atoll
connectedness

Transect
exposure

Size and proximity of adjacent atolls and
level of exposure to currents reflect potential dispersal of larval recruits


 

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)



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