| 1. |
- Bachimanchi, Harshith, et al.
(författare)
-
Deep-learning-powered data analysis in plankton ecology
- 2024
-
Ingår i: Limnology And Oceanography Letters. - 2378-2242.
-
Forskningsöversikt (refereegranskat)abstract
- The implementation of deep learning algorithms has brought new perspectives to plankton ecology. Emerging as an alternative approach to established methods, deep learning offers objective schemes to investigate plankton organisms in diverse environments. We provide an overview of deep-learning-based methods including detection and classification of phytoplankton and zooplankton images, foraging and swimming behavior analysis, and finally ecological modeling. Deep learning has the potential to speed up the analysis and reduce the human experimental bias, thus enabling data acquisition at relevant temporal and spatial scales with improved reproducibility. We also discuss shortcomings and show how deep learning architectures have evolved to mitigate imprecise readouts. Finally, we suggest opportunities where deep learning is particularly likely to catalyze plankton research. The examples are accompanied by detailed tutorials and code samples that allow readers to apply the methods described in this review to their own data.
|
|
| 2. |
- De Wit, Pierre, 1978, et al.
(författare)
-
A decade of progress in marine evolutionary biology
- 2022
-
Ingår i: Evolutionary Applications. - : Wiley. - 1752-4571. ; 16:2, s. 193-201
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- This article summarizes the Evolutionary Applications Special Issue, “A decade of progress in Marine Evolutionary Biology.” The globally connected ocean, from its pelagic depths to its highly varied coastlines, inspired Charles Darwin to develop the theory of evolution during the voyage of the Beagle. As technology has developed, there has been a dramatic increase in our knowledge about life on our blue planet. This Special Issue, composed of 19 original papers and seven reviews, represents a small contribution to the larger picture of recent research in evolutionary biology, and how such advancements come about through the connection of researchers, their fields, and their knowledge. The first European network for marine evolutionary biology, the Linnaeus Centre for Marine Evolutionary Biology (CeMEB), was developed to study evolutionary processes in the marine environment under global change. Though hosted by the University of Gothenburg in Sweden, the network quickly grew to encompass researchers throughout Europe and beyond. Today, more than a decade after its foundation, CeMEB's focus on the evolutionary consequences of global change is more relevant than ever, and knowledge gained from marine evolution research is urgently needed in management and conservation. This Special Issue, organized and developed through the CeMEB network, contains contributions from all over the world and provides a snapshot of the current state of the field, thus forming an important basis for future research directions.
|
|
| 3. |
- De Wit, Pierre, 1978, et al.
(författare)
-
Single nucleotide polymorphisms are suitable for assessing the success of restocking efforts of the European lobster (Homarus gammarus, L.)
- 2022
-
Ingår i: Conservation Genetics Resources. - : Springer Science and Business Media LLC. - 1877-7252 .- 1877-7260. ; 14:1, s. 47-52
-
Tidskriftsartikel (refereegranskat)abstract
- The European lobster (Homarus gammarus) forms the base of an important fishery along the coasts of Europe. However, stocks have been in decline for many years, prompting new regulations in the fishery and also restocking efforts. An important feature of any restocking effort is the assessment of success in the number of released juveniles that stay and become adult over time. Here, we tested the power of a single nucleotide polymorphism (SNP) DNA marker panel developed for population assignment to correctly infer parentage on the maternal side of lobster larvae, in the absence of known fathers, using lobsters included in a current restocking effort on the Swedish west coast. We also examined the power to reconstruct the unknown paternal genotypes, and examined the number of fathers for each larval clutch. We found that the 96-SNP panel, despite only containing 78 informative markers, allowed us to assign all larvae to the correct mother. Furthermore, with ten genotyped larvae or more, confident paternal genotypes could be reconstructed. We also found that 15 out of 17 clutches were full siblings, whereas two clutches had two fathers. To our knowledge, this is the first time a SNP panel of this size has been used to assess parentage in a crustacean restocking effort. Our conclusion is that the panel works well, and that it could be an important tool for the assessment of restocking success of H. gammarus in the future.
|
|
| 4. |
- De Wit, Pierre, 1978, et al.
