Population genetics reveals cryptic lineages and ongoing hybridization in a declining migratory fish species complex

Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression, of two species of anadromous fish with contrasted life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species allis shad that disperse stronger distance compared to the iteroparous species, twaite shad. Individuals caught at sea were assigned at the river level for twaite shad and at the region level for allis shad. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species implicated historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence of contemporary hybridization and introgression between both species. Besides, our results support the existence of cryptic species in the Mediterranean sea. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species’ populations and their hybridization should be carefully considered while implementing conservation programs.

Marine and continental distribution and dynamic of the early spawning migration of twaite shad (Alosa fallax (Lacépède, 1803)) and allis shad (Alosa alosa (Linnaeus, 1758)) in the north-west of the Iberian Peninsula

Knowledge regarding the marine phase of twaite shad (Alosa fallax (Lacépède, 1803)) and allis shad (Alosa alosa (Linnaeus, 1758)) remains limited. To understand the coastal and continental distribution and dynamic of migration of these species, in the present study we collected official data records of marine landings (kg), separated according to species, for all fish markets in Galicia (north-west of the Iberian Peninsula) and undertook freshwater field sampling campaigns. The findings indicate that both species of shad exhibit a coastal distribution near the rivers where they spawn, namely the Minho and Ulla rivers. Catches at sea declined from January, a phenomenon that can be understood as the onset of migration to the rivers. Bycatch reports are important because both A. fallax and A. alosa are listed in the Annex V of the European Union Habitats Directive, which lists animal species whose exploitation and taking in the wild may be subject to management measures. However, for a better management of these species it is necessary to understand the magnitude of displacements and connection of shad populations at sea.