Reef Check News

Where do I place my transect line given a highly variable coral reef and then, how do I avoid bias introduced by variable amounts of soft seabed?


Each month, Reef Check will answer a technical question regarding the monitoring protocol of our coral reef or rocky reef programs. If you have a question you would like answered, please email

Reef Check Tropical: Where do I place my transect line given a highly variable coral reef and then, how do I avoid bias introduced by variable amounts of soft seabed?

Many coral reefs are patchy or formed in shapes that follow the hard substrate. In these reefs, the intervening spaces are often dominated by bare sand or seagrass. Reef Check does not advocate the use of random sampling because it can result in a waste of resources when by chance, transects are clumped together in one area and spread very thinly in another; therefore, additional surveys are needed. But it should be recognized that by choosing the path of the transect line, this may introduce bias.

The goal of Reef Check is not to survey sand or seagrass beds. The goal is to survey areas of reef where hard or soft coral can grow – mainly hard substrate. Therefore, great care should be taken when ensuring that the transect follows the reef. In most cases, the coral cover estimate obtained in this manner will be higher than what would be obtained if the transect passed over areas of sand or seagrass.

Thirty years ago in the Caribbean, staghorn coral or Acropora cervicornis, formed an entire zone that occupied soft sandy reef slopes. That zone no longer exists due to the rarity of this species. In the tropical Pacific, a number of coral species inhabit soft seabed and some can cover large areas. However, most coral is found growing on hard substrate – typically the old reef rock.

Therefore, the amount of hard substrate versus soft seabed on a reef can affect the percentage of coral calculated as given above, particularly in the Caribbean. For example, when surveying a “spur and groove” reef or small patch reefs, the transect will inevitably pass across some significant areas of bare sand between the spurs or patches. This could reduce the total possible coral cover when compared with a uniform reef with little soft seabed. As a rule of thumb, if the areas between reefs exceed 5m then consider restarting the transect where the reef starts again.

Reef Check data sheets are pre-programmed to calculate percentage of all substrate types including hard coral cover. The latter is calculated as the total number of hard coral “hits” recorded on the transect divided by the total number of sample points (160) per transect.  Therefore, in cases where the percentage of hard substrate is variable, alternatives are to calculate the living coral as an index – dividing living by living plus recently killed coral. To minimize bias from variable amounts of soft seabed, simply calculate the index as living coral divided by living plus recently killed coral and rock. This index represents the percentage of hard substrate covered by live coral. As usual, there are many different ways to present data. As long as a clear description is provided of the methods used, the reader will be able to understand the results.