| 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. |
- Pereyra, Ricardo T., 1974, et al.
(författare)
-
Clones on the run: The genomics of a recently expanded partially clonal species
- 2023
-
Ingår i: Molecular Ecology. - 0962-1083. ; 32:15, s. 4209-23
-
Tidskriftsartikel (refereegranskat)abstract
- Why species that in their core areas mainly reproduce sexually become enriched with clones in marginal populations ("geographic parthenogenesis") remains unclear. Earlier hypotheses have emphasized that selection might promote clonality because it protects locally adapted genotypes. On the other hand, it also hampers recombination and adaptation to changing conditions. The aim of the present study was to investigate the early stages of range expansion in a partially clonal species and what drives an increase in cloning during such expansion. We used genome-wide sequencing to investigate the origin and evolution of large clones formed in a macroalgal species (Fucus vesiculosus) during a recent expansion into the postglacial Baltic Sea. We found low but persistent clonality in core populations, while at range margins, large dominant clonal lineages had evolved repeatedly from different sexual populations. A range expansion model showed that even when asexual recruitment is less favourable than sexual recruitment in core populations, repeated bottlenecks at the expansion front can establish a genetically eroded clonal wave that spreads ahead of a sexual wave into the new area. Genetic variation decreases by drift following repeated bottlenecks at the expansion front. This results in the emerging clones having low expected heterozygosity, which corroborated our empirical observations. We conclude that Baker's Law (clones being favoured by uniparental reproductive assurance in new areas) can play an important role during range expansion in partially clonal species, resulting in a complex spatiotemporal mosaic of clonal and sexual lineages that might persist during thousands of generations.
|
|
| 3. |
- Berdan, Emma L, 1983, et al.
(författare)
-
A metabarcoding analysis of the wrackbed microbiome indicates a phylogeographic break along the North Sea-Baltic Sea transition zone
- 2023
-
Ingår i: Environmental Microbiology. - 1462-2912. ; 25:9, s. 1659-73
-
Tidskriftsartikel (refereegranskat)abstract
- Sandy beaches are biogeochemical hotspots that bridge marine and terrestrial ecosystems via the transfer of organic matter, such as seaweed (termed wrack). A keystone of this unique ecosystem is the microbial community, which helps to degrade wrack and re-mineralize nutrients. However, little is known about this community. Here, we characterize the wrackbed microbiome as well as the microbiome of a primary consumer, the seaweed fly Coelopa frigida, and examine how they change along one of the most studied ecological gradients in the world, the transition from the marine North Sea to the brackish Baltic Sea. We found that polysaccharide degraders dominated both microbiomes, but there were still consistent differences between wrackbed and fly samples. Furthermore, we observed a shift in both microbial communities and functionality between the North and Baltic Sea driven by changes in the frequency of different groups of known polysaccharide degraders. We hypothesize that microbes were selected for their abilities to degrade different polysaccharides corresponding to a shift in polysaccharide content in the different seaweed communities. Our results reveal the complexities of both the wrackbed microbial community, with different groups specialized to different roles, and the cascading trophic consequences of shifts in the near shore algal community.
|
|
| 4. |
- 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.
|
|
| 5. |
- Falkenberg, L. J., et al.
(författare)
-
Low sensitivity of reproductive life-stages in the Pacific oyster (Crassostrea gigas) to abamectin
- 2017
-
Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535. ; 182, s. 665-671
-
Tidskriftsartikel (refereegranskat)abstract
- Hard surfaces submerged in the marine environment often become colonised by macro-organisms unless the surfaces have some form of biofouling protection. While protective paints that contain tributyltin or copper work well to prevent biofouling, release of these materials into the environment has been shown to have wider negative impacts. Consequently, new low-release antifouling paints are being developed with alternative active ingredients, such as avermectins, yet little is known about their potential effects on non-target organisms in marine environments. Here we investigated the toxicity of a key avermectin, specifically abamectin, on several aspects of reproduction (sperm motility, fertilisation success, early larval development) in the Pacific oyster, Crassostrea gigas. Oyster reproduction was generally insensitive to the low concentrations of abamectin, although greater concentrations of abamectin did negatively affect all three endpoints – LOECs were 1000μgl−1, 500μgl−1, and 100μgl−1 abamectin for sperm motility, fertilisation success, and larval development, respectively. A similar pattern was found in the EC50s of the three endpoints (mean±SE) 934±59μgl−1, 1076.26±725.61μgl−1, and 140±78μgl−1 abamectin (sperm motility, fertilisation success, and larval development, respectively). Together, these results clearly indicate that of the three endpoints considered, larval development was more sensitive to abamectin (lower LOEC, EC50) than fertilisation success and sperm motility. Although more data are needed from a wider range of marine species and environments to fully assess potential toxicity effects on non-target organisms, our results highlight the potential utility of abamectin in low-release antifouling paints. © 2017 Elsevier Ltd
|
|
| 6. |
- Kinnby, Alexandra, 1990, et al.
