Development of a genetic/morphological databank for the identification of wild eggs of Australian marine fishes (APSF 06-6)

APSF 06-6 | Amount: $ 41,500 | Project Leader: F Neira | Project Period: Jul 2006 - Jul 2009

A project undertaken by the Tasmanian Aquaculture and Fisheries Institute (TAFI), University of Tasmania, Hobart, and supervised by Dr Francisco J. Neira

The project aims to identify field-caught eggs of Australian marine fishes employing molecular (mitochondrial DNA [mtDNA]) and standard morphological techniques, and use these data to assemble the first National reference databank for fish egg identification. Project originated from the need for increased accuracy and resolution in the identification of fish eggs to species, and the use of egg distribution and abundance data in fisheries biomass assessments, as well as wider applications to fish/fisheries biology, ecology, systematics and aquaculture. Main outputs of this project comprise the first morphological/molecular reference library of eggs of Australian marine fishes, and an illustrated identification guide.

Fig. 1. Late-stage eggs of blue mackerel, Scomber australasicus, 1.05-1.30mm diameter, from northern New South Wales.
Fig. 2. Late-stage egg of redbait, Emmelichthys nitidus, 0.91 – 1.11mm diameter, from eastern Tasmania.
Fig. 3. Staff from TAFI (University of Tasmania) retrieving a bongo plankton sampler used in the collection of fish eggs and larvae along shelf waters of eastern Tasmania during October 2005.
Specific objectives of the study are:
  1. To assemble a National reference databank to catalogue eggs of fishes at species level, based on genetic (mtDNA) and morphological techniques.
  2. To produce a descriptive, illustrated identification guide of fish eggs of key fish species.
Advantages of molecular identifications

Molecular techniques to identify fish eggs to species have several advantages over standard morphological techniques, including:

  1. providing precise species identifications regardless of degree of egg development, i.e. from newly-spawned to late-stage eggs;
  2. can be applied to link unidentified eggs to known fish species; and
  3. providing unequivocal means of confirming identifications based on morphological characters. The mtDNA sequencing method provides the most accurate information for the development of a genetic key to identify both intraspecific and intrageneric variation, particularly in the case of closely related species.
The technique

The project involves the extraction of mitochondrial DNA from each egg, segment amplicafication via polymerase chain reaction (PCR), and subsequent sequencing of the protein-coding mitochondrial cytochrome oxidase subunit I (CO I) gene. Sequences are then compared against the species-specific mtDNA fingerprints kept in Genbank (National Centre for Biotechnology Information) and BoLD (Barcode of Life Data) databases to confirm the identitication.


Fish eggs have already been obtained from plankton samples collected throughout south-eastern Australia (southern Queensland to Tasmania) during Commonwealth-funded surveys undertaken between 2002 and 2006. Additional fish eggs are to be obtained from archived ichthyoplankton samples kept at various State research institutions.


Developing a genetic-morphological reference databank for the identification of fish eggs is of National importance. The information obained will have a wide range of direct and indirect applications in future fisheries, ecological and/or biological research. Results from this project will ensure improved accuracy in determining spawning season/area, and thus greatly facilitate the application of egg-based methods to obtain spawning biomass estimates of commercial fishes nationwide. Other significant applications derived from fish egg data include stock differentiation, and fishery-independent indicators of long-term environmental variability of aquatic ecosystems.

Preliminary results

Sequences already developed for most adult fish species in Australia have successfully been applied to identify eggs of blue mackerel (Scomber australasicus) from northern New South Wales, and redbait (Emmelichthys nitidus) from eastern Tasmania, after identifications using morphological features.