Fish abundance estimation

How fish abundance is estimated


Estimating the abundance of wild populations is vital for sustainable management of biological resources, particularly fisheries. It supports the UN’s Sustainable Development Goal 14 “Conserve and sustainably use the oceans, seas and marine resources for sustainable development”. However, abundance is difficult to estimate accurately. This article introduces the methods in place

Different methods for abundance estimation:

  1. Poisoning

  2. Photo identification

  3. Baited remote underwater video

  4. Diver-based Underwater Visual Censuses

  5. Mark-recapture

  6. Close-kin mark-recapture

  1. Poisoning

Historically, fish inventories were carried out via the comprehensive but destructive technique of poisoning a given area of the reef and then collecting and classifying the dead fish. The method consists of installing nets to create an enclosure and then pouring Rotenone, which acts by blocking the cellular uptake of oxygen.

Indigenous fishers have traditionally crushed native rotenone-containing-plants and applied them to marine and freshwater to catch fish. Fishery managers often use large quantities of rotenone to kill-off invasive or unwanted fishes in freshwater systems, then restock the system with native fish to conserve the natural ecosystem or to support recreational fisheries. Scientists have also used rotenone as a tool to assess fish diversity and abundance in marine and freshwater environments. Source

Restrictions on rotenone use in marine research are increasingly being imposed worldwide

  1. Photo identification and Citizen Science

Photo-ID studies have become common in studies of sharks and rays, and provide a means to non-invasively sample species under threat. Photo-ID has been used most recently as the basis for estimating abundance and movements within the eastern Australian GNS population. This method also provides an excellent opportunity for the public to assist research (i.e. citizen science). Even though care must be exercised to account for inherent biases in photo-ID studies, their use in establishing a baseline index of abundance, and with enough time possibly trend, is invaluable. Photo-ID could also be coupled with tissue sampling to assist with assessing the accuracy of photo-ID. Source

  1. Baited remote underwater video (BRUV)

It is a system used in marine biology research. By attracting fish into the field of view of a remotely controlled camera, the technique records fish diversity, abundance and behaviour of species. Sites are sampled by video recording the region surrounding a baited canister which is lowered to the bottom from a surface vessel or less commonly by a submersible or remotely operated underwater vehicle. The video can be transmitted directly to the surface by cable, or recorded for later analysis.

Baited cameras are highly effective at attracting scavengers and subsequent predators, and are a non-invasive method of generating relative abundance indices for a number of marine species.

As a non-extractive technique, it offers a low environmental impact way of understanding changes in fish numbers and diversity over time. BRUV surveys were developed in Australia, and are now used around the world for a variety of projects. This is a low budget monitoring system that is less reliant on the availability of skilled labour and may make sustainable monitoring more practical, over the long term. [Source: Wikipedia]

  1. Diver-based Underwater Visual Censuses

These methods rely on divers identifying species and recording their presence on slates, either by following a precise path or not.

They are key tools in the study of coral reef fish ecology. These techniques, however, have inherent problems that make it difficult to collect accurate numerical data.

One of these problems is the "diver effect" (defined as the reaction of fish to a diver). The presence of a diver can cause some fishes to move away or hide, while others may be attracted, thereby decreasing or increasing counts

The Roving Diver Survey Method

Very popular with citizen science surveys because it only requires the ability to recognise the fish and take notes on a slate. Volunteering divers and snorkelers swim freely throughout a site and record every observed fish species that can be positively identified. Species and approximate abundance scores are recorded on an underwater slate.The Reef Fish Survey, a global program, has been leveraging this method.

The Transect Survey Method

Similar to the previous one, but the diver counts occurrences while moving along a fixed path called "transect". A transect line is any line, marked at regular intervals, that is easy to use in the field. Another type of transect is a "quadrat", represented by a framed area. A frame can be made using PVC pipes, wire hangers bent into squares, hula-hoops, wooden dowels or even cardboard. There are several types of transect. It requires an observer to move along a fixed path and to count occurrences along the path.

  1. Capture-mark-release-recapture method

It is a method commonly used in ecology to estimate an animal population's size where it is impractical to count every individual.[1] A portion of the population is captured, marked, and released. Later, another portion will be captured and the number of marked individuals within the sample is counted. Since the number of marked individuals within the second sample should be proportional to the number of marked individuals in the whole population, an estimate of the total population size can be obtained by dividing the number of marked individuals by the proportion of marked individuals in the second sample.

Advantage: Scientists are able to estimate population size when it is too difficult to count individuals; Disadvantage: Estimates are not always accurate.

Formula for estimating total population:

Total population = (Number caught on day 2 / number observed tagged on day 2) x number tagged on day 1

20 = (4/1) x 5


  1. Close-kin mark-recapture

Differently from the traditional mark-recapture, the method does not require the same specimen to be captured twice, but instead it is based on the principle that an individual’s genotype can be considered a “recapture” of the genotypes of each of its parents.

Uses genetic and statistical techniques to identify family relationships, specifically parent-offspring pairs and half-sibling pairs.

The basic principle is that when the population of a species is small, randomly sampled specimens will be likely to have some level of family relationship. On the contrary, large populations will have a low degree of family relationship. Just imagine visiting a small village and expecting some level of kinship as compared to a big town.

The samples can be collected from the live fish as well from dead ones.

It has been used for estimating the population of bluefin tuna, white sharks, Grey nurse sharks.

When coupled with a species’ demographics model it is possible to use genetic relatedness to derive an absolute contemporary population estimate for the adult population.

Given adequate sampling, the number of kin-pairs found, and their spread in time, can be used in a mathematically sound and transparent mark-recapture framework (Bravington et al. 2016b) to estimate adult abundance, and potentially trend.

Age-at-maturity is an important parameter informing the CKMR model, that’s why it’s important to know the correlation between the size of the fish and its age, to understand if the captured specimen is mature or not.

To know more:

Webinar: Can a Novel Genetic Approach Improve Shortfin Mako Shark Management in the Atlantic Ocean? segment 17’-19’

Close-Kin Mark-Recapture Mark V. Bravington, Hans J. Skaug and Eric C. Anderson

Examples of methods applied in Australia, results and policy impact (Grey Nurse sharks, Weedy Seadragons, …)

Using CKMR the total population of the eastern GNS was estimated to be 2167 with a annual rate of increase of 3.4%

Sizing up Australia’s eastern Grey Nurse Shark population

The species is listed as “vulnerable” on the IUCN Red List of Threatened Species (Pollard & Smith 2009) as a result of observed declines in GNS numbers worldwide. The eastern Australian population has been declared “critically endangered” under the Australian Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act) and as such is the subject of an on-going recovery plan.

How do you collect DNA samples from live fish?