2019
 

Novel DNA methods and instrumentation for species monitoring in fisheries

År: 2019

Novel DNA methods and instrumentation for species monitoring in fisheries

Hansen, B. K., 2019

Research output: Book/ReportPh.D. thesis – Annual report year: 2019Research

Marine fish play a vital role for global food biosecurity and economy, whose continued productivity necessitates proper fisheries management. Successful management relies on the ability to accurately determine and monitor how many fish can be sustainably caught and subsequently ensure correct reporting of catches through fisheries surveillance. However, current monitoring of
marine fish is expensive and limited to annual surveys, if conducted at all. Moreover, current fisheries surveillance is reliant on visual assessment of the catch, which make advantageous onboard bulk storage and processing methods illegal. Thus, tools to improve current monitoring and fisheries surveillance will benefit both commercial fisheries, management and conservation of marine fish
stocks. This present thesis examines novel genetic methods and instruments as an alternative approach or supplement to established fisheries monitoring and surveillance techniques. Utilizing advanced genetic instrumentation and methodologies, the overarching goals of this PhD were to (1) examine
the current knowledge, challenges and perspectives for using modern DNA monitoring and surveillance techniques in applications relevant to fisheries, (2) test a fully automated 2. Generation Environmental Sample Processor (2G ESP) for in-situ environmental DNA (eDNA) analysis, and (3) assess the ability of DNA based methods to identify and quantify species composition in complex
bulk fisheries products. The thesis opens with a general introduction briefly describing the history and present state of genetic applications of relevance to species monitoring and surveillance in fisheries management (chapter I). The introduction extends to review relevant knowledge, contemporary instrumentation and methodological issues in order to put the content of the thesis into an overarching state of the art research context. Hereafter, four manuscripts are provided in chapter II-V. In chapter II we review the wealth studies which have revealed great potential but also challenges related to the use of eDNA in marine fish monitoring. In chapter III we demonstrate that a 2G ESP has the ability to perform autonomous, remote in situ eDNA analysis for real-time monitoring of fish. Further, in chapter IV we show how DNA based methods can detect and quantify proportions of marine fish from complex tissue mixtures in bulk fisheries products, such as fish silage and frozen fish blocks. Finally, chapter V describes and discusses the potential of genetic methods in relation to the European landing obligation in order to prevent, assess and control the catch of non-targeted species. Overall, this thesis presents the immense potential of modern genetics and the rapidly developing
applications in marine fisheries, but also provides critical insights to strengths and weaknesses related to various methods and applications. Further, the thesis highlights the potential of using novel methodologies and instrumentation applicable to fisheries monitoring and surveillance. Of particular note, chapter III provides the first example of a fully autonomous eDNA analysis using the 2G ESP, a finding which has broad perspectives for future monitoring in remote and inaccessible marine areas.
Original languageEnglish
Publication statusPublished - 2019

 

Identifying simple and cost-effective gear solutions for an effective implementation of the new EU Common Fisheries Policy (CFP)

År: 2019

Identifying simple and cost-effective gear solutions for an effective implementation of the new EU Common Fisheries Policy (CFP)

Melli, V., 2019, 153 p.

