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Organisms well suited for the study of ecotype formation have wide distribution ranges, where they adapt to multiple drastically different habitats repeatedly over space and time. Here we study such ecotypes in a Crustacean model, Asellus aquaticus, a commonly occurring isopod found in freshwater habitats as diverse as streams, caves and lakes. Previous studies focusing on cave vs. surface ecotypes have attributed depigmentation, eye loss and prolonged antennae to several south European cave systems. Likewise, surveys across multiple Swedish lakes have identified the presence of dark‐pigmented "reed" and light‐pigmented "stonewort" ecotypes, which can be found within the same lake. In this study, we sequenced the first draft genome of A. aquaticus, and subsequently use this to map reads and call variants in surface stream, cave and two lake ecotypes. In addition, the draft genome was combined with a RADseq approach to perform a quantitative trait locus (QTL) mapping study using a laboratory bred F2 and F4 cave × surface intercross. We identified genomic regions associated with body pigmentation, antennae length and body size. Furthermore, we compared genome‐wide differentiation between natural populations and found several genes potentially associated with these habitats. The assessment of the cave QTL regions in the light–dark comparison of lake populations suggests that the regions associated with cave adaptation are also involved with genomic differentiation in the lake ecotypes. These demonstrate how troglomorphic adaptations can be used as a model for related ecotype formation. [ABSTRACT FROM AUTHOR]

Divergent natural selection is often thought to be the principal factor driving phenotypic differentiation between populations. We studied two ecotypes of the aquatic isopod Asellus aquaticus which have diverged in parallel in several Swedish lakes. In these lakes, isopods from reed belts along the shores colonized new stonewort stands in the centre of the lakes and rapid phenotypic changes in size and pigmentation followed after colonization. We investigated if selection was likely to be responsible for these observed phenotypic changes using indirect inferences of selection ( FST– QST analysis). Average QST for seven quantitative traits were higher than the average FST between ecotypes for putatively neutral markers (AFLPs). This suggests that divergent natural selection has played an important role during this rapid diversification. In contrast, the average QST between the different reed ecotype populations was not significantly different from the mean FST. Genetic drift could therefore not be excluded as an explanation for the minor differences between allopatric populations inhabiting the same source habitat. We complemented this traditional FST– QST approach by comparing the FST distributions across all loci ( n = 67–71) with the QST for each of the seven traits. This analysis revealed that pigmentation traits had diverged to a greater extent and at higher evolutionary rates than size-related morphological traits. In conclusion, this extended and detailed type of FST– QST analysis provides a powerful method to infer adaptive phenotypic divergence between populations. However, indirect inferences about the operation of divergent selection should be analyzed on a per-trait basis and complemented with detailed ecological information. [ABSTRACT FROM AUTHOR]

1. In this study, we examine how a 7-year period of expanding submerged stonewort ( Chara spp.) vegetation during a shift from turbid to clear water in a shallow lake influenced individual growth and population size structure of perch ( Perca fluviatilis). We expected that a shift from phytoplankton to macrophyte dominance and clear water would improve feeding conditions for perch during a critical benthivorous ontogenetic stage, and enhance the recruitment of piscivorous perch. 2. Growth analysis based on opercula showed that growth during the second year of life was significantly higher in years with abundant vegetation than in years with turbid water and sparse vegetation. Growth was not affected during the first, third and fourth year of life. Stable isotope analyses on opercula from 2-year-old perch showed that the increase in growth coincided with a change in carbon source in the diet. Stable nitrogen ratio did not change, indicating that the increased growth was not an effect of any change in trophic position. 3. Following the expansion of submerged vegetation, perch size range and abundance of piscivorous perch increased in central, unvegetated areas of the lake. In stands of stoneworts, however, mainly benthivorous perch were caught, and size range did not change with time. 4. Our findings provide empirical support for the notion that establishment of submerged vegetation may lead to increased recruitment of piscivorous perch, because of improved competitive conditions for perch during the benthivorous stage. This is likely to constitute a benthic-pelagic feedback coupling, in which submerged vegetation and clear water promote the recruitment of piscivorous perch, which, in turn, may increase water clarity through top-down effects in the pelagic. [ABSTRACT FROM AUTHOR]

