DOI: 10.5281/zenodo.17842295
title: Adaptive selection and Resilience Index to environmental change (RIec) in fish species. Data supporting  FISHADAPT WP2-3

description: Local adaptation to environmental conditions was quantified by using sequences of a dataset containing coding sequences of genes randomly distributed across the genomes of three populations of European hake (Atlantic Northern and Southern stocks and Mediterranean). The European hake dataset of coding sequences (i.e. selective dataset) was produced within the FISHADAPT project using the capture-sequencing technique in Rapid Genomics company (USA), and is available from  https://www.ncbi.nlm.nih.gov/sra/PRJNA1380745. The number of signals of adaptation found in the European hake was compared to that obtained using data from three populations of a less exploited fish species (Galician, French, and Norwegian), the ballan wrasse Labrus bergylta, using data produced in https://doi.org/10.1111/mec.17732.

To do comparable neutral datasets from both species, random sequences of 1000 bp length were taken from the whole genome sequences of Ballan wrasse to resemble the neutral dataset obtained for European hake populations (i.e. RADseq, available in  10.5281/zenodo.17839041). To do comparable selective datasets in both species, coding sequences obtained for European hake were blasted against the annotated genome of cod. Then, the ID of the annotated genes in cod was used to get the orthologous ID of Ballan wrasse using the ENSEMBL Biomart application (https://www.ensembl.org ). 

 Local adaptation to environmental conditions was evaluated by pair-wise association analyses among populations as implemented in ANGSD, while balancing selection or ongoing adaptive selection was evaluated using BetaScan software (Siewert & Voight, 2017) for each population. Beta scores higher than 1 were used as the threshold to consider evidence of balancing or ongoing adaptive selection within populations, while p-values of allele differences among populations lower than 1e-6 were considered as evidence of local adaptation. The proportion of mutations with evidence of significantly different allele frequency between populations (i.e. local adaptation) was compared among the neutral (i.e. RADseqs) and the selective datasets for each pair of analysed populations. In the same way, the proportion of loci with beta scores higher than 1 was also compared between neutral and selective datasets for each population. The ratio between selective/neutral datasets was taken as an indication of levels of natural selection within and among populations.

 Expectations for balancing or ongoing selection are:

Ø  ratios higher than 1 -> prevalence of adaptive selection.

Ø  ratios lower than 1 -> prevalence of purifying selection.

Ø  ratios ≈1 -> prevalence of genetic drift (i.e. demography).

Expectations for local adaptation are:

Ø  ratios higher than 1 -> local adaptation/population differentiation.

Ø  ratios lower than 1 -> no local adaptation/undifferenced populations.

Outcome and results:

Results indicated lower global levels of natural 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 (Table 1).

Ratios of selective/neutral datasets >1, giving evidence of local adaptation, were only found in the comparisons between Ballan wrasse North population to the other two Southern populations, and very low levels in European hake (Table 2), in agreement to the observed low levels of genetic differentiation found for this species in https://doi.org/10.1093/icesjms/fsaf231. 

Table 1. Assessment of balancing/ongoing adaptive selection in each species population. Selective and Neutral columns show the proportion of loci with a beta score higher than 1.




 
 


Selective



Neutral



Ratio Selective/Neutral





Ballan wrasse



AT



0.21



0.30



0.69





NOR



0.18



0.32



0.55





FR



0.21



0.29



0.73





European hake



AT



0.21



0.22



0.95





NOR



0.21



0.21



0.99





MED



0.20



0.22



0.92





Table 2. Assessment of local adaptation. Selective and Neutral columns show the proportion of mutations with significantly different allele frequency among population pairs.




 


Population-pairs



Selective



Neutral



Ratio Selective/Neutral





Ballan wrasse



AT-FR



9.8e-5



2.6e-4



0.38





AT-NOR



3.2e-2



2.3e-2



1.37





FR-NOR



2.7e-2



2.0e-2



1.37





European hake



AT-MED



1.7e-4



1.2e-3



0.14





AT-NOR



1.1e-4



5.9e-4



0.19





MED-NOR



1.7e-4



1.5e-3



0.12





A Resilience Index to environmental changes (RIec) was designed 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.

Avg.pop.dec (i.e. Average decreases in effective population size) = Average Nea/Nec between the population’s pairs. Nea= ancestral effective population size, and Nec= current effective population size.

la (i.e. local adaptation index) is the ratio of selective/neutral as estimated in Table 2.

oa (i.e. ongoing adaptation) is the ratio selective/neutral as estimated in Table 1.

The estimated RIec was 0.27 for Ballan wrasse, and 1.07e-4 for European hake, indicating decreased levels of adaptive potential to environmental changes in European hake when compared to Ballan wrasse populations, besides their ancestral bigger effective population size, connectivity,  and abundances.

The results show a huge effect of harvesting in European hake, reducing the levels of genetic diversity in more than 300 times their sizes of 50 years ago (https://doi.org/10.1093/icesjms/fsaf231).