Research output: Book/ReportPh.D. thesis – Annual report year: 2019Research

With the new Common Fisheries Policy (CFP) the European Union (EU) aimed at
eliminating the discard of commercial species, introducing the obligation to land
all catches (“landing obligation”). This catch-based approach, where all sizes of
regulated species have to be landed and counted against quota, is designed to
encourage fishermen to minimize unwanted catches. Therefore, fishermen are
now in need of fishing gear options to cope with the variability in unwanted
catches and maximize their profit within the allowed catch limits. Flexible and
specialized gear solutions, which can be used on a haul-by-haul basis to adjust
size and species selectivity, can lead to an effective implementation of the CFP
while maintaining the economic viability of the fishery. These solutions are
particularly urgent in mixed trawl fisheries, where “choke” species can limit the
exploitation of more productive stocks. Therefore, this study focused on the
Danish Nephrops (Nephrops norvegicus) directed mixed trawl fishery, one of the
economically most important fisheries in Europe. This multispecies fishery has
one of the highest rates of unwanted catches, and is expected to be strongly
affected by a fully implemented and controlled landing obligation. We investigated flexible gear modifications that could support alternative harvest strategies, such as the reduction of both undersized and commercial sized fish bycatch or the retention of only the most valuable bycatch species and sizes. The thesis consists of a review and four papers. Paper I contains the development and test of the first counter-herding device for Nephrops-directed trawl fisheries. This flexible anterior modification, easily mountable and de-mountable on the gear at a haul-by-haul level, was designed to lead fish out of the trawl path. Its efficiency varied across species and sizes, but was consistent regardless of diel period. The results showed a major reduction of catches of potentially unwanted fish species, in particular haddock (Melanogrammus aeglefinus) and whiting (Merlangius merlangus), with no effect on Nephrops catches. Paper II focuses on a horizontally divided trawl codend, which could lead to a flexible separation of the catch in different compartments of the trawl. We attempted to use visual stimulation to improve species separation. Using Light Emitting Diodes (LED), we investigated if either positive or negative phototaxis could be used to improve fish vertical separation from Nephrops. The results showed significant changes in vertical separation but no clear species-specific phototactic response. Moreover, overall LED lights increased the proportion of individuals entering the lower compartment together with Nephrops. Paper III continues the research on the horizontally divided trawl codend, but applying other types of behavioural stimulators. We investigated if and to which extent it is possible to improve the vertical separation of fish from Nephrops by adding active stimulators designed to exploit fish avoidance behaviour. We tested two types of behaviour stimulators: a chain curtain at the entrance of the lower compartment and a set of rising float-lines ahead of the point of separation. The results showed that species separation can be partially improved by the stimulators, but the effect may not be sufficient to justify the additional complexity in design respect to the baseline. Paper IV describes a meta-analytical approach to predict the size-selectivity of a gear with a combination of Bycatch Reduction Devices (BRDs) and to compare their performance under different catch scenarios. We applied this theoretical
approach to the Nephrops-directed trawl fishery, to identify the most pertinent
BRDs combinations and the alternative harvest strategies that they could
support. By including the results obtained in the previous papers, as well as
relevant BRDs available in literature, we predicted the selectivity of up to 100
possible combinations. Their performance was investigated for the target
species, Nephrops, and two bycatch species, cod (Gadus morhua) and haddock.
This meta-analytical approach can accelerate the process of identifying optimal
uses of flexible gear solutions, broadening fishermen’s options when coping with the EU landing obligation.
Original languageEnglish
Number of pages153
Publication statusPublished - 2019

 

Defense mechanisms in phytoplankton: traits and trade–offs

År: 2019

Defense mechanisms in phytoplankton: traits and trade–offs

Mohr, M. P., 2019, 99 p.

Research output: Book/ReportPh.D. thesis – Annual report year: 2019Research

In aquatic ecosystems, phytoplankton form the base of the food webs. They generate nearly half of the global primary productivity and consequently play a vital role in regulating Earth’s climate via carbon cycling. In addition, phytoplankton community composition impacts the biogeochemical cycles of inorganic elements since different functional groups of phytoplankton have different requirements and acquisition modes for nutrients. Therefore, since phytoplankton community composition impacts the global climate and the functioning of aquatic ecosystems, it is important to understand what mechanisms in turn determine the community composition. Evidently, one such mechanism is predation and the subsequent employment of defensive strategies, which promotes coexistence and species diversity. However,
the promotion of species diversity requires trade–offs. This implies that the
advantage of a defense mechanism must come at a cost, otherwise all species
would evolve towards a state of equal defense and the community composition
would no longer be promoted by predation. Based on the available evidence,
it appears that the function of many proposed defensive traits in phytoplankton
remains unclear and the trade–offs undocumented or unquantified. In many
cases, experimental evidence even suggests that defenses are costless. Here, we
propose that some costs may materialize only under natural conditions, while
other may become evident under resource–deficient conditions when a rivalry
for limiting resources between growth and defense occurs. For that reason, a
mechanistic understanding of the hypothesized component processes is required for evaluation of costs that are realized under natural conditions, while the magnitude of the costs must be assessed under conditions of resource limitation. As stated above, the role of many proposed defenses remains elusive including the protective role of silicified cell walls in diatoms. While it seems intuitive that the siliceous wall may have evolved as a mechanical protection against grazing, many other roles of a siliceous shell have been proposed and direct evidence of defense is limited. In addition, the anticipated benefits must be traded off against the costs; since deposition of silica in diatoms is determined by their growth rates, this dependency can be regarded as one of the costs of silicification. We experimentally demonstrate the protective role of silicified cell walls against adult copepods and nauplii, with near inversely proportional relationship between predation risk and silica wall thickness. On the other hand, our empirical data reveal that the increased cell wall thickness is inconsequential to protozoan grazers that engulf their prey. Additionally, we demonstrate that the deposition of silica in diatoms decreases with increasing growth rates, suggesting a possible cost to silicification. Overall, it appears that the silica wall is an efficient defense mechanism against copepods, implying that the plasticity of silicification in diatoms has likely evolved as a response to copepod grazing whose specialized tools to break open silicified walls have co–evolved with their prey. Another common trait observed in phytoplankton is the production of chemical compounds, yet often the evolution and the function of such compounds remain unclear. Often, a defensive role of toxin production is anticipated, and this interpretation is supported by observations of increased toxin synthesis in the presence of grazers, which in some cases leads to reduced predation mortality. On the other hand, experiments have consistently failed to observe any costs of toxin production, but a mechanistic understanding of the underlying processes may allow their quantification — i.e. that the production of nitrogen–rich compounds likely depends on ambient nitrogen levels. We demonstrate with a simple fitness optimization model that the cost of toxin production is indeed negligible when nitrogen and light are plentiful. However, when nitrogen or light is limiting cell growth and when grazers are abundant, the model predicts substantial costs that lead to a significant reduction in cell division rates. Our results indicate that the investment in toxin production pays–off since defended cells experience reduced grazing mortality, which consequently leads to the net growth rates that are twice as high as of undefended cells. In this PhD work, I provided an overview of defense mechanisms in phytoplankton and associated trade–offs. In search for defense trade–offs, I identified which traits lack experimental evidence supporting their defensive function (e.g. silicified cell walls), and proposed ways to assess the costs in future experimental or theoretical studies (e.g. toxin production).
Original languageEnglish
Number of pages99
Publication statusPublished - 2019

