Ecogeochemistry potential in deep time biodiversity illustrated using a modern deep-water case study

Trueman, Clive N.; Chung, Ming‐Tsung; Shores, Diana

doi:10.1098/rstb.2015.0223

Cited by 32 publications

(38 citation statements)

References 73 publications

(115 reference statements)

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“…To test whether C. rupestris shows an ontogenetic depth migration 78,79 from shallow as juveniles to deeper as adults, we assigned individuals to age cohorts and modelled depth change over years. Cohorts of fish spawned between 1996 and 2003 were used to assess depth change over the first 12 years of life.…”

Section: Ontogenetic Depth Migrationmentioning

confidence: 99%

Genomics of habitat choice and adaptive evolution in a deep-sea fish

et al. 2018

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W hile longitudinal and latitudinal habitat transitions have been proposed to define marine communities and promote intraspecific differentiation 1-3 , little is known about the importance of transitions along ocean depth gradients 4,5 , although substantial changes in species assemblages with depth have been recorded (for example, ref. 6 ), and relatively narrow depth ranges may distinguish closely related species (for example, refs 7,8 ). Understanding the relevant mechanisms will contribute significantly to our understanding of eco-evolutionary processes and the origin of marine biodiversity. We chose the roundnose grenadier (Coryphaenoides rupestris) as a model system because it is a widespread species that can inhabit a comparatively broad range of depths 9 from ~180 m to 2,600 m. It is a batch spawner, producing up to 69,000 pelagic eggs per female 10 . It has a spawning season peaking in autumn 11 (recent observations were in September at 1,500 m; ref. 12 ), preys on fish, cephalopods and invertebrates in both benthic and pelagic habitats 13 , and shows minor genetic differentiation across its geographic range [14][15][16] .Adaptation to habitat can occur among populations within a species, and if disruptive selection is associated with assortative mating has the potential to promote incipient speciation through ecological processes in sympatry 17 . When environmental change exposes new habitats and niche potential, adaptive radiations may rapidly generate a new lineage of species 18,19 . To the extent that differential selection can retain polymorphisms within or among populations, this may facilitate the process of adaptive radiation. Here, we focus on one of the key habitat transitions in the oceans-between the photic mesopelagic region and the aphotic regions below (together with the more contiguous changes associated with increasing depth). There is the potential for species (such as the roundnose grenadier), whose habitat range extends across this boundary or along the depth gradient, to experience differential selective pressures. We tested hypotheses about adaptation to these deep-sea habitats using genome sequence data together with data on the ecology and life history of the subject species. We found that juvenile fish of this species are found primarily in relatively shallow depths (near the transition between the mesopelagic and bathypelagic zones) and then migrate as they mature to different depths, and this is strongly associated with their genotype at a set of functional loci. In particular, all adults below ~1,800 m share the same homozygous genotype at each locus. There is evidence for strong selection maintaining this difference, but no clear evidence for differentiation driven by assortative mating. Results and discussionWe produced an annotated reference genome for C. rupestris with a total length of 0.829 gigabase pairs, a mean depth of 104× and an N50 of 159,738 (see Supplementary Methods for details). We used this draft genome to map 60 additional genomes sequenced to a mean depth ...

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Section: Ontogenetic Depth Migrationmentioning

confidence: 99%

Genomics of habitat choice and adaptive evolution in a deep-sea fish

et al. 2018

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“…Otoliths are an important tool in fisheries management to evaluate migration patterns of fish stocks or populations using trace element analyses (e.g. McGowan et al, ; Izzo et al, ; Limburg & Elfman, ) and for studies on ecogeochemistry (see Trueman, Chung & Shores, ). They are also used by ecologists in trophic studies when analysing stomach contents of marine mammals (e.g.…”

Section: Introductionmentioning

confidence: 99%

Enigmatic ear stones: what we know about the functional role and evolution of fish otoliths

et al. 2018

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Otoliths in bony fishes play an important role in the senses of balance and hearing. Otolith mass and shape are, among others, likely to be decisive factors influencing otolith motion and thus ear functioning. Yet our knowledge of how exactly these factors influence otolith motion is incomplete. In addition, experimental studies directly investigating the function of otoliths in the inner ear are scarce and yield partly conflicting results. Herein, we discuss questions and hypotheses on how otolith mass and shape, and the relationship between the sensory epithelium and overlying otolith, influence otolith motion. We discuss (i) the state‐of‐the‐art knowledge regarding otolith function, (ii) gaps in knowledge that remain to be filled, and (iii) future approaches that may improve our understanding of the role of otoliths in ear functioning. We further link these functional questions to the evolution of solid teleost otoliths instead of numerous tiny otoconia as found in most other vertebrates. Until now, the selective forces and/or constraints driving the evolution of solid calcareous otoliths and their diversity in shape in teleosts are largely unknown. Based on a data set on the structure of otoliths and otoconia in more than 160 species covering the main vertebrate groups, we present a hypothetical framework for teleost otolith evolution. We suggest that the advent of solid otoliths may have initially been a selectively neutral ‘by‐product’ of other key innovations during teleost evolution. The teleost‐specific genome duplication event may have paved the way for diversification in otolith shape. Otolith shapes may have evolved along with the considerable diversity of, and improvements in, auditory abilities in teleost fishes. However, phenotypic plasticity may also play an important role in the creation of different otolith types, and different portions of the otolith may show different degrees of phenotypic plasticity. Future studies should thus adopt a phylogenetic perspective and apply comparative and methodologically integrative approaches, including fossil otoliths, when investigating otoconia/otolith evolution and their function in the inner ear.

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“…A general lack of understanding of potentially complex population demographic processes across broad oceanic areas and behaviours limits the ability for an effective management. A combination of tools ( e.g ., genetic and geochemical approaches) have potential to inform on the mechanisms for population connectivity and reveal insights in terms of the duration of different life stages (Trueman et al , ).…”

Section: Population Connectivity and Stock Identitymentioning

confidence: 99%

Deep‐water fisheries along the British Isles continental slopes: status, ecosystem effects and future perspectives

Vieira

Trueman

Readdy

et al. 2019

Journal of Fish Biology

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In this paper, we revisit the state of deep‐water fisheries to the west of the British Isles and aim to provide an overview on the key drivers behind community changes along continental margins. The deep‐water fisheries to the west of the British Isles that extend from the shelf‐slope break down to the lower slope and along banks and seamounts of the Rockall Basin, mainly target blue ling Molva dypterygia, roundnose grenadier Coryphaenoides rupestris, orange roughy Hoplostethus atlanticus, with by‐catches of black scabbardfish Aphanopus carbo and tusk Brosme brosme. These fishing grounds experienced a long period of exhaustive exploitation until the early 2000s, but subsequently the implementation of management strategies has helped to relieve excessive fishing pressure. It is widely accepted that a better understanding of the long‐term implications of disturbance is needed to understand patterns in deep‐water communities and what sustainable use and exploitation of resources might look like in this context.

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Ecogeochemistry potential in deep time biodiversity illustrated using a modern deep-water case study

Cited by 32 publications

References 73 publications

Genomics of habitat choice and adaptive evolution in a deep-sea fish

Genomics of habitat choice and adaptive evolution in a deep-sea fish

Enigmatic ear stones: what we know about the functional role and evolution of fish otoliths

Deep‐water fisheries along the British Isles continental slopes: status, ecosystem effects and future perspectives

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