Extensive field data was collected from lake complexes in the Romanian part of the Danube Delta, to assess the occurrence of harmful cyanobacterial blooms. Since detailed long-term monitoring data were missing from those lakes, from sediment cores we:
reconstructed occurrence and structure of cyanobacterial blooms by PCR
evaluated the presence of toxic genes by PCR
resurrected Daphnia from resting eggs
tested pre- and post-eutrophication Daphnia populations for local adaptation to cyanobacterial blooms in laboratory experiments.
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title => protected'Long term diversity and distribution of non-photosynthetic cyanobacteria in peri-Alpine lakes' (93 chars)
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categories => protected'Melainabacteria; ML635J-21; Sericytochromatia; metabarcoding; sedimentary DN A; distance-decay relationship; meta-community; anthropocene' (136 chars)
description => protected'The phylum Cyanobacteria comprises a non-photosynthetic lineage. The diversi ty and distribution of non-photosynthetic cyanobacteria (NCY) across aquatic environments are currently unknown, including their ecology. Here, we repor t about composition and phylogenetic diversity of two clades of NCY in ten l akes of the European peri-Alpine region, over the past ~100 years. Using 16S rDNA sequences obtained from dated sediment cores, we found almost equal pr oportion of taxa assigned to Melainabacteria and the deepest-branching group Sericytochromatia (ML635J-21) (63 total detected taxa). The topology of our reconstructed phylogenies reflected evolutionary relationships expected fro m previous work, that is, a clear separation between the deepest branching S ericytochromatia, the Melainabacteria, and the photosynthetic cyanobacteria clades. While different lakes harbored distinct NCY communities, the diversi ty of NCY assemblages within and between lakes (alpha and beta diversity) di d not significantly change over the last century. This is in contrast with w hat was previously reported for photosynthetic cyanobacteria. Unchanged comm unity phylogenetic similarity over geographic distance indicated no dispersa l limitation of NCY at the regional scale. Our results solicit studies linki
-scale anthropogenic environmental changes. This is the first attempt to stu dy the diversity and distribution of NCY taxa across temperate lakes. It pro vides a first step towards understanding their distribution and ecological f unction in pelagic aquatic habitats, where these organisms seem to be preval ent.' (1752 chars)
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authors => protected'Monchamp, M.-E.; Spaak, P.; Domaizon, I.; Dubois, N.; Bo uffard, D.; Pomati, F.' (108 chars)
title => protected'Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication' (101 chars)
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description => protected'Human impacts on biodiversity are well recognized, but uncertainties remain regarding patterns of diversity change at different spatial and temporal sca les. Changes in microbial assemblages are, in particular, not well understoo d, partly due to the lack of community composition data over relevant scales of space and time. Here, we investigate biodiversity patterns in cyanobacte rial assemblages over one century of eutrophication and climate change by se quencing DNA preserved in the sediments of ten European peri-Alpine lakes. W e found species losses and gains at the lake scale, while species richness i ncreased at the regional scale over approximately the past 100 years. Our da ta show a clear signal for beta diversity loss, with the composition and phy logenetic structure of assemblages becoming more similar across sites in the most recent decades, as have the general environmental conditions in and ar ound the lakes. We attribute patterns of change in community composition to raised temperatures affecting the strength of the thermal stratification and , as a consequence, nutrient fluctuations, which favoured cyanobacterial tax a able to regulate buoyancy. Our results reinforce previous reports of human -induced homogenization of natural communities and reveal how potentially to xic and bloom-forming cyanobacteria have widened their geographic distributi on in the European temperate region.' (1404 chars)
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title => protected'Sedimentary and egg-bank DNA from 3 European lakes reveal concurrent changes in the composition and diversity of cyanobacterial and <em>Daphnia</em> com munities' (160 chars)
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categories => protected'long-term change; eutrophication; microsatellite genotyping; high-throughput amplicon sequencing; Danube Delta; pre-alpine lakes' (128 chars)