The study is based on monitoring data on the seasonal variation during four (1996–1999) vegetation periods, as well as long-term summer data on submerged vegetation, nutrients, light, phytoplankton and zooplankton in Lake Krankesjo¨n, a shallow, calcium-rich, moderately eutrophic lake in southern Sweden.The lake has been in the clear water state with abundant submerged vegetation since the end of the 1980s. Somewhat lower summer biomass of submerged macrophytes during 1997 and 1999 indicates a temporary instability of the clear water state. During these 2 years, summer transparency was about 1.2–2.1 m, while concentrations of total phosphorus and chlorophyll (Chl) a were about 26–40 and 8–18 μg l−1, respectively.Summer biomass of submerged macrophytes was higher during 1996 and 1998. In both years, a distinct increase in light availability and decrease in concentrations of nutrients and chlorophyll occurred simultaneously with the development of dense Chara vegetation. Summer values for transparency were about 2.0–2.5 m, while concentrations of total phosphorus and Chl a were about 20–32 and 4–11 μg l−1, respectively.Summer biomass of crustacean zooplankton was below 250 μg l−1 during all 4 years. A peak abundance of Cladocera (mainly Bosmina longirostris) during May or June caused only a short-term reduction in chlorophyll concentrations that was more pronounced in 1997 than in 1996.Measured light attenuation during 1999 was closely correlated with light attenuation calculated from the amount of suspended solids, chlorophyll concentrations, and water colour. Detritus contributed most to the total amount of suspended solids, while chlorophyll was the main contributor to light attenuation.A long-term decrease of the ratios between chlorophyll and total phosphorus suggests that phytoplankton in the clear water state is limited by factors other than total phosphorus concentrations. Increased sedimentation rate, carbon limitation, allelopathy and a lower bioavailable fraction of the total amount of phosphorus are possible explanations, while nitrogen limitation and grazing from zooplankton probably are of minor importance.Possible reasons for the “instability” of the clear water state during 1997 and 1999 are discussed. Unusually high water level as well as cold and windy weather during the spring of 1996–1999 may have caused a slow and late growth of the plants and thus a temporary instability. However, a tendency for an increase in total phosphorus concentrations and sediment accumulation along the wind-protected shores during the clear water state indicate the possibility of a long-term destabilization which contradicts the alternative stable states model. [Copyright &y& Elsevier]

1. We studied vertical and horizontal distribution of macroinvertebrates within a dense stand of Chara spp. in Lake Krankesjön, southern Sweden. Invertebrates were sampled at three depths within the vegetation and at three distances from the vegetation edge during day and night in July and August. Corresponding samples of oxygen content of the water were taken. 2. The densities (number of invertebrates per unit plant biomass) of most invertebrate taxa were generally lower in the upper layers of the vegetation than in the layers close to the sediment. The densities of several taxa (Asellus aquaticus, Cloëon sp. and Polycentropodidae), as well as total density of invertebrates, were higher at the edge than in the innermost parts of the macrophyte stand, whereas snail densities generally were highest at the innermost sites. 3. Densities of A. aquaticus, Chironomidae larvae and Helobdella stagnalis generally increased at night. These taxa appear to undertake a diel vertical migration within the vegetation, towards, or even down to the sediment in daytime and up into the vegetation, in some cases to the vegetation surface, at night. Factors underlying the diel vertical migration are discussed, as are their ecological consequences. [ABSTRACT FROM AUTHOR]