(författare)
-
Climate Change Increases Susceptibility to Grazers in a Foundation Seaweed : Increased Seaweed Susceptibility to Grazers
- 2021
-
Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- Climate change leads to multiple effects caused by simultaneous shifts in several physical factors which will interact with species and ecosystems in complex ways. In marine systems the effects of climate change include altered salinity, increased temperature, and elevated pCO2 which are currently affecting and will continue to affect marine species and ecosystems. Seaweeds are primary producers and foundation species in coastal ecosystems, which are particularly vulnerable to climate change. The brown seaweed Fucus vesiculosus (bladderwrack) is an important foundation species in nearshore ecosystems throughout its natural range in the North Atlantic Ocean and the Baltic Sea. This study investigates how individual and interactive effects of temperature, salinity, and pCO2 affect F. vesiculosus, using a fully crossed experimental design. We assessed the effects on F. vesiculosus in terms of growth, biochemical composition (phlorotannin content, C:N ratio, and ∂13C), and susceptibility to the specialized grazer Littorina obtusata. We observed that elevated pCO2 had a positive effect on seaweed growth in ambient temperature, but not in elevated temperature, while growth increased in low salinity at ambient but not high temperature, regardless of pCO2-level. In parallel to the statistically significant, but relatively small, positive effects on F. vesiculosus growth, we found that the seaweeds became much more susceptible to grazing in elevated pCO2 and reduced salinity, regardless of temperature. Furthermore, the ability of the seaweeds to induce chemical defenses (phlorotannins) was strongly reduced by all the climate stressors. Seaweeds exposed to ambient conditions more than doubled their phlorotannin content in the presence of grazers, while seaweeds exposed to any single or combined stress conditions showed only minor increases in phlorotannin content, or none at all. Despite the minor positive effects on seaweed growth, the results of this study imply that climate change can strongly affect the ability of fucoid seaweeds to induce chemical defenses and increase their susceptibility to grazers. This will likely lead to widespread consequences under future climate conditions, considering the important role of F. vesiculosus and other fucoids in many coastal ecosystems.
|
|
| 7. |
- Kinnby, Alexandra, 1990, et al.
(författare)
-
Combining an Ecological Experiment and a Genome Scan Show Idiosyncratic Responses to Salinity Stress in Local Populations of a Seaweed
- 2020
-
Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- Climate change-related effects threaten species worldwide; within-species populations may react differently to climate-induced stress due to local adaptation and partial isolation, particularly in areas with steep environmental gradients. Populations of the marine foundation seaweed Fucus vesiculosus are established over a steep salinity gradient at the entrance of the brackish water in the Baltic Sea (NE Atlantic). First, we analyzed the genetic differentiation among populations using thousands of genetic markers. Second, we measured the physiological tolerance to reduced salinity, a predicted effect of climate change in the study area, by measuring growth, phlorotannin (defense compounds) content, and maximum photochemical yield in tissue of the same individuals exposed to both current and projected future salinities. Our results show that despite short geographic distances (max 100 km), most populations were genetically well separated. Furthermore, populations responded very differently to a salinity decrease of four practical salinity units (psu) corresponding to projected future salinity. At the high salinity end of the gradient, some populations maintained growth at the cost of reduced phlorotannin production. However, at the low salinity end, mortality increased and growth was strongly reduced in one population, while a second population from similar salinity instead maintained growth and phlorotannin production. Among genetic markers that appeared as outliers (showing more genetic differentiation than the majority of loci), we found that four were associated with genes that were potential candidates for being under selection. One of these, a calcium-binding protein gene, also showed a significant genotype-phenotype relationship in the population where this genetic marker was variable. We concluded that local selection pressure, genetic affinity, and possibly also population history could explain the very different responses to reduced salinity among these populations, despite being from the same geographic area. Our results highlight the importance of local perspective in the management of species.
|
|
| 8. |
- Kinnby, Alexandra, 1990, et al.