(författare)
-
Spatial genetic structure in a crustacean herbivore highlights the need for local considerations in Baltic Sea biodiversity management
- 2020
-
Ingår i: Evolutionary Applications. - : Wiley. - 1752-4563 .- 1752-4571. ; 13:5, s. 974-990
-
Tidskriftsartikel (refereegranskat)abstract
- Incorporating species' eco-evolutionary responses to human-caused disturbances remains a challenge in marine management efforts. A prerequisite is knowledge of geographic structure and scale of genetic diversity and connectivity—the so-called seascape genetic patterns. The Baltic Sea is an excellent model system for studies linking seascape genetics with effects of anthropogenic stress. However, seascape genetic patterns in this area are only described for a few species and are completely unknown for invertebrate herbivores, which constitute a critical part of the ecosystem. This information is crucial for sustainable management, particularly under future scenarios of rapid environmental change. Here, we investigate the population genetic structure among 31 locations throughout the Baltic Sea, of which 45% were located in marine protected areas, in one of the most important herbivores of this region, the isopod crustacean Idotea balthica, using an array of 33,774 genome-wide SNP markers derived from 2b-RAD sequencing. In addition, we generate a biophysical connectivity matrix for I. balthica from a combination of oceanographic current models and estimated life history traits. We find population structure on scales of hundreds of kilometers across the Baltic Sea, where genomic patterns in most cases closely match biophysical connectivity, indicating passive transport with oceanographic currents as an important mean of dispersal in this species. We also find a reduced genetic diversity in terms of heterozygosity along the main salinity gradient of the Baltic Sea, suggesting periods of low population size. Our results provide crucial information for the management of a key ecosystem species under expected changes in temperature and salinity following global climate change in a marine coastal area. © 2019 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.
|
|
| 5. |
- Durland, Evan, et al.
(författare)
-
Genetic changes in larval oysters are more abundant and dynamic than can be explained by rare events or error. A response to Hedgecock (2022)
- 2022
-
Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 289:1976
-
Tidskriftsartikel (refereegranskat)abstract
- In our recent paper [1], we reported surprisingly dynamic patterns of allele fre- quency change over larval development of Pacific oysters (Crassostrea gigas). In brief, we found that 27% (n = 127) of all loci with significant temporal changes had bi-directional trajectories of minor allele frequencies (MAF). The majority (62%; n = 282) of all loci with any changes in MAF during larval development had subsequent changes in the opposite direction, balancing the overall distor- tion in MAF across this period. We used these and other findings to propose a hypothesis of temporally balancing selection in developing oyster larvae whereby the variable morphological landscape of larval development has potentially heterogeneous selective effects on genes associated with many loci in the oyster genome. In his comment, Hedgecock [2] objects to our interpretation of the results of our study, postulating that the dynamic patterns of MAF changes we report are confounded by complex genomic architectures, variability in parental repro- ductive success, and methodological issues. Some of the points he raises are conceptually valid, but they ignore the design of our study and the nature of our findings. Moreover, Hedgecock presents our findings and interpretations as disagreeing with those of previous studies investigating genetic changes in larval oysters, while we contend that no such fundamental conflict exists. Below, we respond to these critical issues raised by Hedgecock.
|
|
| 6. |
- Durland, Evan, et al.
(författare)
-
Larval development in the Pacific oyster and the impacts of ocean acidification: Differential genetic effects in wild and domesticated stocks
- 2021
-
Ingår i: Evolutionary Applications. - : Wiley. - 1752-4571. ; 14:9, s. 2258-2272
-
Tidskriftsartikel (refereegranskat)abstract
- The adaptive capacity of marine calcifiers to ocean acidification (OA) is a topic of great interest to evolutionary biologists and ecologists. Previous studies have provided evidence to suggest that larval resilience to high pCO2 seawater for these species is a trait with a genetic basis and variability in natural populations. To date, however, it remains unclear how the selective effects of OA occur within the context of complex genetic interactions underpinning larval development in many of the most vulnerable taxa. Here we evaluated phenotypic and genetic changes during larval development of Pacific oysters (Crassostrea gigas) reared in ambient (~400 µatm) and high (~1600 µatm) pCO2 conditions, both in domesticated and naturalized “wild” oysters from the Pacific Northwest, USA. Using pooled DNA samples, we determined changes in allele frequencies across larval development, from early “D-stage” larvae to metamorphosed juveniles (spat), in both groups and environments. Domesticated larvae had ~26% fewer loci with changing allele frequencies across developmental stages and <50% as many loci affected by acidified culture conditions, compared to larvae from wild broodstock. Functional enrichment analyses of genetic markers with significant changes in allele frequency revealed that the structure and function of cellular membranes were disproportionately affected by high pCO2 conditions in both groups. These results indicate the potential for a rapid adaptive response of oyster populations to OA conditions; however, underlying genetic changes associated with larval development differ between these wild and domesticated oyster stocks and influence their adaptive responses to OA conditions.
|
|
| 7. |
- Durland, Evan, et al.
(författare)
-
Temporally balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring
- 2021
-
Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 288
-
Tidskriftsartikel (refereegranskat)abstract
- Balancing selection is one of the mechanisms which has been proposed to explain the maintenance of genetic diversity in species across generations. For species with large populations and complex life histories, however, hetero- geneous selection pressures may create a scenario in which the net effects of selection are balanced across developmental stages. With replicated cultures and a pooled sequencing approach, we show that genotype-dependent mor- tality in larvae of the Pacific oyster (Crassostrea gigas) is largely temporally dynamic and inconsistently in favour of a single genotype or allelic variant at each locus. Overall, the patterns of genetic change we observe to be taking place are more complex than what would be expected under classical examples of additive or dominant genetic interactions. They are also not easily explained by our current understanding of the effects of genetic load. Collectively, temporally heterogeneous selection pressures across different larval developmental stages may act to maintain genetic diversity, while also inherently sheltering genetic load within oyster populations.
|
|
| 8. |
- Eriksson, Martin, et al.