description => protected'Eutrophication generally favours the growth of cyanobacteria over eukaryotic green algae in freshwater lakes. Cyanobacteria constitute a poor food sourc e for the waterflea <em>Daphnia</em>, an important primary consumer of phyto plankton in lakes. While it is known that some <em>Daphnia</em> species are adapted to eutrophic conditions and can cope with cyanobacteria in their die t, it is less known whether cyanobacterial community composition can influen ce <em>Daphnia</em> population structure in lakes. We studied the variation in genetic diversity of <em>Daphnia</em> resting eggs and cyanobacterial DNA preserved in sediment cores from three European lakes impacted by eutrophic ation. Our retrospective analysis confirms that <em>D. galeata</em> invaded the two pre-alpine lakes around the middle of the twentieth century, hybridi zed with and became dominant over <em>D. longispina</em>. This coincides wit h the presence in all lakes and the increase in the proportion of colonial a nd filamentous cyanobacteria in the pre-alpine lakes. The recent re-oligotro phication of the lakes did not reverse the cyanobacterial and <em>Daphnia</e m> assemblages to their pre-eutrophication composition and genetic structure , suggesting that both changed irreversibly due to anthropogenic influence o n the ecosystems. Genetic analyses applied to lake sedimentary archives have the potential to unveil how different compartments of the food web covary i n a changing environment.' (1469 chars)
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authors => protected'Fontana, S.; Thomas, M. K.; Moldoveanu, M.; Spaak, P.; Pomati, F.' (95 chars)
title => protected'Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness' (117 chars)
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description => protected'Understanding how microbial diversity influences ecosystem properties is of paramount importance. Cellular traits – which determine responses to the a biotic and biotic environment – may help us rigorously link them. However, our capacity to measure traits in natural communities has thus far been lim ited. Here we compared the predictive power of trait richness (trait space c overage), evenness (regularity in trait distribution) and divergence (preval ence of extreme phenotypes) derived from individual-based measurements with two species-level metrics (taxonomic richness and evenness) when modelling t he productivity of natural phytoplankton communities. Using phytoplankton da ta obtained from 28 lakes sampled at different spatial and temporal scales, we found that the diversity in individual-level morphophysiological traits s trongly improved our ability to predict community resource-use and biomass y ield. Trait evenness – the regularity in distribution of individual cells/ colonies within the trait space – was the strongest predictor, exhibiting a robust negative relationship across scales. Our study suggests that quanti fying individual microbial phenotypes in trait space may help us understand how to link physiology to ecosystem-scale processes. Elucidating the mechani sms scaling individual-level trait variation to microbial community dynamics could there improve our ability to forecast changes in ecosystem properties across environmental gradients.' (1476 chars)
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title => protected'Sedimentary DNA reveals cyanobacterial community diversity over 200 years in two perialpine lakes' (97 chars)
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description => protected'We reconstructed cyanobacterial community structure and phylogeny using DNA that was isolated from layers of stratified sediments spanning 200 years of lake history in the perialpine lakes Greifensee and Lake Zurich (Switzerland ). Community analysis based on amplification and sequencing of a 400-nucleot ide (nt)-long 16S rRNA fragment specific to <em>Cyanobacteria</em> revealed operational taxonomic units (OTUs) capturing the whole phylum, including rep resentatives of a newly characterized clade termed <em>Melainabacteria</em>, which shares common ancestry with <em>Cyanobacteria</em> and has not been p reviously described in lakes. The reconstruction of cyanobacterial richness and phylogenetic structure was validated using a data set consisting of 40 y ears of pelagic microscopic counts from each lake. We identified the OTUs as signed to common taxa known to be present in Greifensee and Lake Zurich and found a strong and significant relationship (adjusted <em>R</em><sup>2</sup> = 0.89; <em>P</em> < 0.001) between pelagic species richness in water an d OTU richness in the sediments. The water-sediment richness relationship va ried between cyanobacterial orders, indicating that the richness of <em>Chro ococcales</em> and <em>Synechococcales</em> may be underestimated by microsc opy. PCR detection of the microcystin synthetase gene <em>mcyA</em> confirme d the presence of potentially toxic cyanobacterial taxa over recent years in Greifensee and throughout the last century in Lake Zurich. The approach pre sented in this study demonstrates that it is possible to reconstruct past pe lagic cyanobacterial communities in lakes where the integrity of the sedimen tary archive is well preserved and to explore changes in phylogenetic and fu nctional diversity over decade-to-century timescales.' (1801 chars)
