The work plan to achieve the scientific objectives was originally divided in five work packages:
WP 1: NEUTRAL DATASET AND CONNECTIVITY. Datasets of genomics neutral sequences of European hake and Ballan wrasse populations were analysed to get estimates of genetic diversity, neutrality index, current, ancestral and historical effective population sizes, and genetic connectivity among populations.
The results indicated that harvesting activities on European hake populations have decreased their levels of genetic diversity changing the genetic differentiation among them, though genetic flow could have been historically high. Moreover, levels of genetic diversity were lower in the Mediterranean (MED) population than in the North Sea (NOR) & Galician (AT) populations as expected because this population has been considered vulnerable to extinction by IUCN since the middle of the 80s.
For Ballan Wrasse lower levels of genetic diversity and higher deviation of neutrality index were found for the more intensively harvested North population, though this population has ancestrally reduced effective population size compared to the other two. Moreover, the historically smaller effective population sizes when compared to European hake have probably produced reduced ancestral genetic flow between Spain & France populations to the North population.
WP2: SELECTION. Datasets of coding sequences (i.e. selective) from populations of Ballan wrasse and European hake populations were analysed to get insight into the levels of local adaptation and balancing or ongoing adaptive selection.
Results indicated lower global levels of balancing/ongoing adaptive selection in European hake than in Ballan wrasse populations. Ratios of selective/neutral datasets ≈1 were found in European hake, indicating the prevalence of genetic drift (i.e. demography) driving the populations' evolution, whereas some levels of purifying selection are observed in Ballan wrasse.
Ratios of selective/neutral datasets >1, giving evidence of local adaptation were only found in the comparisons between the Ballan wrasse North population to the other two Southern populations, and very low levels in European hake, in agreement with the observed low levels of genetic differentiation found for this species in WP1.
In summary, the analyses performed within this Work Package indicated global levels of natural selection higher in Ballan wrasse than in European hake. Although higher connectivity among populations of European hake could have allowed ancient high levels of balancing selection among populations favouring high levels of adaptation to multiple environments, the huge declines experienced by these populations as found in WP1, probably eroded this adaptive potential. Moreover, increased levels of local adaptation and low genetic flow among Northern vs Southern populations of Ballan wrasse can also be limiting the species' capacity to adapt to changes in the local environmental conditions.
WP3: RESILIENCE INDEX AND QUANTIFICATION OF THE HARVESTING EFFECT. Given the results obtained in WP1 and WP2 a Resilience Index to environmental changes (RIec) was designed within the FISHADAPT project as RIec = (∑_(i=1)^n(connectivity*(local_adaptation_index+ongoing_adaptation_index))/(average population declines))/n.Where: n is the number of population pairs; Connectivity = 1-FST index, among population pairs from WP1; Average pairwise population declines= Average Nea/Nec between the population’s pairs from WP1; local adaptation index is the ratio selective/neutral mutations as estimated in WP2; ongoing adaptation index is the ratio selective/neutral loci as estimated in WP2.
In summary, results indicated that fishing activities have decreased the levels of genetic diversity and adaptive potential to environmental change of populations and that the comparative Resilience Index RIec designed within this WP is a good first approach for the detection of this effect. Moreover, results show that long-term artisanal fishing activities produced small effects on the levels of genetic diversity in the Galician population, in contrast to those found for recent intensive fishing activities in the North population of Ballan wrasse and in the three analysed populations of European hake. This loss of genetic diversity was correlated to the loss of biomass and Inbreeding Depression in populations of European hake, indicating a profound genetic effect of harvesting on the populations of European hake, which could be threatening these populations to extinction if genetic parameters are not considered within stock assessments.
WP4: GENETIC LOTTERY HYPOTHESIS. Within FISHADAPT project it was sequenced a pool of more than 500 larvae from 17 nests of Ballan wrasse plain morphotype collected in the year 2019 in the Galician region. Mutations with evidence of being adaptive in WP2 were screened in the larvae pool.
The results showed that only ~2.6% of alleles presenting significant differences between adult populations NOR versus AT were present in the larvae pool. Therefore, the genetic lottery hypothesis is likely false for this species as the genetic flow of adaptive mutations to local conditions is limited. Further studies should evaluate this hypothesis for different species with different degrees of genetic flow among them.
WP5: LIKELIHOOD OF ADAPTATION TO ENVIRONMENTAL CHANGE. Within this work package, the progress done was the literature research on the state of the art for the methods estimating the likelihood of adaptation to environmental change. This research shows a very incipient state, requiring the design of new methodologies including machine learning, and complex simulations taking into account the demographic history and the life traits of the species being studied. Nonetheless, the results obtained in WP3 (i.e. the resilience index) have shown to be a good first predictor of the likelihood of adaptation to environmental change in harvested populations.