(författare)
-
Adaptive, maladaptive, neutral, or absent plasticity: Hidden caveats of reaction norms
- 2022
-
Ingår i: Evolutionary Applications. - : Wiley. - 1752-4571. ; 16:2, s. 486-503
-
Tidskriftsartikel (refereegranskat)abstract
- Adaptive phenotypic plasticity may improve the response of individuals when faced with new environmental conditions. Typically, empirical evidence for plasticity is based on phenotypic reaction norms obtained in reciprocal transplant experiments. In such experiments, individuals from their native environment are transplanted into a different environment, and a number of trait values, potentially implicated in individuals' response to the new environment, are measured. However, the interpretations of reaction norms may differ depending on the nature of the assessed traits, which may not be known beforehand. For example, for traits that contribute to local adaptation, adaptive plasticity implies nonzero slopes of reaction norms. By contrast, for traits that are correlated to fitness, high tolerance to different environments (possibly due to adaptive plasticity in traits that contribute to adaptation) may, instead, result in flat reaction norms. Here we investigate reaction norms for adaptive versus fitness-correlated traits and how they may affect the conclusions regarding the contribution of plasticity. To this end, we first simulate range expansion along an environmental gradient where plasticity evolves to different values locally and then perform reciprocal transplant experiments in silico. We show that reaction norms alone cannot inform us whether the assessed trait exhibits locally adaptive, maladaptive, neutral, or no plasticity, without any additional knowledge of the traits assessed and species' biology. We use the insights from the model to analyse and interpret empirical data from reciprocal transplant experiments involving the marine isopod Idotea balthica sampled from two geographical locations with different salinities, concluding that the low-salinity population likely has reduced adaptive plasticity relative to the high-salinity population. Overall, we conclude that, when interpreting results from reciprocal transplant experiments, it is necessary to consider whether traits assessed are locally adaptive with respect to the environmental variable accounted for in the experiments or correlated to fitness.
|
|
| 9. |
- Gustafsson, Malin, et al.
(författare)
-
Unlocking the secret life of blue mussels: Exploring connectivity in the Skagerrak through biophysical modeling and population genomics
- 2024
-
Ingår i: Evolutionary Applications. - 1752-4571. ; 17
-
Tidskriftsartikel (refereegranskat)abstract
- Knowledge of functional dispersal barriers in the marine environment can be used to inform a wide variety of management actions, such as marine spatial planning, restoration efforts, fisheries regulations, and invasive species management. Locations and causes of dispersal barriers can be studied through various methods, including movement tracking, biophysical modeling, demographic models, and genetics. Combining methods illustrating potential dispersal, such as biophysical modeling, with realized dispersal through, e.g., genetic connectivity estimates, provides particularly useful information for teasing apart potential causes of observed barriers. In this study, we focus on blue mussels (Mytilus edulis) in the Skagerrak—a marginal sea connected to the North Sea in Northern Europe—and combine biophysical models of larval dispersal with genomic data to infer locations and causes of dispersal barriers in the area. Results from both methods agree; patterns of ocean currents are a major structuring factor in the area. We find a complex pattern of source-sink dynamics with several dispersal barriers and show that some areas can be isolated despite an overall high dispersal capability. Finally, we translate our finding into management advice that can be used to sustainably manage this ecologically and economically important species in the future.
|
|
| 10. |
- Li, Ao, et al.
(författare)
-
Genome architecture and selective signals compensatorily shape plastic response to a new environment
- 2023
-
Ingår i: The Innovation. - 2666-6758. ; 4:4
-
Tidskriftsartikel (refereegranskat)abstract
- Transcriptional plasticity interacts with natural selection in complex ways and is crucial for the survival of species under rapid climate change. How 3D genome architecture affects transcriptional plasticity and its interaction with genetic adaptation are unclear. We transplanted estuarine oysters to a new environment and found that genes located in active chromatin regions exhibited greater transcriptional plasticity, and changes in these regions were negatively correlated with selective signals. This indicates a trade-off be- tween 3D active regions and selective signals in shaping plastic responses to a new environment. Specifically, a mutation, lincRNA, and changes in the accessibility of a distal enhancer potentially affect its interaction with the ManIIa gene, which regulates the muscle function and survival of oysters. Our findings reveal that 3D genome architecture compensates for the role of genetic adaptation in environmental response to new environments and provide insights into synergetic genetic and epigenetic interactions critical for fitness-related trait and survival in a model marine species.
|
|
