Replication data and scripts for: Harbor porpoise losing its edge: genetic time series suggests a rapid population decline in Iberian waters over the last 30 years

Data and scripts related to the study Ben Chehida Y, Stelwagen T, Hoekendijk JPA, Ferreira M, Eira C, Pereira AT, Nicolau L, Thumloup J, Fontaine MC. 2023. Harbor porpoise losing its edges: genetic time series suggests a rapid population decline in Iberian waters over the last 30 years. Accepted in the journal Ecology and Evolution (Wiley) (biorXiv preprint doi: https://doi.org/10.1101/2021.08.19.456945)

Content summary
- Input data and scripts required to replicate the demographic inference by Approximate Bayesian Computation (ABC).
- Mitochondrial DNA sequence alignments generated in the present study.
- Input data and scripts used to compute the Hudson et al 1992 estimator of FST as well as the Excoffier et al 1992 estimator of PhiST.
- Input data and script used to compute haplotype diversity in each population.
- Input data and settings used to build the phylogenetic tree.
- Input data and script to replicate the rarefaction analysis for the estimators of mtDNA genetic diversity.

Research abstract
Impact of climate changes on species is expected to be especially visible at the extremities of the species distribution, where they meet sub-optimal conditions. In Mauritania and Iberia, two genetically isolated populations of harbor porpoises form a distinct ecotype and are presumably locally adapted to the upwelling waters. By analyzing the evolution of mitochondrial genetic variation in the Iberian population between two temporal cohorts (1990-2002 vs. 2012-2015), we report a dramatic decrease in genetic diversity. Phylogenetic analyses including neighboring populations identified two porpoises in southern Iberia carrying a divergent haplotype close to the Mauritanian population, yet forming a distinctive lineage. This suggests that Iberian porpoises may not be as isolated as previously thought with immigration from Mauritania or an unknown population in between, but none from the northern ecotype. The rapid decline in the Iberian mitochondrial diversity may be driven by either genetic drift, or by a dramatic decline in census population size possibly resulting from environmental stochasticity, prey depletion, or acute fishery bycatches. These results illustrate the value of genetics time series to inform demographic trends and emphasize the urgent need for conservation measures to ensure the viability of this small harbor porpoise population in Iberia.