Shum, P
2016,
Diversification of beaked redfish, Sebastes mentella, along a depth gradient in the central North Atlantic
, PhD thesis, University of Salford.
Abstract
Despite the striking physical and environmental gradients associated with depth variation
in the oceans, relatively little is known about their impact on population diversification,
adaptation and speciation. The pelagic beaked redfish, Sebastes mentella, exhibits depthassociated
patterns of population genetic substructure in the central North Atlantic, with a
widely distributed population inhabiting waters between 200 and 550m depth and localised
putative populations dwelling at greater depths, between 550 and 900m. This PhD project
implements a multidisciplinary approach to explore and understand aspects of this
biological complexity, in the context of depth.
To investigate depth as a factor driving population divergence and adaptation,
sampling was carried out to target S. mentella at different depth layers and across most of
its distribution range. Through the use of mitochondrial and nuclear markers on samples
spanning a period between 2006 and 2013, the existence of two strongly divergent
evolutionary lineages is revealed, with significantly different geographic distribution
patterns and dwelling at different depths. The first empirical evidence to explicitly test
genotype and phenotype of Sebastes vision associated with shifts in habitat depth is
presented, by conducting spectral analysis of rod visual pigments. Additionally, de novo
RNA-seq analysis of redfish retina transcriptome is presented for a subset of “shallow” and
“deep” individuals, in order to characterise differential expression of candidate genes
involved in visual perception in organisms adapted to different depths. Furthermore, a
market accuracy survey of redfish sampled across Europe from various retailers was crossreferenced
against data currently held in public databases. Results revealed the existence of
inaccurate reference sequences in data bases, likely stemming from species
misidentification from previous studies, which currently hinders the efficacy of DNA
methods for the identification of Sebastes products. Overall, we cast new light on the role
of depth in maintaining biodiversity in the oceans, and consider the practical implications
of such findings.
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