Why genetic structure matters: a fisheries conservation perspective

Why assess population genetic structure and connectivity in marine species?

One of the great challenges of fishery sustainability is to ensure that the spatial units of management reflect those of fished stocks so that conservation measures are suitable and effective. Population structure and connectivity –effectively the extent to which local stocks of species are interdependent and interrelated to one another– hold major implications for conservation management. By example, where the spatial boundaries of a population are known, fishery managers can be confident that representative monitoring of key biological parameters such as abundance, size structure and maturation rates allows them to set effective recommendations on catch and effort. However, if multiple disconnected stocks have differing biological parameters but are wrongly assumed to be one population, then a one-size-fits-all regulatory approach may be incompatible with maintaining sufficient biomass to safeguard future harvests. To this end, scientists investigate spatial population structure (i.e. the geographic extents of population units), and the connectivity between them (i.e. their recruitment dynamics with other stocks). For biologists studying species on land, physical tags are useful to evidence connectivity –bird rings and satellite tags are good examples– as they enable observations of how individuals disperse, migrate, and interbreed with other populations. However, most marine species produce many small offspring that are incompatible with physical tagging, and so marine scientists often utilise genetics to investigate the geographic boundaries of populations and the extent to which individuals move between them.

Above: baby crawfish start off life as translucent phyllosoma, and take up to a year to grow to a couple of centimetres in size while adrift on ocean currents, so are much too small and delicate to enable physical tagging. Photo by E. Poza.

Population genomics of European crawfish

One such species for which knowledge of broad-scale stock interrelatedness is either lacking or based on methods lacking the power of modern genetic tools is the European spiny lobster or crawfish, Palinurus elephas. Through their propensity to migrate in large social groups –which make it possible to entangle a whole ‘family’ together in a single gill-net– and their lack of claws –which makes it possible for divers to capture them by hand– crawfish have been susceptible to overfishing. Most crawfish stocks have declined over 90% since the middle of the twentieth century, and point-of-sale prices exceeding £100/kg continue to fuel pressure on remaining stocks. In southwest England & Wales, crawfish were practically wiped out for several decades until fresh recruitment began accumulating during the 2010s. This comeback had clearly not come from local sources (since there were insufficient adults to produce significant larval supply), so fishery managers wanted to assess the origins of these new recruits in order better understand stock dynamics and to manage stocks more effectively into the future. Our research group at Exeter were engaged to assess the wider population genetic structure of the species to see if we could assign the spatial origins of these newly-settled crawfish, so collected sub-lethal tissue clips from crawfish in 3 locations in the SW UK, and compared their genetic profiles to samples from 7 locations from the wider Atlantic range, and 5 locations in the Mediterranean (349 crawfish in total). Isolating over 7,500 variable SNP loci (a type of genetic marker) from across the genome, we found little evidence of sub-structuring beyond two meta-populations associated to their basin of origin, simply the Atlantic or the Med. Because each of these units was effectively homogenous, the SW UK crawfish could not be attributed to any particular region within the Atlantic, with even stocks as distantly separated as the Hebrides and Portugal (over 1,500 miles apart) showing no genetic divergence.

Above: A lone crawfish forages on a maerl bed in Cornwall's Falmouth Bay, where the species has made a recent recovery. Photo by Matt Slater of Cornwall Wildlife Trust.

Comparison to European lobsters

With this analysis complete, we the compared crawfish genetic structure to that of a similar species with different biological parameters across the same spatial range. We collected tissue clips from 214 European lobsters, Homarus gammarus, across 32 locations encompassing its range (the Med and NE Atlantic, including E Britain and W Scandinavia where crawfish do not inhabit), and genotyped these at almost 6,500 SNP loci. Lobster showed the same genetic break between Atlantic and Mediterranean that characterises crawfish structure, but within these clusters, sub-structuring was apparent in discreet regional stocks attributed to: Scandinavia; the NE Atlantic (within which there was also a subtle latitudinal cline of differentiation); the Western Med.; the Adriatic Sea, and; the Aegean Sea. Between locations, measures of genetic divergence were typically up to 10x higher in lobster than they were in crawfish, while lobsters were also more differentiated with increasing geographic distance between stocks, a pattern surprisingly not evident in crawfish.

Above: Plots for lobster (left) and crawfish (right) depicting the results of Discriminant Analyses of Principal Components, a method to characterise genetic differentiation. Circular dots depict individual animals, while rectangular labels denote the mean of each geographic fishery sample, with both coloured by assignment to their regional stock as per the key at the top of each plot.

Implications for conservation management

We attribute the comparative lack of crawfish population structuring to their greater dispersal tendencies via a longer pelagic larval duration and sporadic adult movements; typical larval drifts of crawfish last 6-12 months (compared to only about a month for lobster), and tagged crawfish have been recaptured over 500 miles from their site of return. Although our genetic results are not directly equivalent to measures of demographic connectivity, and the exchange of only a handful of immigrants each generation is required to prevent genetic divergence of otherwise separate stocks, our finding of genetic homogeneity in Atlantic crawfish suggests that fragmented and inconsistent conservation legislation threatens their widespread overexploitation. By example, even areas with progressive regulations may not maintain sufficient local recruitment if most of their own larvae drift to other regions, and other regions which supply much of their juvenile settlement are depleted by ineffective management. So, for crawfish, cooperative and transnational management is more likely to be required to ensure regionally sustainable yields. Meanwhile, our finding of more spatial structuring in lobsters indicates that their stocks are more likely to self-recruit, making them more susceptible to localised overfishing, but also implying that local measures which maintain spawning stock biomass should contribute effectively towards safeguarding fishery productivity.

By Charlie Ellis, 18/07/2023. This summary is derived from my new study, published with Open Access in the Journal of Biogeography:

Ellis CD, MacLeod KL, Jenkins TL, Rato LD, Jézéquel Y, Pavičić M, Díaz D, Stevens JR. (2023) Shared and distinct patterns of genetic structure in two sympatric large decapods. Journal of Biogeography, 50 (7), 1271-1284. https://doi.org/10.1111/jbi.14623

Above: The author comes face to face with a crawfish landed by a Cornish fisherman kind enough to allow me to collect small sub-lethal tissue samples of his catch.