Estimating absolute size of endangered marine populations from genetically identified parent-offpring pairs – GenoPopTaille

A novel method was recently developed for estimating absolute population size (number of individuals) of animal populations based on identifying parent-offspring pairs genetically. The principle of the method is that of the well proven capture-mark-recapture approach but with genetic marking of parents and recapture via their offspring. The genetic markers used in the project were SNP (Single Nucleotide Polymorphism) markers. A SNP is a location in the genome at which, in a given population, individuals differ by a single nucleotide base. There are two versions (two alleles) of each SNP. As each individual has two homologous DNA strands, it has two copies of each SNP each inherited from one of its two parents. Thus, the two individuals in a parent-offspring pair share at least one copy for each SNP. In contrast, two siblings do not have necessarily a copy in common at each SNP, although they received their copies from there two parents and the number of shared SNPs between half-siblings is even fewer. Therefore several thousand SNP markers were genotyped by the project to identify both parent-offspring pairs, siblings and half-sib pairs. The central statistical part of the project was then to estimate the number of individuals in the population using a dedicated population dynamics model and the number of related individuals among the sampled individuals (around 7000 thousand) as input data.

The study of the meta-population structure of thornback ray using genetic data and simulations revealed three broad entities, one on the European shelf, one around the Azores and the last in the Mediterranean Sea. Depending on the assumed migration scenario, more demographical units were identified on a lower spatial scale. Based upon genomic data, a DNA chip of more than 7000 SNP markers was developed for genotyping several thousand individuals.
A dedicated theme session on the contribution of genetics to assessing marine exploited populations was co-organised with international partners at the annual science conference of
the International Council for the Exploration of the Sea (ICES). The session illustrated the perspectives offered by the genetic-based mark-recapture abundance estimation method trialed in the project. Part of the project team continues the sampling, the genotyping and the statistical analysis in the European funded PANDORA project.

The future prospect of the projet is the development of a genetic method for estimating fish populations abundances. The method apply to rare to moderatly abundant populations, for which usual fisheries science method based upon fitting populations dynamic models to catch and survey data often fail, primary because data ara scarce.

The scientific production covers several aspects of thornback ray populations:
• Abundance estimation in the Bay of Biscay;
• Metapopulation structure;
• Effective population size, which is useful for conservation purposes. The project demonstrated that a large number of individuals need to be sampled for reliable estimation, i.e. similar magnitude then needed for genetic-based mark-recapture;
• Population biomass, estimated using commercial landings and scientific survey data;
• Identification of sex-linked SNPs and sex-determination system.
Lastly, the project showed that the impact of current scientific monitoring on ecosystems could be reduced, including by using the genetic-based mark-recapture abundance estimation method applied in this project.

At ecosystem level, sustainable exploitation of fisheries resources depends not only on the status of populations of target species but also on that of populations of bycatch species, some of which are more sensitive to exploitation than target species. This is the case for a number of ray and shark species whose abundance declined during the 20th century, in certain cases severely. Further, the biology of rays and sharks is still poorly known and traditional fisheries stock assessment methods using fisheries catches and scientific survey data for estimating abundance are expensive or even inapplicable due to the small numbers observed.
Recently a new method based on the genetic identification of parent-offspring pairs has been developed to estimate the absolute size of small populations. The method relies on the principle of capture-mark-recapture which is well tested using physical tags, but using genetic marking of parents and recapture via their offsprings. However, this method is still very little used for marine fisheries resources, with few final results published, because of the costs and technical difficulties of applying of genetic tools at the scale of a whole marine population.
The rapid progress of genomic technics during the last decade now allows for high-throughput sequencing and genotyping of large samples for several hundreds or thousands of genetic tags. The GenoPopTaille project will develop a novel application of these genomic technics to estimate the absolute number of thornback ray, Raja clavata, in the Bay of Biscay based on genetic identification of parent-offspring pairs. The thornback ray was chosen for this project because its total abundance is presumed small enough for the method to be applicable and the sampling of a large number of individuals from catches of commercial fisheries is feasible.
The project GenoPopTaille will first apply RAD sequencing technics to evaluate the genetic structure and gene flow in thornback ray populations from the northeast Atlantic based upon several thousand of SNP (Single Nucleotide Polymorphism) tags. The most informative SNPs for the Bay of Biscay population will then be chosen to be genotyped for a large sample (~7000) of adults and juveniles for a large number (~200) of SNPs. These genetic data will be used to identify parent-offspring pairs. The number of parent-offspring pairs will be used in a population dynamics model for estimating the abundance of spawners, accounting for factors such as individual fecundity and mortality. The feasability of using other parental links (e.g. sibs and half-sibs) for estimating population size will also be evaluated. Further, the use of stranded egg capsules to genetically monitor the abundance of ray populations will be tested using capsules collected by an on-going participative science programme along the French coast.
The challenges taken up by this project are first of all statistical (development population dynamics models and parameter estimation) but also the novel application of genetic tools. The project includes a cost-benefit analysis to evaluate the applicability of the method to other fish populations, in particular declining or endangered species, for which population abundance cannot easily be estimated using other methods.