We use cookies to ensure that we give you the best experience on our website. By continuing to browse this repository, you give consent for essential cookies to be used. You can read more about our Privacy and Cookie Policy.

Durham Research Online
You are in:

Genomic data suggest environmental drivers of fish population structure in the deep sea : a case study for the orange roughy (Hoplostethus atlanticus).

Gonçalves da Silva, Anders and Barendse, William and Kijas, James and England, Phillip R. and Hoelzel, A. Rus (2020) 'Genomic data suggest environmental drivers of fish population structure in the deep sea : a case study for the orange roughy (Hoplostethus atlanticus).', Journal of applied ecology., 57 (2). pp. 296-306.


The accurate identification of conservation units is central to effective management strategies. However, marine environment populations often have large census sizes and few obvious boundaries to gene flow. Poorly understood species in the deep sea are especially at risk of being erroneously managed as a single interbreeding stock (panmictic). However, mistaking cryptic structure for panmixia can have important consequences leading to ineffective management and population decline. Furthermore, characteristics of populations essential for their survival may reflect local adaptation, not evident from surveys using neutral genetic markers. We use genomic methodologies to test hypotheses about potential drivers of cryptic population structure among marine fish populations in the deep sea. In particular, we consider the possibility of isolation by distance along habitat corridors for a species dependent on a specific depth range and test for differentiation at functional loci across potential ecological habitat boundaries. For a species previously understood to be panmictic in the North Atlantic, we reveal neutral genetic differentiation among regional populations isolated by distance along deep‐water channels. We also reveal a distinct pattern of cryptic genetic structure for putative functional loci, despite apparently high levels of gene flow. Synthesis and applications. This example reflects the life history and ecology of a broad range of deep‐sea species currently exploited in intensive fisheries or as bycatch. In many cases where these populations are managed as a single stock, more effective management could be achieved using the methods we describe to identify relevant eco‐evolutionary processes, facilitated by genomic methods, permitting the recognition of cryptic stock structure. This approach also allows managers to more directly promote the essential but elusive conservation of adaptive potential.

Item Type:Article
Full text:(AM) Accepted Manuscript
Download PDF
Publisher Web site:
Publisher statement:This is the accepted version of the following article: Gonçalves da Silva, Anders, Barendse, William, Kijas, James, England, Phillip R. & Hoelzel, A. Rus (2020). Genomic data suggest environmental drivers of fish population structure in the deep sea: A case study for the orange roughy (Hoplostethus atlanticus). Journal of Applied Ecology 57(2): 296-306 which has been published in final form at This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for self-archiving.
Date accepted:07 October 2019
Date deposited:10 January 2020
Date of first online publication:12 December 2019
Date first made open access:12 December 2020

Save or Share this output

Look up in GoogleScholar