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authors => protected'Drugă, B.; Turko, P.; Spaak, P.; Pomati, F.' (64 chars)
title => protected'Cyanobacteria affect fitness and genetic structure of experimental <I>Daphni a</I> populations' (93 chars)
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description => protected'Zooplankton communities can be strongly affected by cyanobacterial blooms, e specially species of genus <I>Daphnia</I>, which are key-species in lake eco systems. Here, we explored the effect of microcystin/nonmicrocystin (MC/non- MC) producing cyanobacteria in the diet of experimental <I>Daphnia galeata</ I> populations composed of eight genotypes. We used <I>D. galeata</I> clones hatched from ephippia 10 to 60 years old, which were first tested in monocu ltures, and then exposed for 10 weeks as mixed populations to three food tre atments consisting of green algae combined with cyanobacteria able/unable of producing MC. We measured the expression of nine genes potentially involved in <I>Daphnia</I> acclimation to cyanobacteria: six protease genes, one ubi quitin-conjugating enzyme gene, and two rRNA genes, and then we tracked the dynamics of the genotypes in mixed populations. The expression pattern of on e protease and the ubiquitin-conjugating enzyme genes was positively correla ted with the increased fitness of competing clones in the presence of cyanob acteria, suggesting physiological plasticity. The genotype dynamics in mixed populations was only partially related to the growth rates of clones in mon ocultures and varied strongly with the food. Our results revealed strong int raspecific differences in the tolerance of <I>D. galeata</I> clones to MC/no n-MC-producing cyanobacteria in their diet, suggesting microevolutionary eff ects.' (1449 chars)
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authors => protected'Tardent, N.; Tellenbach, C.; Turko, P.; Spaak, P.' (69 chars)
title => protected'Clonal structure and depth selection during a <em>Caullerya mesnili</em> epi demic in a hybridizing population of the <em>Daphnia longispina</em> complex' (152 chars)
journal => protected'Hydrobiologia' (13 chars)
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categories => protected'diel vertical migration; microenvironment; parasite; Greifensee' (63 chars)
description => protected'<em>Daphnia</em> perform diel vertical migration (DVM), a predator-avoidance strategy to migrate towards deeper and colder layers in the water column in the morning and movement to the algae-rich surface layers in the evening. H owever, individuals performing DVM incur several trade-offs since they might suffer from resource limitation and a slower instantaneous birth rate in de eper depths. DVM patterns may be modified by abiotic factors such as tempera ture, food concentration, or pH and vary among different <em>Daphnia</em> sp ecies and genotypes. Furthermore, <em>Daphnia</em> host a variety of micropa rasites that might pose an additional factor influencing DVM behaviour. For infected individuals, migration into cooler temperature layers might slow do wn parasite growth. Moreover, parasites can increase opacity of their hosts. Non-migrating individuals might then be selectively purged from the upper l ayers by visually hunting predators. With these premises we asked, whether e pidemics of the ichthyosporean parasite <em>Caullerya mesnili</em> affect or are affected by the DVM behaviour of <em>Daphnia</em> in Lake Greifensee, S witzerland by analysing the vertical distribution of <em>Daphnia</em> during day and night on two dates. Furthermore, we were interested whether a poten tial interaction depends on host genotype. We therefore studied the genotypi c composition of the integrated population in regular sampling intervals ove r the course of one year and on a fine-grained vertical resolution during th e <em>Caullerya</em> epidemic in late summer. Since <em>Caullerya</em>-infec ted <em>Daphnia</em> migrated equally well as uninfected ones, the findings of this study suggest that <em>Caullerya</em> epidemics neither affected nor were affected by the DVM behaviour of <em>Daphnia</em>. We observed clonal succession in the lake but could not link this succession to the <em>Cauller ya</em> epidemic; all except one of the common multilocus genotypes were und er-infected. In addition...' (2226 chars)
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Long term diversity and distribution of non-photosynthetic cyanobacteria in peri-Alpine lakes
