Diversification of beaked redfish, Sebastes mentella, along a depth gradient in the central North Atlantic

Doctoral thesis English OPEN
Shum, P

Despite the striking physical and environmental gradients associated with depth variation\ud in the oceans, relatively little is known about their impact on population diversification,\ud adaptation and speciation. The pelagic beaked redfish, Sebastes mentella, exhibits depthassociated\ud patterns of population genetic substructure in the central North Atlantic, with a\ud widely distributed population inhabiting waters between 200 and 550m depth and localised\ud putative populations dwelling at greater depths, between 550 and 900m. This PhD project\ud implements a multidisciplinary approach to explore and understand aspects of this\ud biological complexity, in the context of depth.\ud To investigate depth as a factor driving population divergence and adaptation,\ud sampling was carried out to target S. mentella at different depth layers and across most of\ud its distribution range. Through the use of mitochondrial and nuclear markers on samples\ud spanning a period between 2006 and 2013, the existence of two strongly divergent\ud evolutionary lineages is revealed, with significantly different geographic distribution\ud patterns and dwelling at different depths. The first empirical evidence to explicitly test\ud genotype and phenotype of Sebastes vision associated with shifts in habitat depth is\ud presented, by conducting spectral analysis of rod visual pigments. Additionally, de novo\ud RNA-seq analysis of redfish retina transcriptome is presented for a subset of “shallow” and\ud “deep” individuals, in order to characterise differential expression of candidate genes\ud involved in visual perception in organisms adapted to different depths. Furthermore, a\ud market accuracy survey of redfish sampled across Europe from various retailers was crossreferenced\ud against data currently held in public databases. Results revealed the existence of\ud inaccurate reference sequences in data bases, likely stemming from species\ud misidentification from previous studies, which currently hinders the efficacy of DNA\ud methods for the identification of Sebastes products. Overall, we cast new light on the role\ud of depth in maintaining biodiversity in the oceans, and consider the practical implications\ud of such findings.
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