 

Lipid content in overwintering Calanus finmarchicus across the Subpolar Eastern North Atlantic Ocean

År: 2019

Lipid content in overwintering Calanus finmarchicus across the Subpolar Eastern North Atlantic Ocean

Jónasdóttir, S. H., Wilson, R. J., Gislason, A. & Wilson, R. J., 2019, (Accepted/In press) In : Limnology and Oceanography.

Research output: Contribution to journalJournal article – Annual report year: 2019Researchpeer-review

The boreal copepod Calanus finmarchicus accumulates lipid reserves during summer feeding in surface ocean waters, which enable it to stay at depth and survive famine during overwintering. Respiration of lipids during prolonged overwintering at ocean depths (> 1000 m in some areas) has been shown to result in a net sequestration of carbon into the deep ocean: the so-called “lipid pump.” Here, we provide a comprehensive synthesis of the geographic and vertical variations in lipid content of overwintering animals across the Subpolar Eastern North Atlantic and, on the basis of this, we revise the estimates of carbon sequestration. Wax ester content ranged from 40 to 190 μg individual−1 at > 250 m depths, with highest concentrations in the coldest (< 0C) waters at 400–600 m depth at the slope east of Faroe Islands and east of Greenland and lowest in the warmer (> 4C) Irminger Sea and Rockall Basin. Our new analysis results in about 44% higher estimates of carbon sequestration at up to 11.5 g C m−2
Original languageEnglish
JournalLimnology and Oceanography
ISSN0024-3590
DOIs
Publication statusAccepted/In press - 2019

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Statistical modeling of patterns in annual reproductive rates

År: 2019

Statistical modeling of patterns in annual reproductive rates

Brooks, M. E., Kristensen, K., Darrigo, M. R., Rubim, P., Uriarte, M., Bruna, E. & Bolker, B. M., 2019, (Accepted/In press) In : Ecology. e02706.

Research output: Contribution to journalJournal article – Annual report year: 2019Researchpeer-review

Reproduction by individuals is typically recorded as count data (e.g. number of fledglings from a nest or inflorescences on a plant) and commonly modeled using Poisson or negative binomial distributions, which assume that variance is greater than or equal to the mean. However, distributions of reproductive effort are often underdispersed (i.e., variance <mean). When used in hypothesis tests, models that ignore underdispersion will be overly conservative and may fail to detect significant patterns. Here we show that generalized Poisson (GP) and Conway-Maxwell-Poisson (CMP) distributions are better choices for modeling reproductive effort because they can handle both overdispersion and underdispersion; we provide examples of how ecologists can use GP and CMP distributions in generalized linear models (GLMs) and generalized linear mixed models (GLMMs) to quantify patterns in reproduction. Using a new R package, glmmTMB, we construct GLMMs to investigate how rainfall and population density influence the number of fledglings in the warbler Oreothlypis celata and how flowering rate of Heliconia acuminata differs between fragmented and continuous forest. We also demonstrate how to deal with zero-inflation, which occurs when there are more zeros than expected in the distribution, e.g. due to complete reproductive failure by some individuals. This article is protected by copyright. All rights reserved.
Original languageEnglish
Article numbere02706
JournalEcology
ISSN0012-9658
DOIs
Publication statusAccepted/In press - 2019