Summary1. We measured the abundance and biomass of filter-feeding microcrustacean zooplankton and calculated their grazing impact on phytoplankton biomass during summer in five shallow, mesotrophic to eutrophic lakes. For three of the lakes data exist both from years with dense submerged vegetation and low turbidity (the clearwater state), as well as from years characterised by sparse vegetation and high turbidity (the turbid state). In the other two lakes data are available only for clearwater conditions. 2. In all lakes conditions of dense vegetation and clear water coincided with a low abundance of crustacean plankton during summer. In the three lakes that shifted, the calculated biovolume ingested by crustacean plankton (filtering rate) was 3–11 times lower during clearwater conditions compared with turbid conditions. Because phytoplankton biomass was lower during clearwater conditions, however, daily grazing pressure from microcrustacea (expressed as percentage of phytoplankton biomass) did not differ between states. In three of the five lakes, grazers were estimated to take less than 10% of the phytoplankton biomass per day, indicating filtration by zooplankton was not the most important mechanism to maintain clearwater conditions. 3. High densities of Cladocera were found in three of the lakes within dense stands of Charophyta. However, these samples were dominated by plant-associated taxa that even during the night were rarely found outside the vegetation. This indicates that plant-associated zooplankton has no major influence on the maintenance of water clarity outside the vegetation. 4. Spring peak abundance of Cladocera was observed in three of the lakes. In two of these, where seasonal development was studied in both the clearwater and the turbid state, spring peaks were lower during the clearwater state. 5. Predation, low food availability or a combination of both may explain the low zooplankton densities. Phytoplankton may be limited by low phosphorus availability in the lakes dominated by Charophyta. Our results indicate that the importance of zooplankton grazing may have minor importance for the maintenance of the clearwater state in lakes with dense, well-established submerged vegetation. [ABSTRACT FROM AUTHOR]

Organisms well suited for the study of ecotype formation have wide distribution ranges, where they adapt to multiple drastically different habitats repeatedly over space and time. Here we study such ecotypes in a Crustacean model, Asellus aquaticus, a commonly occurring isopod found in freshwater habitats as diverse as streams, caves and lakes. Previous studies focusing on cave vs. surface ecotypes have attributed depigmentation, eye loss and prolonged antennae to several south European cave systems. Likewise, surveys across multiple Swedish lakes have identified the presence of dark-pigmented "reed" and light-pigmented "stonewort" ecotypes, which can be found within the same lake. In this study, we sequenced the first draft genome of A. aquaticus, and subsequently use this to map reads and call variants in surface stream, cave and two lake ecotypes. In addition, the draft genome was combined with a RADseq approach to perform a quantitative trait locus (QTL) mapping study using a laboratory bred F 2 and F 4 cave × surface intercross. We identified genomic regions associated with body pigmentation, antennae length and body size. Furthermore, we compared genome-wide differentiation between natural populations and found several genes potentially associated with these habitats. The assessment of the cave QTL regions in the light-dark comparison of lake populations suggests that the regions associated with cave adaptation are also involved with genomic differentiation in the lake ecotypes. These demonstrate how troglomorphic adaptations can be used as a model for related ecotype formation., (© 2021 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Divergent natural selection is often thought to be the principal factor driving phenotypic differentiation between populations. We studied two ecotypes of the aquatic isopod Asellus aquaticus which have diverged in parallel in several Swedish lakes. In these lakes, isopods from reed belts along the shores colonized new stonewort stands in the centre of the lakes and rapid phenotypic changes in size and pigmentation followed after colonization. We investigated if selection was likely to be responsible for these observed phenotypic changes using indirect inferences of selection (F(ST)-Q(ST) analysis). Average Q(ST) for seven quantitative traits were higher than the average F(ST) between ecotypes for putatively neutral markers (AFLPs). This suggests that divergent natural selection has played an important role during this rapid diversification. In contrast, the average Q(ST) between the different reed ecotype populations was not significantly different from the mean F(ST). Genetic drift could therefore not be excluded as an explanation for the minor differences between allopatric populations inhabiting the same source habitat. We complemented this traditional F(ST)-Q(ST) approach by comparing the F(ST) distributions across all loci (n = 67-71) with the Q(ST) for each of the seven traits. This analysis revealed that pigmentation traits had diverged to a greater extent and at higher evolutionary rates than size-related morphological traits. In conclusion, this extended and detailed type of F(ST)-Q(ST) analysis provides a powerful method to infer adaptive phenotypic divergence between populations. However, indirect inferences about the operation of divergent selection should be analyzed on a per-trait basis and complemented with detailed ecological information.