The phylum Cyanobacteria comprises a non-photosynthetic lineage. The diversity and distribution of non-photosynthetic cyanobacteria (NCY) across aquatic environments are currently unknown, including their ecology. Here, we report about composition and phylogenetic diversity of two clades of NCY in ten lakes of the European peri-Alpine region, over the past ~100 years. Using 16S rDNA sequences obtained from dated sediment cores, we found almost equal proportion of taxa assigned to Melainabacteria and the deepest-branching group Sericytochromatia (ML635J-21) (63 total detected taxa). The topology of our reconstructed phylogenies reflected evolutionary relationships expected from previous work, that is, a clear separation between the deepest branching Sericytochromatia, the Melainabacteria, and the photosynthetic cyanobacteria clades. While different lakes harbored distinct NCY communities, the diversity of NCY assemblages within and between lakes (alpha and beta diversity) did not significantly change over the last century. This is in contrast with what was previously reported for photosynthetic cyanobacteria. Unchanged community phylogenetic similarity over geographic distance indicated no dispersal limitation of NCY at the regional scale. Our results solicit studies linking in-lake environmental factors to the composition of these microorganisms’ communities, whose assembly appeared not to have been influenced by large-scale anthropogenic environmental changes. This is the first attempt to study the diversity and distribution of NCY taxa across temperate lakes. It provides a first step towards understanding their distribution and ecological function in pelagic aquatic habitats, where these organisms seem to be prevalent.
Monchamp, M.-E.; Spaak, P.; Pomati, F. (2019) Long term diversity and distribution of non-photosynthetic cyanobacteria in peri-Alpine lakes, Frontiers in Microbiology, 9, 3344 (11 pp.), doi:10.3389/fmicb.2018.03344, Institutional Repository
Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication
Human impacts on biodiversity are well recognized, but uncertainties remain regarding patterns of diversity change at different spatial and temporal scales. Changes in microbial assemblages are, in particular, not well understood, partly due to the lack of community composition data over relevant scales of space and time. Here, we investigate biodiversity patterns in cyanobacterial assemblages over one century of eutrophication and climate change by sequencing DNA preserved in the sediments of ten European peri-Alpine lakes. We found species losses and gains at the lake scale, while species richness increased at the regional scale over approximately the past 100 years. Our data show a clear signal for beta diversity loss, with the composition and phylogenetic structure of assemblages becoming more similar across sites in the most recent decades, as have the general environmental conditions in and around the lakes. We attribute patterns of change in community composition to raised temperatures affecting the strength of the thermal stratification and, as a consequence, nutrient fluctuations, which favoured cyanobacterial taxa able to regulate buoyancy. Our results reinforce previous reports of human-induced homogenization of natural communities and reveal how potentially toxic and bloom-forming cyanobacteria have widened their geographic distribution in the European temperate region.
Monchamp, M.-E.; Spaak, P.; Domaizon, I.; Dubois, N.; Bouffard, D.; Pomati, F. (2018) Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication, Nature Ecology & Evolution, 2, 317-324, doi:10.1038/s41559-017-0407-0, Institutional Repository
Sedimentary and egg-bank DNA from 3 European lakes reveal concurrent changes in the composition and diversity of cyanobacterial and Daphnia communities
Eutrophication generally favours the growth of cyanobacteria over eukaryotic green algae in freshwater lakes. Cyanobacteria constitute a poor food source for the waterflea Daphnia, an important primary consumer of phytoplankton in lakes. While it is known that some Daphnia species are adapted to eutrophic conditions and can cope with cyanobacteria in their diet, it is less known whether cyanobacterial community composition can influence Daphnia population structure in lakes. We studied the variation in genetic diversity of Daphnia resting eggs and cyanobacterial DNA preserved in sediment cores from three European lakes impacted by eutrophication. Our retrospective analysis confirms that D. galeata invaded the two pre-alpine lakes around the middle of the twentieth century, hybridized with and became dominant over D. longispina. This coincides with the presence in all lakes and the increase in the proportion of colonial and filamentous cyanobacteria in the pre-alpine lakes. The recent re-oligotrophication of the lakes did not reverse the cyanobacterial and Daphnia assemblages to their pre-eutrophication composition and genetic structure, suggesting that both changed irreversibly due to anthropogenic influence on the ecosystems. Genetic analyses applied to lake sedimentary archives have the potential to unveil how different compartments of the food web covary in a changing environment.
