Comparison of visual and molecular taxonomic methods to identify ichthyoplankton in the North Sea

Mateos‐Rivera, Alejandro; Skern‐Mauritzen, Rasmus; Dahle, Geir; Sundby, Svein; Mozfar, Bahar; Thorsén, Anders; Wehde, Henning; Krafft, Bjørn A.

doi:10.1002/lom3.10387

Cited by 12 publications

(5 citation statements)

References 25 publications

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“…DNA from eggs was isolated as described by Mateos‐Rivera et al. ( 2020 ), while cod tissue was suspended in lysis buffer from the DNAdvance kit (Beckman Coulter, CA, USA) and processed using a Biomek i5 Automated Workstation (Beckman Coulter), following the manufacturer's instructions.…”

Section: Methodsmentioning

confidence: 99%

Genetic analyses verify sexually mature escaped farmed Atlantic cod and farmed cod eggs in the natural environment

Jorde,

van der Meeren,

Quintela

et al. 2024

Evolutionary Applications

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Elucidating the effects of domesticated organisms escaping into the natural environment represents a topic of importance in both evolutionary and conservation biology. However, when excluding the abundant data on salmonids, there is a lack of knowledge on this topic for marine fish aquaculture, which continues to expand globally. In order to bridge this empirical gap, we investigated a suspected escape of sexually mature domesticated Atlantic cod from a commercial marine fish farm in northern Norway. This involved genotyping samples of fish from cages on the farm, putatively identified escapees and wild cod captured in the region and samples of recently spawned eggs collected in the sea. Genetic analyses confirmed a farmed ancestry of the suspected escapees, and significantly, 27% of the sampled cod eggs. Furthermore, statistical analyses revealed a strong reduction in genetic variation in all samples of the farmed cod, including low effective population size and high degree of siblingship. These results thus document the escape of sexually mature adult cod and the release of fertilized domesticated cod eggs into the natural environment. Although it is possible that some of the mature escapees spawned post‐escape, the fact that only a single egg of potential hybrid farmed × wild origin was identified, together with the high number of mature cod in the farm, points to within cage spawning as the primary source of these eggs. This suggestion is supported by oceanic particle‐drift modelling, verifying that transport of eggs between the farm and the egg sampling locations was plausible. This study represents a rare documentation of interaction between domesticated and wild populations for a marine fish, pointing towards potential impacts on the local wild population.

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Section: Methodsmentioning

confidence: 99%

Genetic analyses verify sexually mature escaped farmed Atlantic cod and farmed cod eggs in the natural environment

Jorde,

van der Meeren,

Quintela

et al. 2024

Evolutionary Applications

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“…Both mtDNA genes were amplified in a 15‐μL PCR mix consisting of 1x Buffer, 2 mM MgCl 2 , 0.15 mM dNTP, 1 U GoTaq polymerase (Promega), 0.4 μM of each primer, and 3 μL of the template. PCR amplification was performed at 95°C; 35 cycles of 94°C for 30 s, 48°C for 30 s, 72°C for 1 min; and 72°C 7 min; and purified following the procedure described in Mateos‐Rivera et al ( 2020 ), before being sent for sequencing in duplicates (one per each direction) to Eurofins Genomics.…”

Section: Methodsmentioning

confidence: 99%

Aquaculture‐driven evolution of the salmon louse mtDNA genome

Rutle,

Skern‐Mauritzen,

Nilsen

et al. 2023

Evolutionary Applications

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Resistance toward the antiparasitic pyrethroid, deltamethrin, is reported in the Atlantic salmon louse (Lepeophtheirus salmonis salmonis), a persistent ectoparasite of farmed and wild salmonids. The resistance mechanism is linked to mitochondrial DNA (mtDNA), where genetic markers for resistance have been identified. Here, we investigated how widespread pyrethroid use in aquaculture may have influenced mtDNA variation in lice, and the dispersion of resistant haplotypes across the North Atlantic, using historical (2000–2002 “pre‐resistance”) and contemporary (2014–2017 “post‐resistance”) samples. To study this, we sequenced ATPase 6 and cytochrome b, genotyped two genetic markers for deltamethrin resistance, and genotyped microsatellites as “neutral” controls of potential population bottlenecks. Overall, we observed a modest reduction in mtDNA diversity in the period 2000–2017, but no reduction in microsatellite variation was observed. The reduction in mtDNA variation was especially distinct in two of the contemporary samples, fixed for one and two haplotypes, respectively. By contrast, all historical samples consisted of close to one mtDNA haplotype per individual. No population genetic structure was detected among the historical samples for mtDNA nor microsatellites. By contrast, significant population genetic differentiation was observed for mtDNA among some of the contemporary samples. However, the observed population genetic structure was tightly linked with the pattern of deltamethrin resistance, and we therefore conclude that it primarily reflects the transient mosaic of pyrethroid usage in time and space. Two historically undetected mtDNA haplotypes dominated in the contemporary samples, both of which were linked to deltamethrin resistance, demonstrating primarily two origins of deltamethrin resistance in the North Atlantic. Collectively, these data demonstrate that the widespread use of pyrethroids in commercial aquaculture has substantially altered the patterns of mtDNA diversity in lice across the North Atlantic, and that long‐distance dispersion of resistance is rapid due to high level of genetic connectivity that is observed in this species.

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“…Afterwards, 50 μL of the neutralizing solution (Tris-HCl 40 mM, pH 5) were added to the mixture. Upon DNA isolation, PCR amplification targeting the mitochondrial COI gene was performed following the methods described in Mateos-Rivera et al (2020). We refer to Table S1 for details on PCR amplification, purification, and sequencing.…”

Section: Morphological and Molecular Taxonomic Methodsmentioning

confidence: 99%

Composition and diversity of larval fish in the Indian Ocean using morphological and molecular methods

et al. 2021

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Although vital in fisheries management, no comprehensive studies on ichthyoplankton have been conducted in Sri Lankan waters in the north central Indian Ocean hitherto. Hence, this study is the first detailed account of diversity and species composition of larval fish based on samples collected during the southwest monsoon in 2018. In total, 80 species belonging to 69 families were identified using morphological and molecular methods targeting the COI gene. The larval fish diversity varied significantly between regions: east (North East, Central East, and South East) and west (North West, South West, and South). In their larval stages, mesopelagic families were associated with the offshore waters whereas demersal and pelagic families were related with shelf regions in the South, South East, and Central East. The larvae of pelagic families are likely dispersed by the South Monsoon Current from the west to the east regions, while demersal fish seem to be confined to the same area as conspecific adults. The most abundant larval species observed were Selar crumenophthalmus, Cubiceps pauciradiatus, and Dipterygonotus balteatus. High abundances of several commercially important larval tuna species were found in the South East, Central East, and South regions indicating that these waters could be important nursery grounds. Furthermore, Callionymus simplicicornis was recorded for the first time in the Indian Ocean, and seven additional species were found new to Sri Lankan waters. The results from this study also highlight the importance of using combined morphological and molecular methods and the need for strengthening fish nucleotide databases in poorly studied areas of the Indian Ocean.

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Comparison of visual and molecular taxonomic methods to identify ichthyoplankton in the North Sea

Cited by 12 publications

References 25 publications

Genetic analyses verify sexually mature escaped farmed Atlantic cod and farmed cod eggs in the natural environment

Genetic analyses verify sexually mature escaped farmed Atlantic cod and farmed cod eggs in the natural environment

Aquaculture‐driven evolution of the salmon louse mtDNA genome

Composition and diversity of larval fish in the Indian Ocean using morphological and molecular methods

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