Our final example of molecular ecology in a wider context is fishing. A quick perusal through the contents of the journal Molecular Ecology reveals numerous studies that are important to commercial and sports fisheries. Many species of fish are in decline, and in this section we will look at a few examples that show us how population genetics can help us to understand why fish populations are dwindling so rapidly, and can assist us with the evaluation of stock enhancement programmes.


Over the past few decades, overfishing has become a global concern that has serious repercussions for marine and freshwater ecosystems, and also profound and lasting economic and social impacts. Canada's northern cod fishing industry, for example, was at its peak in 1968, when 810 000 tonnes of cod were caught in a single year. A steady decline since then means that the current cod stock is now estimated at less than 2 per cent of what it was 20 years ago, and the fishery was closed indefinitely as of 2003. According to some estimates, 90 per cent of all large fish have disappeared from the world's oceans (Myers and Worm, 2003) and fishing quotas are now in effect in many countries around the world for numerous fish and shellfish species. Overfishing owes much to a complex mix of politics, economics and social concerns, but has also been influenced by a historically poor understanding of the population ecology of different species.

The census size of a population often provides a starting point for unravelling population dynamics, although obtaining accurate counts of marine populations can be logistically challenging. One commonly used method, known as virtual population analysis, is based on commercial catches, although estimates derived in this way may be inaccurate for a number of reasons, including flawed reporting. Another approach is known as the annual egg production method. This combines estimates of the number of planktonic fish eggs with various population parameters, such as average female fecundity and population sex ratio, to obtain a size estimate of the total breeding population. This technique requires accurate identification of fish eggs, which can be problematic because multiple species produce eggs of a similar size and appearance. A recent study used species-specific probes in quantitative PCR reactions to determine just what proportion of codlike eggs in the Irish Sea had actually been laid by cod. Only 34 per cent of positively identified eggs were cod, whereas 8 per cent were haddock and 58 per cent were whiting. This study shows how breeding populations may be grossly overestimated following the inaccurate identification of morphologically similar fish eggs (Fox et al., 2005).

Even if census population size estimates are reasonably accurate, recent studies have suggested that the census population size may actually tell us very little about the effective population size (Ne), and hence the genetic diversity, of fish populations. Loss of genetic diversity was for many years considered to be a relatively unimportant factor in the demise of fish stocks because the numbers of dramatically depleted stocks may still be in the millions, and population genetics theory tells us that genetic diversity will not deplete substantially until population sizes become much smaller than that. However, this is true only of the effective population size. In one study, researchers used archived scale samples from a population of New Zealand snapper (Pagrus auratus) to calculate Ne based on temporal changes in allele frequencies (Chapter 3), and Ne was found to be approximately five orders of magnitude smaller than the census population size, Nc (Hauser et al., 2002). As a result, a population of several million snappers could have genetic properties more typical of a population of several hundred fish. In this particular example the discrepancy was at least partially attributable to a high variation in individual reproductive success. It is clear from this study that Nc may be a grossly inaccurate method for estimating the genetic diversity, and hence the long-term viability, of fish populationse.

Figure 8.4 The Ne/Nc ratios of Chinook salmon in four different populations in the Upper Fraser River watershed. The Ne values were calculated from temporal variations in allele frequencies across three time intervals over a 25-year period. Adapted from Shrimpton and Heath (2003)

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Relatively small effective population sizes are being discovered in a growing number of fish populations. The temporal variance in allele frequencies was used to calculate the Ne of red drum (Sciaenops ocellatus) in the northern Gulf of Mexico, and subsequent calculations put the Ne/Nc ratio at around 0.001 (Turner, Wares and Gold, 2002). The same approach was used to calculate Ne from scale samples that were collected over a 20-year period from five populations of Chinook salmon (Oncorhynchus tshawytscha) from the Upper Fraser River watershed in British Columbia, Canada. Recent increases in the census population sizes suggested that management practices have been successful, but low Ne/Nc ratios showed that simple censuses of populations provide incomplete pictures of their recovery (Figure 8.4). In Chinook salmon, reduced Ne values have been attributed to a combination of fluctuating Nc, uneven sex ratios, and variation in reproductive success (Shrimpton and Heath, 2003). Recent findings such as these are highlighting the need to manage depleted fishing stocks on the basis of their Ne as opposed to their Nc, because the former will give us a more accurate picture of the future adaptability and persistence of fish populations.

Stock enhancement

Remedial action aimed at halting or reversing the decline of fish populations often involves stock enhancement programmes that supplement wild populations with hatchery-reared individuals. The success of these programmes will depend in part on the survival rates of hatchery fish once they have been released into the wild, and also on the fitness of hatchery--wild hybrids. One way in which the success of stock enhancement programmes can be monitored is through genetic tags, such as a mitochondrial haplotype or an allozyme that is rare in the wild population. If the frequency of this marker increases over time then the programme is considered to be a success because this could occur only if the hatchery-reared fish were interbreeding with the natural population and producing viable offspring (Hansen et al., 1995). Another way to monitor enhanced populations is through mixed stock analysis, a general approach for determining which of a number of possible populations are contributing to a particular mixed stock. This can be used to calculate the proportion of wild and hatchery-reared fish in an enhanced population (Debevec et al., 2000).

Parentage analysis is yet another approach that was used to evaluate the fitness of wild fish, hatchery-reared fish, and wild--hatchery hybrids in a population of rainbow trout (Oncorhynchus mykiss). The authors of this study used six microsatellite loci that were sufficiently variable (up to 24 alleles at each locus) to exclude all but one parent-pair for each sampled offspring (Miller, Close and Kapuscinski, 2004). The survival of offspring in each class was then monitored. Survival of hatchery offspring, hybrids and back-crosses relative to the wild offspring was 0.21, 0.59 and 0.37, respectively. Survival is clearly reduced in both hatchery-produced fish and hatchery--wild hybrids, meaning that stock enhancement may actually be lowering the chances that this population will survive in the long term. Table 8.4 outlines some other ways in which molecular markers can help to assess whether or not the addition of cultured fish to wild populations has been beneficial or detrimental.

Table 8.4 Some of the genetic effects that may follow the supplementation of a wild fish population with cultured stocks. Adapted from Utter and Epifanio (2002) and references therein

Genetic effect


Reduced Ne/Nc following introduction of Compare Ne of populations with similar Nc that hatchery stock that has relatively low genetic have and have not been subjected to stock diversity

Reduced Ne following either an increase in competition or the introduction of pathogens Reduced genetic diversity following genetic swamping of the wild fish by the cultured fish Reduced fitness (and Ne) in hybrids following the loss of adaptive alleles (outbreeding depression) Reduced fitness (and Ne) in hybrids following the loss of a co-adapted genome (outbreeding depression)

enhancement As above

Mixed stock analysis to determine the proportion of wild, cultured and hybrid fish over several generations Compare fitness of parents and hybrid offspring

Compare fitness of parents with F2 and subsequent generations of offspring


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