Monchamp, M.-E.; Enache, I.; Turko, P.; Pomati, F.; Rîşnnoveanu, G.; Spaak, P. (2017) Sedimentary and egg-bank DNA from 3 European lakes reveal concurrent changes in the composition and diversity of cyanobacterial and Daphnia communities, Hydrobiologia, 800, 155-172, doi:10.1007/s10750-017-3247-7, Institutional Repository
Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness
Understanding how microbial diversity influences ecosystem properties is of paramount importance. Cellular traits – which determine responses to the abiotic and biotic environment – may help us rigorously link them. However, our capacity to measure traits in natural communities has thus far been limited. Here we compared the predictive power of trait richness (trait space coverage), evenness (regularity in trait distribution) and divergence (prevalence of extreme phenotypes) derived from individual-based measurements with two species-level metrics (taxonomic richness and evenness) when modelling the productivity of natural phytoplankton communities. Using phytoplankton data obtained from 28 lakes sampled at different spatial and temporal scales, we found that the diversity in individual-level morphophysiological traits strongly improved our ability to predict community resource-use and biomass yield. Trait evenness – the regularity in distribution of individual cells/colonies within the trait space – was the strongest predictor, exhibiting a robust negative relationship across scales. Our study suggests that quantifying individual microbial phenotypes in trait space may help us understand how to link physiology to ecosystem-scale processes. Elucidating the mechanisms scaling individual-level trait variation to microbial community dynamics could there improve our ability to forecast changes in ecosystem properties across environmental gradients.
Fontana, S.; Thomas, M. K.; Moldoveanu, M.; Spaak, P.; Pomati, F. (2018) Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness, ISME Journal, 12, 356-366, doi:10.1038/ismej.2017.160, Institutional Repository
Sedimentary DNA reveals cyanobacterial community diversity over 200 years in two perialpine lakes
We reconstructed cyanobacterial community structure and phylogeny using DNA that was isolated from layers of stratified sediments spanning 200 years of lake history in the perialpine lakes Greifensee and Lake Zurich (Switzerland). Community analysis based on amplification and sequencing of a 400-nucleotide (nt)-long 16S rRNA fragment specific to Cyanobacteria revealed operational taxonomic units (OTUs) capturing the whole phylum, including representatives of a newly characterized clade termed Melainabacteria, which shares common ancestry with Cyanobacteria and has not been previously described in lakes. The reconstruction of cyanobacterial richness and phylogenetic structure was validated using a data set consisting of 40 years of pelagic microscopic counts from each lake. We identified the OTUs assigned to common taxa known to be present in Greifensee and Lake Zurich and found a strong and significant relationship (adjusted R2 = 0.89; P < 0.001) between pelagic species richness in water and OTU richness in the sediments. The water-sediment richness relationship varied between cyanobacterial orders, indicating that the richness of Chroococcales and Synechococcales may be underestimated by microscopy. PCR detection of the microcystin synthetase gene mcyA confirmed the presence of potentially toxic cyanobacterial taxa over recent years in Greifensee and throughout the last century in Lake Zurich. The approach presented in this study demonstrates that it is possible to reconstruct past pelagic cyanobacterial communities in lakes where the integrity of the sedimentary archive is well preserved and to explore changes in phylogenetic and functional diversity over decade-to-century timescales.
