Extent of the HyMap survey area and location of the field sites and key locations at Ningaloo Reef.

<p>Outlines of the state and Commonwealth marine park boundaries are also indicated.</p

Overview of the northern region of the Ningaloo Reef with insets illustrating selected habitat maps and corresponding subsurface reflectance.

<p>(Ar) Subsurface reflectance of nearshore, sublittoral pavement along a rocky shore, (A) habitats of extensive macro-algae, limestone pavement and sand. (Br) Subsurface reflectance of outer reef flat, (B) spur and groove structures with coral and macro-algae transitioning to tabulate coral and sand in the deeper lagoon. (Cr) Subsurface reflectance of the littoral alluvial fan off Yardie Creek, (C) habitats with limestone pavement and adjacent macro-algae with sparse coral. (Dr) Subsurface reflectance of the back reef, (D) back reef on the northern edge of the reef pass with clusters of bommies south and east of the reef flats. Legend from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070105#pone-0070105-g005" target="_blank">Figure 5</a> applies.</p

Summary of areas and percentage components of the main cover types mapped in the four regions at Ningaloo Reef.

<p>Summary of areas and percentage components of the main cover types mapped in the four regions at Ningaloo Reef.</p

Example of benthic habitats for the Turquoise Bay area of Ningaloo Reef at the thematic classification level 4a.

<p><b>Legend codes explained in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070105#pone-0070105-t001" target="_blank"><b>Table 1</b></a><b>.</b></b></p

PCA transformed data from image-derived spectra viewed in a two-dimensional space showing continuous (>90% cover) coral classes as well as the tabulate/digitate cluster from Ningaloo Reef.

<p>Axes created through the PCA process removed correlations evident in untransformed spectra and allowed identification of outliers, trends and groups.</p

Illustration of the hierarchical system of classification levels used in the Ningaloo Reef marine habitats look-up table.

<p>Illustration of the hierarchical system of classification levels used in the Ningaloo Reef marine habitats look-up table.</p

Summary of the labelling approach for benthic components at Ningaloo Reef using class label and percentage cover.

<p>Summary of the labelling approach for benthic components at Ningaloo Reef using class label and percentage cover.</p

New hyperspectrally derived (left) and existing (Bancroft and Sheridan) [6], [7] (right) habitat maps for two selected areas in the northern (upper panels) and central regions (lower panels) of Ningaloo Reef.

<p>(A) Reef channel west of Sandy Bay is characterized by a mix of macro-algae and pavement in the new map, contrasting with mostly coral cover in the existing map <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070105#pone.0070105-Bancroft1" target="_blank">[6]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070105#pone.0070105-CALM1" target="_blank">[7]</a>. Spur and groove patterns are evident on the reef flats north and south of the channel, a feature which is missed in the panel on the right. (B) Coral communities around Coral Bay with distinct transitions between coral and macro-algae dominated cover as well as clusters of bommies adjacent to the sandy lagoons which are overrepresented in area in the existing map. Legend for the maps in the left hand panels is the same as on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070105#pone-0070105-g007" target="_blank">Figure 7</a>.</p

Spectral reflectance (mean values) for selected hard corals (top), macro-algae (centre) and abiotic cover (bottom) at Ningaloo Reef.

<p>Spectral reflectance (mean values) for selected hard corals (top), macro-algae (centre) and abiotic cover (bottom) at Ningaloo Reef.</p

Overview of the central region of the Ningaloo Reef with insets illustrating selected habitat maps and corresponding subsurface reflectance.

<p>(Ar) Subsurface reflectance of the edge of the reef flat on the southern edge of a reef pass, (A) habitats of the edge of the reef flat with transition from pavement to patchy macro-algae with a number of coral bommies. (Br) Subsurface reflectance of northern part of a large bay, (B) oval patterns of pavement and sparse macro-algae, with a large bommie in the centre (possibly grazing halos). (Cr) Subsurface reflectance of the Five Fingers Reef, (C) linear limestone ridges with dominant hard coral surrounded by macro-algae due west. (Dr) Subsurface reflectance of a nearshore area south of Pelican Point, (D) complex habitat pattern in the nearshore area with the subtidal platform characterized by pavement, sparse coral, macro-algae and sand. Legend from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070105#pone-0070105-g005" target="_blank">Figure 5</a> applies.</p