DiMaS · Retrospective genomic analyses of shortfin Mako shark (Isurus oxyrinchus) using DNA from archived jaws

Retrospective genomic analyses of shortfin Mako shark (Isurus oxyrinchus) using DNA from archived jaws

The project DiMaS focused on evaluating long-term changes in population connectivity and genetic diversity of the endangered shortfin mako shark (Isurus oxyrinchus) throughout its distribution range. Shortfin mako is a migratory top predator, with a world-wide distribution in the tropical and warm-temperate oceans. The species is currently targeted commercially throughout its distribution, both directly and as by-catch from longline fisheries. Intense exploitation coupled with inadequate catch-and-landing statistics, led to a worldwide population decline, with shortifin mako currently listed as Endangered by the IUCN’s Red List of Threatened Species, and included in Appendix II of the CITES convention. In particular, recent declines in abundance have been observed in the Northeast Atlantic where catch rates have declined by 50%, or more, due to 10-fold under-reporting of catches. Declines in population abundance can have repercussions on genetic diversity levels, and consequently in the long-term evolutionary potential of a species. However, little is known regarding the evolutionary history of shortfin mako, as previous molecular studies have employed a small number of molecular markers and focused on contemporary samples only. Temporal genetic data can, thus, provide information on population range shifts, fluctuations in population size and direct adaptive genetic changes in response to exploitation, allowing inferences to be drawn regarding the evolutionary history of shortfin mako. In this context, DiMaS employed a retrospective genomics approach making use of historical samples archived in national and regional museums, national fishery institutes and personal collections, as well as contemporary samples obtained from fishery institutes, throughout the species’ distribution range, to investigate if reported declines had impacted its genetic diversity and evolutionary history. Using a novel exome-targeted sequencing approach, genome-wide markers were generated for 471 samples, spanning all oceans and time periods from 1790 – 2018. Our aims were to assess spatio-temporal population sub-structuring, estimate long-term genetic diversity levels and effective population size and understand the most likely mechanisms and processes influencing the evolutionary history of shorting mako through time and space. Overall, the results generated in DiMaS suggest a complex evolutionary history of this species. Analyses of spatio-temporal patterns of genetic diversity did not reveal significant losses of genetic diversity in line with an increase in exploitation pressures (from 1980 onwards). In addition, weak signals of break in gene flow are reported between individuals caught in the Northwest Atlantic (USA), Southwest Atlantic (Brazil), South Africa, New Zealand and Eastern Pacific (Gulf of California). This differentiation patterns were not constant through time, and point to a complex migratory behaviour. Our findings suggest that gene flow and genetic drift as the most likely micro-evolutionary mechanisms shaping the evolutionary history of shortfin mako, and this project leaves many doors open to understand the complex evolutionary history of this endangered shark.

Data: CORDIS, © European Union