(författare)
-
Factors affecting formation of adventitious branches in the seaweeds Fucus vesiculosus and F. radicans
- 2019
-
Ingår i: Bmc Ecology. - : Springer Science and Business Media LLC. - 1472-6785. ; 19
-
Tidskriftsartikel (refereegranskat)abstract
- BackgroundIn the brackish Baltic Sea, shedding of adventitious branches is central to asexual recruitment of new thalli in the brown algae Fucus vesiculosus and F. radicans. To test which factors influence the formation of adventitious branches in brackish and in more marine conditions, we sampled 29 Fucus sites in the Baltic Sea (salinity 3-11) and 18 sites from the Danish straits, Kattegat, Skagerrak, and the North Sea (salinity 15-35). Separately for each area, we used structural equation modelling to determine which of eight predictor factors (phosphate, nitrate, chlorophyll-a (as a proxy for turbidity), temperature, salinity, oxygen, grazing pressure, and thallus area) best explained observed numbers of adventitious branches.ResultsIn more marine waters, high yearly average values of phosphate, salinity and turbidity had positive effects on the formation of adventitious branches. In brackish-waters, however, high numbers of adventitious branches were found in areas with low yearly average values of temperature, salinity and oxygen. Grazing intensity had no significant effect in either of the two study areas, contrasting findings from studies in other areas. In areas with both sexually and asexually reproducing Fucus individuals, clones had on average more adventitious branches than unique genotypes, although there was strong variation among clonal lineages.ConclusionThis study is the first to investigate multiple potential drivers of formation of adventitious branches in natural populations of Fucus. Our results suggest that several different factors synergistically and antagonistically affect the growth of adventitious branches in a complex way, and that the same factor (salinity) can have opposing effects in different areas.
|
|
| 9. |
- Kinnby, Alexandra, 1990
(författare)
-
Habitat-Forming Seaweeds in a Changing Climate
- 2021
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Climate change is an umbrella term encompassing some of the largest and most potent selective pressures currently acting on ecosystems. It can have diverse effects on marine systems; the most powerful of which are changes to salinity through altered patterns of precipitation and evaporation, temperature through increased global temperature, and pH through the dissolution of CO2 into seawater where it ultimately reacts with water to form carbonate (CO32-) and hydrogen ions (2H+). All these changes may impact marine organisms, in particular above the thermocline and in coastal waters. The studies included in this thesis were all performed in or close to the transition zone between the North Sea and the Baltic Sea. This area is a shallow coastal water mass influenced by the fully oceanic North Sea and the brackish Baltic Sea. Brown seaweeds are important habitat-forming seaweeds in this area, and bladderwrack (Fucus vesiculosus) is one of the most widespread and abundant. The general objective of this thesis is to evaluate the effects of climate change on habitat forming seaweeds in a coastal area and to experimentally address the complexity caused by the multiple factors changing simultaneously as a consequence of climate change. For example, including both separate and interactive effects of changes in seawater temperature, pH, salinity, and grazing pressure on both adult and early life stages of primarily Fucus vesiculosus in the experiments. By conducting field and lab experiments and combining physiological, chemical, and genetic approaches, I detect different aspects of responses to climate induced stress. My findings show that F. vesiculosus responds to climate change variables differently in different populations, and it responds to combinations of variables in ways that are not easily predicted based on experiments with single variables. I found that this seaweed will likely increase in growth by area but not weight under future climate change, and that its ability to induce chemical defence to grazing will be dramatically reduced. Furthermore, I found that F. vesiculosus and two other species of brown seaweeds may reduce their calcium content and tissue strength, which leads to increased risk of physical damage from storms and grazing and could result in population declines. This could in turn lead to significant effects on coastal ecosystems, and if these patterns are also true for other habitat-forming species they could have wide-reaching effects.
|
|
| 10. |
- Kinnby, Alexandra, 1990, et al.
(författare)
-
Ocean acidification decreases grazing pressure but alters morphological structure in a dominant coastal seaweed.
- 2021
-
Ingår i: PloS one. - : Public Library of Science (PLoS). - 1932-6203. ; 16:1
-
Tidskriftsartikel (refereegranskat)abstract
- Ocean acidification driven by anthropogenic climate change is causing a global decrease in pH, which is projected to be 0.4 units lower in coastal shallow waters by the year 2100. Previous studies have shown that seaweeds grown under such conditions may alter their growth and photosynthetic capacity. It is not clear how such alterations might impact interactions between seaweed and herbivores, e.g. through changes in feeding rates, nutritional value, or defense levels. Changes in seaweeds are particularly important for coastal food webs, as they are key primary producers and often habitat-forming species. We cultured the habitat-forming brown seaweed Fucus vesiculosus for 30 days in projected future pCO2 (1100 μatm) with genetically identical controls in ambient pCO2 (400 μatm). Thereafter the macroalgae were exposed to grazing by Littorina littorea, acclimated to the relevant pCO2-treatment. We found increased growth (measured as surface area increase), decreased tissue strength in a tensile strength test, and decreased chemical defense (phlorotannins) levels in seaweeds exposed to high pCO2-levels. The herbivores exposed to elevated pCO2-levels showed improved condition index, decreased consumption, but no significant change in feeding preference. Fucoid seaweeds such as F. vesiculosus play important ecological roles in coastal habitats and are often foundation species, with a key role for ecosystem structure and function. The change in surface area and associated decrease in breaking force, as demonstrated by our results, indicate that F. vesiculosus grown under elevated levels of pCO2 may acquire an altered morphology and reduced tissue strength. This, together with increased wave energy in coastal ecosystems due to climate change, could have detrimental effects by reducing both habitat and food availability for herbivores.
|
|