Monchamp, M.-E.; Walser, J.-C.; Pomati, F.; Spaak, P. (2016) Sedimentary DNA reveals cyanobacterial community diversity over 200 years in two perialpine lakes, Applied and Environmental Microbiology, 82(21), 6472-6482, doi:10.1128/AEM.02174-16, Institutional Repository
Cyanobacteria affect fitness and genetic structure of experimental Daphnia populations
Zooplankton communities can be strongly affected by cyanobacterial blooms, especially species of genus Daphnia, which are key-species in lake ecosystems. Here, we explored the effect of microcystin/nonmicrocystin (MC/non-MC) producing cyanobacteria in the diet of experimental Daphnia galeata populations composed of eight genotypes. We used D. galeata clones hatched from ephippia 10 to 60 years old, which were first tested in monocultures, and then exposed for 10 weeks as mixed populations to three food treatments consisting of green algae combined with cyanobacteria able/unable of producing MC. We measured the expression of nine genes potentially involved in Daphnia acclimation to cyanobacteria: six protease genes, one ubiquitin-conjugating enzyme gene, and two rRNA genes, and then we tracked the dynamics of the genotypes in mixed populations. The expression pattern of one protease and the ubiquitin-conjugating enzyme genes was positively correlated with the increased fitness of competing clones in the presence of cyanobacteria, suggesting physiological plasticity. The genotype dynamics in mixed populations was only partially related to the growth rates of clones in monocultures and varied strongly with the food. Our results revealed strong intraspecific differences in the tolerance of D. galeata clones to MC/non-MC-producing cyanobacteria in their diet, suggesting microevolutionary effects.
Drugă, B.; Turko, P.; Spaak, P.; Pomati, F. (2016) Cyanobacteria affect fitness and genetic structure of experimental Daphnia populations, Environmental Science and Technology, 50(7), 3416-3424, doi:10.1021/acs.est.5b05973, Institutional Repository
Clonal structure and depth selection during a Caullerya mesnili epidemic in a hybridizing population of the Daphnia longispina complex
Daphnia perform diel vertical migration (DVM), a predator-avoidance strategy to migrate towards deeper and colder layers in the water column in the morning and movement to the algae-rich surface layers in the evening. However, individuals performing DVM incur several trade-offs since they might suffer from resource limitation and a slower instantaneous birth rate in deeper depths. DVM patterns may be modified by abiotic factors such as temperature, food concentration, or pH and vary among different Daphnia species and genotypes. Furthermore, Daphnia host a variety of microparasites that might pose an additional factor influencing DVM behaviour. For infected individuals, migration into cooler temperature layers might slow down parasite growth. Moreover, parasites can increase opacity of their hosts. Non-migrating individuals might then be selectively purged from the upper layers by visually hunting predators. With these premises we asked, whether epidemics of the ichthyosporean parasite Caullerya mesnili affect or are affected by the DVM behaviour of Daphnia in Lake Greifensee, Switzerland by analysing the vertical distribution of Daphnia during day and night on two dates. Furthermore, we were interested whether a potential interaction depends on host genotype. We therefore studied the genotypic composition of the integrated population in regular sampling intervals over the course of one year and on a fine-grained vertical resolution during the Caullerya epidemic in late summer. Since Caullerya-infected Daphnia migrated equally well as uninfected ones, the findings of this study suggest that Caullerya epidemics neither affected nor were affected by the DVM behaviour of Daphnia. We observed clonal succession in the lake but could not link this succession to the Caullerya epidemic; all except one of the common multilocus genotypes were under-infected. In addition, outbreak and course of this Caullerya epidemic seemed to rely mainly on environmental cues. Because this first study only provides a snapshot of time, we hope that further studies will be done to verify our results.
Tardent, N.; Tellenbach, C.; Turko, P.; Spaak, P. (2017) Clonal structure and depth selection during a Caullerya mesnili epidemic in a hybridizing population of the Daphnia longispina complex, Hydrobiologia, 798(1), 33-44, doi:10.1007/s10750-015-2632-3, Institutional Repository
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